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Lee HK, Jung NH, Lee DE, Lee H, Yang J, Kim YS, Han SS, Han N, Kim IW, Oh JM. Discovery of Biomarkers Related to Interstitial Fibrosis and Tubular Atrophy among Kidney Transplant Recipients by mRNA-Sequencing. J Pers Med 2023; 13:1242. [PMID: 37623492 PMCID: PMC10455123 DOI: 10.3390/jpm13081242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Interstitial fibrosis and tubular atrophy (IF/TA) after kidney transplantation causes a chronic deterioration of graft function. IF/TA can be diagnosed by means of a graft biopsy, which is a necessity as non-invasive diagnostic methods are unavailable. In this study, we identified IF/TA-related differentially expressed genes (DEGs) through next-generation sequencing using peripheral blood mononuclear cells. Blood samples from kidney transplant recipients undergoing standard immunosuppressive therapy (tacrolimus/mycophenolate mofetil or mycophenolate sodium/steroid) and diagnosed as IF/TA (n = 41) or normal (controls; n = 41) at their one-year protocol biopsy were recruited between January of 2020 and August of 2020. DEGs were derived through mRNA sequencing and validated by means of a quantitative real-time polymerase chain reaction. We identified 34 DEGs related to IF/TA. ADAMTS2, PLIN5, CLDN9, and KCNJ15 demonstrated a log2(fold change) of >1.5 and an area under the receiver operating characteristic curve (AUC) value of >0.6, with ADAMTS2 showing the largest AUC value and expression levels, which were 3.5-fold higher in the IF/TA group relative to that observed in the control group. We identified and validated DEGs related to IF/TA progression at one-year post-transplantation. Specifically, we identified ADAMTS2 as a potential IF/TA biomarker.
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Affiliation(s)
- Hyun Kyung Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea; (H.K.L.)
| | - Na Hyun Jung
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea; (H.K.L.)
| | - Da Eun Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea; (H.K.L.)
| | - Hajeong Lee
- Division of Nephrology, Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea (Y.S.K.)
- Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jaeseok Yang
- Transplantation Center, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Division of Nephrology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Yon Su Kim
- Division of Nephrology, Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea (Y.S.K.)
- Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Seung Seok Han
- Division of Nephrology, Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea (Y.S.K.)
- Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Nayoung Han
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea; (H.K.L.)
- College of Pharmacy, Jeju National University, Jeju 63243, Republic of Korea
| | - In-Wha Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea; (H.K.L.)
| | - Jung Mi Oh
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea; (H.K.L.)
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2
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Yepes-Calderón M, Sotomayor CG, Rasmussen DGK, Hijmans RS, te Velde-Keyzer CA, van Londen M, van Dijk M, Diepstra A, Berger SP, Karsdal MA, Bemelman FJ, de Fijter JW, Kers J, Florquin S, Genovese F, Bakker SJL, Sanders JS, Van Den Born J. Biopsy-Controlled Non-Invasive Quantification of Collagen Type VI in Kidney Transplant Recipients: A Post-Hoc Analysis of the MECANO Trial. J Clin Med 2020; 9:3216. [PMID: 33036366 PMCID: PMC7600059 DOI: 10.3390/jcm9103216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 01/15/2023] Open
Abstract
The PRO-C6 assay, a reflection of collagen type VI synthesis, has been proposed as a non-invasive early biomarker of kidney fibrosis. We aimed to investigate cross-sectional and longitudinal associations between plasma and urine PRO-C6 and proven histological changes after kidney transplantation. The current study is a post-hoc analysis of 94 participants of the MECANO trial, a 24-month prospective, multicenter, open-label, randomized, controlled trial aimed at comparing everolimus-based vs. cyclosporine-based immunosuppression. PRO-C6 was measured in plasma and urine samples collected 6 and 24 months post-transplantation. Fibrosis was evaluated in biopsies collected at the same time points by Banff interstitial fibrosis/tubular atrophy (IF/TA) scoring and collagen staining (Picro Sirius Red; PSR); inflammation was evaluated by the tubulo-interstitial inflammation score (ti-score). Linear regression analyses were performed. Six-month plasma PRO-C6 was cross-sectionally associated with IF/TA score (Std. β = 0.34), and prospectively with 24-month IF/TA score and ti-score (Std. β = 0.24 and 0.23, respectively) (p < 0.05 for all). No significant associations were found between urine PRO-C6 and any of the biopsy findings. Fibrotic changes and urine PRO-C6 behaved differentially over time according to immunosuppressive therapy. These results are a first step towards non-invasive fibrosis detection after kidney transplantation by means of collagen VI synthesis measurement, and further research is required.
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Affiliation(s)
- Manuela Yepes-Calderón
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands; (M.Y.-C.); (R.S.H.); (C.A.t.V.-K.); (M.v.L.); (M.v.D.); (S.P.B.); (S.J.L.B.); (J.-S.S.); (J.V.D.B.)
| | - Camilo G. Sotomayor
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands; (M.Y.-C.); (R.S.H.); (C.A.t.V.-K.); (M.v.L.); (M.v.D.); (S.P.B.); (S.J.L.B.); (J.-S.S.); (J.V.D.B.)
| | | | - Ryanne S. Hijmans
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands; (M.Y.-C.); (R.S.H.); (C.A.t.V.-K.); (M.v.L.); (M.v.D.); (S.P.B.); (S.J.L.B.); (J.-S.S.); (J.V.D.B.)
| | - Charlotte A. te Velde-Keyzer
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands; (M.Y.-C.); (R.S.H.); (C.A.t.V.-K.); (M.v.L.); (M.v.D.); (S.P.B.); (S.J.L.B.); (J.-S.S.); (J.V.D.B.)
| | - Marco van Londen
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands; (M.Y.-C.); (R.S.H.); (C.A.t.V.-K.); (M.v.L.); (M.v.D.); (S.P.B.); (S.J.L.B.); (J.-S.S.); (J.V.D.B.)
| | - Marja van Dijk
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands; (M.Y.-C.); (R.S.H.); (C.A.t.V.-K.); (M.v.L.); (M.v.D.); (S.P.B.); (S.J.L.B.); (J.-S.S.); (J.V.D.B.)
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands;
| | - Stefan P. Berger
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands; (M.Y.-C.); (R.S.H.); (C.A.t.V.-K.); (M.v.L.); (M.v.D.); (S.P.B.); (S.J.L.B.); (J.-S.S.); (J.V.D.B.)
| | | | - Frederike J. Bemelman
- Department of Nephrology, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Johan W. de Fijter
- Department of Nephrology, Leiden University Medical Center, University of Leiden, 2300 RC Leiden, The Netherlands;
| | - Jesper Kers
- Amsterdam Institute for Infection and Immunity (AII), Amsterdam UMC, University of Amsterdam, 1098 XH Amsterdam, The Netherlands; (J.K.); (S.F.)
- Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- Leiden Transplant Center, Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Van ‘t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Sandrine Florquin
- Amsterdam Institute for Infection and Immunity (AII), Amsterdam UMC, University of Amsterdam, 1098 XH Amsterdam, The Netherlands; (J.K.); (S.F.)
- Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- Leiden Transplant Center, Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Federica Genovese
- Nordic Bioscience A/S, 2730 Herlev, Denmark; (D.G.K.R.); (M.A.K.); (F.G.)
| | - Stephan J. L. Bakker
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands; (M.Y.-C.); (R.S.H.); (C.A.t.V.-K.); (M.v.L.); (M.v.D.); (S.P.B.); (S.J.L.B.); (J.-S.S.); (J.V.D.B.)
| | - Jan-Stephan Sanders
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands; (M.Y.-C.); (R.S.H.); (C.A.t.V.-K.); (M.v.L.); (M.v.D.); (S.P.B.); (S.J.L.B.); (J.-S.S.); (J.V.D.B.)
| | - Jacob Van Den Born
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands; (M.Y.-C.); (R.S.H.); (C.A.t.V.-K.); (M.v.L.); (M.v.D.); (S.P.B.); (S.J.L.B.); (J.-S.S.); (J.V.D.B.)
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3
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Hofmann BB, Krapp N, Li Y, De La Torre C, Sol M, Braun JD, Kolibabka M, Pallavi P, Krämer BK, Yard BA, Kälsch AI. N-Octanoyl-Dopamine inhibits cytokine production in activated T-cells and diminishes MHC-class-II expression as well as adhesion molecules in IFNγ-stimulated endothelial cells. Sci Rep 2019; 9:19338. [PMID: 31853095 PMCID: PMC6920350 DOI: 10.1038/s41598-019-55983-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 11/29/2019] [Indexed: 01/06/2023] Open
Abstract
IFNγ enhances allograft immunogenicity and facilitates T-cell mediated rejection. This may cause interstitial fibrosis and tubular atrophy (IFTA), contributing to chronic allograft loss. We assessed if inhibition of T-cell activation by N-octanoyl dopamine (NOD) impairs adherence of activated T-cells to endothelial cells and the ability of activated T-cells to produce IFNγ. We also assessed if NOD affects IFNγ mediated gene expression in endothelial cells. The presence of NOD during T-cell activation significantly blunted their adhesion to unstimulated and cytokine stimulated HUVEC. Supernatants of these T-cells displayed significantly lower concentrations of TNFα and IFNγ and were less capable to facilitate T-cell adhesion. In the presence of NOD VLA-4 (CD49d/CD29) and LFA-1 (CD11a/CD18) expression on T-cells was reduced. NOD treatment of IFNγ stimulated HUVEC reduced the expression of MHC class II transactivator (CIITA), of MHC class II and its associated invariant chain CD74. Since IFTA is associated with T-cell mediated rejection and IFNγ to a large extent regulates immunogenicity of allografts, our current data suggest a potential clinical use of NOD in the treatment of transplant recipients. Further in vivo studies are warranted to confirm these in vitro findings and to assess the benefit of NOD on IFTA in clinically relevant models.
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Affiliation(s)
- Björn B Hofmann
- Department of Nephrology, Endocrinology and Rheumatology, Fifth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Nicolas Krapp
- Department of Nephrology, Endocrinology and Rheumatology, Fifth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Yingchun Li
- Department of Nephrology, Endocrinology and Rheumatology, Fifth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Carolina De La Torre
- Center of Medical Research, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Marloes Sol
- Department of Medical Biology and Pathology, University Medical Center Groningen, Groningen, Netherlands
| | - Jana D Braun
- Department of Nephrology, Endocrinology and Rheumatology, Fifth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Matthias Kolibabka
- Department of Nephrology, Endocrinology and Rheumatology, Fifth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Prama Pallavi
- Department of Nephrology, Endocrinology and Rheumatology, Fifth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Bernhard K Krämer
- Department of Nephrology, Endocrinology and Rheumatology, Fifth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Benito A Yard
- Department of Nephrology, Endocrinology and Rheumatology, Fifth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.
| | - Anna-Isabelle Kälsch
- Department of Nephrology, Endocrinology and Rheumatology, Fifth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
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4
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Biomarker Guidelines for High-Dimensional Genomic Studies in Transplantation: Adding Method to the Madness. Transplantation 2018; 101:457-463. [PMID: 28212255 DOI: 10.1097/tp.0000000000001622] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Bontha SV, Maluf DG, Archer KJ, Dumur CI, Dozmorov M, King A, Akalin E, Mueller TF, Gallon L, Mas VR. Effects of DNA Methylation on Progression to Interstitial Fibrosis and Tubular Atrophy in Renal Allograft Biopsies: A Multi-Omics Approach. Am J Transplant 2017; 17:3060-3075. [PMID: 28556588 PMCID: PMC5734859 DOI: 10.1111/ajt.14372] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/01/2017] [Accepted: 05/20/2017] [Indexed: 01/25/2023]
Abstract
Progressive fibrosis of the interstitium is the dominant final pathway in renal destruction in native and transplanted kidneys. Over time, the continuum of molecular events following immunological and nonimmunological insults lead to interstitial fibrosis and tubular atrophy and culminate in kidney failure. We hypothesize that these insults trigger changes in DNA methylation (DNAm) patterns, which in turn could exacerbate injury and slow down the regeneration processes, leading to fibrosis development and graft dysfunction. Herein, we analyzed biopsy samples from kidney allografts collected 24 months posttransplantation and used an integrative multi-omics approach to understand the underlying molecular mechanisms. The role of DNAm and microRNAs on the graft gene expression was evaluated. Enrichment analyses of differentially methylated CpG sites were performed using GenomeRunner. CpGs were strongly enriched in regions that were variably methylated among tissues, implying high tissue specificity in their regulatory impact. Corresponding to this methylation pattern, gene expression data were related to immune response (activated state) and nephrogenesis (inhibited state). Preimplantation biopsies showed similar DNAm patterns to normal allograft biopsies at 2 years posttransplantation. Our findings demonstrate for the first time a relationship among epigenetic modifications and development of interstitial fibrosis, graft function, and inter-individual variation on long-term outcomes.
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Affiliation(s)
- Sai Vineela Bontha
- Translational Genomics Transplant Laboratory, Transplant Division, University of Virginia, Department of Surgery, PO Box 800625. 409 Lane Rd, Charlottesville, VA, 22908- 0625, USA
| | - Daniel G. Maluf
- Translational Genomics Transplant Laboratory, Transplant Division, University of Virginia, Department of Surgery, PO Box 800625. 409 Lane Rd, Charlottesville, VA, 22908- 0625, USA
| | - Kellie J. Archer
- Division of Biostatistics, The Ohio State University, 1841 Neil Avenue, 240 Cunz Hall, Columbus, OH 43210
| | - Catherine I. Dumur
- Department of Pathology, Virginia Commonwealth University, PO Box 980662, 1101 E. Marshall Street, Richmond, VA 23298-0662
| | - Mikhail Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, One Capitol Square, room 730, 830 East Main Street, Richmond, Virginia 23298
| | - Anne King
- Division of Nephrology, Internal Medicine. Virginia commonwealth University, VA, 1101 E. Marshall Street, Richmond, VA 23298-0662
| | - Enver Akalin
- Departments of Clinical Medicine and Surgery, Albert Einstein College of Medicine Montefiore Medical Center, 11 E 210th St, Bronx, NY 10467
| | - Thomas F. Mueller
- Division of Nephorology, Internal Medicine, University Hospital Zurich, Ramistrasse 100, Zurich-8091
| | - Lorenzo Gallon
- Department of Medicine-Nephrology, Northwestern University676 N St Clair St # 100, Chicago, IL 60611
| | - Valeria R. Mas
- Translational Genomics Transplant Laboratory, Transplant Division, University of Virginia, Department of Surgery, PO Box 800625. 409 Lane Rd, Charlottesville, VA, 22908- 0625, USA
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van de Vrie M, Deegens JK, Eikmans M, van der Vlag J, Hilbrands LB. Urinary MicroRNA as Biomarker in Renal Transplantation. Am J Transplant 2017; 17:1160-1166. [PMID: 27743494 PMCID: PMC5434819 DOI: 10.1111/ajt.14082] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 09/30/2016] [Accepted: 10/02/2016] [Indexed: 01/25/2023]
Abstract
Urine represents a noninvasive source in which proteins and nucleic acids can be assessed. Such analytes may function as biomarkers to monitor kidney graft pathology at every desired frequency, thereby providing a time window to prevent graft damage by therapeutic intervention. Recently, several proteins have been measured in urine as markers of graft injury. However, the specificity is limited, and measuring urinary proteins generally lacks the potential to predict early kidney graft damage. Currently, urinary mRNA and microRNA are being investigated to evaluate the prognostic value of changes in gene expression during the initial stages of graft damage. At such time point, a change in treatment regimen and dosage is expected to have maximum potency to minimize future decline in graft function. Both mRNA and microRNAs have shown promising results in both detection and prediction of graft injury. An advantage of microRNAs compared to mRNA molecules is their stability, a characteristic that is beneficial when working with urine samples. In this review, we provide the current state of urinary biomarkers in renal transplantation, with a focus on urinary microRNA. In addition, we discuss the methods used to study urinary microRNA expression.
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Affiliation(s)
- M. van de Vrie
- Department of NephrologyRadboud University Medical CenterNijmegenthe Netherlands
| | - J. K. Deegens
- Department of NephrologyRadboud University Medical CenterNijmegenthe Netherlands
| | - M. Eikmans
- Department of ImmunohematologyLeiden University Medical CenterLeidenthe Netherlands
| | - J. van der Vlag
- Department of NephrologyRadboud University Medical CenterNijmegenthe Netherlands
| | - L. B. Hilbrands
- Department of NephrologyRadboud University Medical CenterNijmegenthe Netherlands
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Stribos EGD, Nielsen SH, Brix S, Karsdal MA, Seelen MA, van Goor H, Bakker SJL, Olinga P, Mutsaers HAM, Genovese F. Non-invasive quantification of collagen turnover in renal transplant recipients. PLoS One 2017; 12:e0175898. [PMID: 28430784 DOI: 10.1371/journal.pone.0175898] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 04/02/2017] [Indexed: 12/17/2022] Open
Abstract
Kidney allograft failure due to chronic injury/rejection remains the main cause of graft loss in renal transplant recipients (RTR). Here, we investigated whether specific biomarkers of extracellular matrix (ECM) turnover are associated with allograft function and chronic kidney disease (CKD) stage in RTR. Seventy-eight patients who attended the University Medical Center Groningen for a routine check-up after kidney transplantation were enrolled in the study. Plasma and/or 24h-urine samples were collected and specific matrix-metalloproteinase-generated neo-epitope fragments of collagens were measured by enzyme-linked immunosorbent assay. Our results demonstrated that urinary levels of C3M, a marker for collagen type III degradation, correlated with estimated glomerular filtration rate (eGFR; r = 0.58, p<0.0001), with lower levels detected in the urine of patients with advanced CKD. In addition, plasma levels of Pro-C6, a marker for collagen type VI formation, significantly increased with disease progression and correlated with eGFR (r = -0.72, p<0.0001). Conversely, plasma C3M and urinary Pro-C6 levels showed no correlation with renal function. We identified two neo-epitope biomarkers of tissue turnover associated with ECM remodeling and fibrosis that can stratify patients by CKD stage. This is as promising first step towards non-invasive monitoring of ECM turnover in the kidneys.
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Affiliation(s)
- Elisabeth G D Stribos
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, Groningen Research Institute of Pharmacy, Groningen, The Netherlands
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Signe Holm Nielsen
- Nordic Bioscience A/S, Herlev, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Marc A Seelen
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Harry van Goor
- Department of Pathology and Medical Biology, Division of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stephan J L Bakker
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter Olinga
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, Groningen Research Institute of Pharmacy, Groningen, The Netherlands
| | - Henricus A M Mutsaers
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, Groningen Research Institute of Pharmacy, Groningen, The Netherlands
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Novianti PW, Jong VL, Roes KCB, Eijkemans MJC. Meta-analysis approach as a gene selection method in class prediction: does it improve model performance? A case study in acute myeloid leukemia. BMC Bioinformatics 2017; 18:210. [PMID: 28399794 PMCID: PMC5387259 DOI: 10.1186/s12859-017-1619-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 03/30/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Aggregating gene expression data across experiments via meta-analysis is expected to increase the precision of the effect estimates and to increase the statistical power to detect a certain fold change. This study evaluates the potential benefit of using a meta-analysis approach as a gene selection method prior to predictive modeling in gene expression data. RESULTS Six raw datasets from different gene expression experiments in acute myeloid leukemia (AML) and 11 different classification methods were used to build classification models to classify samples as either AML or healthy control. First, the classification models were trained on gene expression data from single experiments using conventional supervised variable selection and externally validated with the other five gene expression datasets (referred to as the individual-classification approach). Next, gene selection was performed through meta-analysis on four datasets, and predictive models were trained with the selected genes on the fifth dataset and validated on the sixth dataset. For some datasets, gene selection through meta-analysis helped classification models to achieve higher performance as compared to predictive modeling based on a single dataset; but for others, there was no major improvement. Synthetic datasets were generated from nine simulation scenarios. The effect of sample size, fold change and pairwise correlation between differentially expressed (DE) genes on the difference between MA- and individual-classification model was evaluated. The fold change and pairwise correlation significantly contributed to the difference in performance between the two methods. The gene selection via meta-analysis approach was more effective when it was conducted using a set of data with low fold change and high pairwise correlation on the DE genes. CONCLUSION Gene selection through meta-analysis on previously published studies potentially improves the performance of a predictive model on a given gene expression data.
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Affiliation(s)
- Putri W. Novianti
- Biostatistics & Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
- Department of Epidemiology and Biostatistics, VU University medical center, Amsterdam, The Netherlands
- Department of Pathology, VU University medical center, Amsterdam, The Netherlands
| | - Victor L. Jong
- Biostatistics & Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
- Viroscience Laboratory, Erasmus Medical Center Rotterdam, 3015 CE Rotterdam, The Netherlands
| | - Kit C. B. Roes
- Biostatistics & Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - Marinus J. C. Eijkemans
- Biostatistics & Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
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Astragaloside IV from Astragalus membranaceus ameliorates renal interstitial fibrosis by inhibiting inflammation via TLR4/NF-кB in vivo and in vitro. Int Immunopharmacol 2017; 42:18-24. [DOI: 10.1016/j.intimp.2016.11.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/07/2016] [Accepted: 11/08/2016] [Indexed: 12/31/2022]
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10
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Epigenetics in Kidney Transplantation: Current Evidence, Predictions, and Future Research Directions. Transplantation 2016; 100:23-38. [PMID: 26356174 DOI: 10.1097/tp.0000000000000878] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Epigenetic modifications are changes to the genome that occur without any alteration in DNA sequence. These changes include cytosine methylation of DNA at cytosine-phosphate diester-guanine dinucleotides, histone modifications, microRNA interactions, and chromatin remodeling complexes. Epigenetic modifications may exert their effect independently or complementary to genetic variants and have the potential to modify gene expression. These modifications are dynamic, potentially heritable, and can be induced by environmental stimuli or drugs. There is emerging evidence that epigenetics play an important role in health and disease. However, the impact of epigenetic modifications on the outcomes of kidney transplantation is currently poorly understood and deserves further exploration. Kidney transplantation is the best treatment option for end-stage renal disease, but allograft loss remains a significant challenge that leads to increased morbidity and return to dialysis. Epigenetic modifications may influence the activation, proliferation, and differentiation of the immune cells, and therefore may have a critical role in the host immune response to the allograft and its outcome. The epigenome of the donor may also impact kidney graft survival, especially those epigenetic modifications associated with early transplant stressors (e.g., cold ischemia time) and donor aging. In the present review, we discuss evidence supporting the role of epigenetic modifications in ischemia-reperfusion injury, host immune response to the graft, and graft response to injury as potential new tools for the diagnosis and prediction of graft function, and new therapeutic targets for improving outcomes of kidney transplantation.
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Rudnicki M, Perco P, D Haene B, Leierer J, Heinzel A, Mühlberger I, Schweibert N, Sunzenauer J, Regele H, Kronbichler A, Mestdagh P, Vandesompele J, Mayer B, Mayer G. Renal microRNA- and RNA-profiles in progressive chronic kidney disease. Eur J Clin Invest 2016; 46:213-26. [PMID: 26707063 DOI: 10.1111/eci.12585] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 12/20/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) contribute to chronic kidney disease (CKD) progression via regulating mRNAs involved in renal homeostasis. However, their association with clinical outcome remains poorly understood. MATERIALS AND METHODS We performed miRNA and mRNA expression profiling on renal biopsy sections by qPCR (miRNA) and microarrays (mRNA) in a discovery (n = 43) and in a validation (n = 29) cohort. miRNAs differentiating stable and progressive cases were inversely correlated with putative target mRNAs, which were further characterized by pathway analysis using KEGG pathways. RESULTS miR-30d, miR-140-3p, miR-532-3p, miR-194, miR-190, miR-204 and miR-206 were downregulated in progressive cases. These seven miRNAs correlated with upregulated 29 target mRNAs involved in inflammatory response, cell-cell interaction, apoptosis and intra-cellular signalling. In particular, miR-206 and miR-532-3p were associated with distinct biological processes via the expression of their target mRNAs: Reduced expression of miR-206 in progressive disease correlated with the upregulation of target mRNAs participating in inflammatory pathways (CCL19, CXCL1, IFNAR2, NCK2, PTK2B, PTPRC, RASGRP1 and TNFRSF25). Progressive cases also showed a lower expression of miR-532-3p and an increased expression of target transcripts involved in apoptosis pathways (MAP3K14, TNFRSF10B/TRAIL-R2, TRADD and TRAF2). In the validation cohort, we confirmed the decreased expression of miR-206 and miR-532-3p, and the inverse correlation of these miRNAs with the expression of nine of the 12 target genes. The levels of the identified miRNAs and the target mRNAs correlated with clinical parameters and histological damage indices. CONCLUSIONS These results suggest the involvement of specific miRNAs and mRNAs in biological pathways associated with the progression of CKD.
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Affiliation(s)
- Michael Rudnicki
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | - Paul Perco
- Emergentec Biodevelopment GmbH, Vienna, Austria
| | | | - Johannes Leierer
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | | | | | - Ninella Schweibert
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | - Judith Sunzenauer
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria.,Department of Nephrology, KH Elisabethinen, Linz, Austria
| | - Heinz Regele
- Institute of Pathology, Medical University Vienna, Vienna, Austria
| | - Andreas Kronbichler
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | | | | | - Bernd Mayer
- Emergentec Biodevelopment GmbH, Vienna, Austria
| | - Gert Mayer
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
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Factors affecting the accuracy of a class prediction model in gene expression data. BMC Bioinformatics 2015; 16:199. [PMID: 26093633 PMCID: PMC4475623 DOI: 10.1186/s12859-015-0610-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/30/2015] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Class prediction models have been shown to have varying performances in clinical gene expression datasets. Previous evaluation studies, mostly done in the field of cancer, showed that the accuracy of class prediction models differs from dataset to dataset and depends on the type of classification function. While a substantial amount of information is known about the characteristics of classification functions, little has been done to determine which characteristics of gene expression data have impact on the performance of a classifier. This study aims to empirically identify data characteristics that affect the predictive accuracy of classification models, outside of the field of cancer. RESULTS Datasets from twenty five studies meeting predefined inclusion and exclusion criteria were downloaded. Nine classification functions were chosen, falling within the categories: discriminant analyses or Bayes classifiers, tree based, regularization and shrinkage and nearest neighbors methods. Consequently, nine class prediction models were built for each dataset using the same procedure and their performances were evaluated by calculating their accuracies. The characteristics of each experiment were recorded, (i.e., observed disease, medical question, tissue/cell types and sample size) together with characteristics of the gene expression data, namely the number of differentially expressed genes, the fold changes and the within-class correlations. Their effects on the accuracy of a class prediction model were statistically assessed by random effects logistic regression. The number of differentially expressed genes and the average fold change had significant impact on the accuracy of a classification model and gave individual explained-variation in prediction accuracy of up to 72% and 57%, respectively. Multivariable random effects logistic regression with forward selection yielded the two aforementioned study factors and the within class correlation as factors affecting the accuracy of classification functions, explaining 91.5% of the between study variation. CONCLUSIONS We evaluated study- and data-related factors that might explain the varying performances of classification functions in non-cancerous datasets. Our results showed that the number of differentially expressed genes, the fold change, and the correlation in gene expression data significantly affect the accuracy of class prediction models.
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Boor P, Floege J. Renal allograft fibrosis: biology and therapeutic targets. Am J Transplant 2015; 15:863-86. [PMID: 25691290 DOI: 10.1111/ajt.13180] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/30/2014] [Accepted: 12/19/2014] [Indexed: 01/25/2023]
Abstract
Renal tubulointerstitial fibrosis is the final common pathway of progressive renal diseases. In allografts, it is assessed with tubular atrophy as interstitial fibrosis/tubular atrophy (IF/TA). IF/TA occurs in about 40% of kidney allografts at 3-6 months after transplantation, increasing to 65% at 2 years. The origin of renal fibrosis in the allograft is complex and includes donor-related factors, in particular in case of expanded criteria donors, ischemia-reperfusion injury, immune-mediated damage, recurrence of underlying diseases, hypertensive damage, nephrotoxicity of immunosuppressants, recurrent graft infections, postrenal obstruction, etc. Based largely on studies in the non-transplant setting, there is a large body of literature on the role of different cell types, be it intrinsic to the kidney or bone marrow derived, in mediating renal fibrosis, and the number of mediator systems contributing to fibrotic changes is growing steadily. Here we review the most important cellular processes and mediators involved in the progress of renal fibrosis, with a focus on the allograft situation, and discuss some of the challenges in translating experimental insights into clinical trials, in particular fibrosis biomarkers or imaging modalities.
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Affiliation(s)
- P Boor
- Division of Nephrology and Clinical Immunology, RWTH University of Aachen, Aachen, Germany; Department of Pathology, RWTH University of Aachen, Aachen, Germany; Institute of Molecular Biomedicine, Bratislava, Slovakia
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Rogers NM, Ferenbach DA, Isenberg JS, Thomson AW, Hughes J. Dendritic cells and macrophages in the kidney: a spectrum of good and evil. Nat Rev Nephrol 2014; 10:625-43. [PMID: 25266210 PMCID: PMC4922410 DOI: 10.1038/nrneph.2014.170] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Renal dendritic cells (DCs) and macrophages represent a constitutive, extensive and contiguous network of innate immune cells that provide sentinel and immune-intelligence activity; they induce and regulate inflammatory responses to freely filtered antigenic material and protect the kidney from infection. Tissue-resident or infiltrating DCs and macrophages are key factors in the initiation and propagation of renal disease, as well as essential contributors to subsequent tissue regeneration, regardless of the aetiological and pathogenetic mechanisms. The identification, and functional and phenotypic distinction of these cell types is complex and incompletely understood, and the same is true of their interplay and relationships with effector and regulatory cells of the adaptive immune system. In this Review, we discuss the common and distinct characteristics of DCs and macrophages, as well as key advances that have identified the renal-specific functions of these important phagocytic, antigen-presenting cells, and their roles in potentiating or mitigating intrinsic kidney disease. We also identify remaining issues that are of priority for further investigation, and highlight the prospects for translational and therapeutic application of the knowledge acquired.
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Affiliation(s)
- Natasha M Rogers
- Vascular Medicine Institute and Thomas E. Starzl Transplantation Institute, University of Pittsburgh School of Medicine, W1544 Biomedical Science Tower, 200 Lothrop Street, Pittsburgh, PA 15261, USA
| | - David A Ferenbach
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Jeffrey S Isenberg
- Vascular Medicine Institute and Thomas E. Starzl Transplantation Institute, University of Pittsburgh School of Medicine, W1544 Biomedical Science Tower, 200 Lothrop Street, Pittsburgh, PA 15261, USA
| | - Angus W Thomson
- Vascular Medicine Institute and Thomas E. Starzl Transplantation Institute, University of Pittsburgh School of Medicine, W1544 Biomedical Science Tower, 200 Lothrop Street, Pittsburgh, PA 15261, USA
| | - Jeremy Hughes
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
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Novianti PW, Roes KCB, Eijkemans MJC. Evaluation of gene expression classification studies: factors associated with classification performance. PLoS One 2014; 9:e96063. [PMID: 24770439 PMCID: PMC4000205 DOI: 10.1371/journal.pone.0096063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 04/03/2014] [Indexed: 12/22/2022] Open
Abstract
Classification methods used in microarray studies for gene expression are diverse in the way they deal with the underlying complexity of the data, as well as in the technique used to build the classification model. The MAQC II study on cancer classification problems has found that performance was affected by factors such as the classification algorithm, cross validation method, number of genes, and gene selection method. In this paper, we study the hypothesis that the disease under study significantly determines which method is optimal, and that additionally sample size, class imbalance, type of medical question (diagnostic, prognostic or treatment response), and microarray platform are potentially influential. A systematic literature review was used to extract the information from 48 published articles on non-cancer microarray classification studies. The impact of the various factors on the reported classification accuracy was analyzed through random-intercept logistic regression. The type of medical question and method of cross validation dominated the explained variation in accuracy among studies, followed by disease category and microarray platform. In total, 42% of the between study variation was explained by all the study specific and problem specific factors that we studied together.
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Affiliation(s)
- Putri W Novianti
- Biostatistics & Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kit C B Roes
- Biostatistics & Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marinus J C Eijkemans
- Biostatistics & Research Support, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
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Maluf DG, Dumur CI, Suh JL, Scian MJ, King AL, Cathro H, Lee JK, Gehrau RC, Brayman KL, Gallon L, Mas VR. The urine microRNA profile may help monitor post-transplant renal graft function. Kidney Int 2014; 85:439-49. [PMID: 24025639 PMCID: PMC3946645 DOI: 10.1038/ki.2013.338] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 06/06/2013] [Accepted: 06/20/2013] [Indexed: 02/08/2023]
Abstract
Noninvasive, cost-effective biomarkers that allow accurate monitoring of graft function are needed in kidney transplantation. Since microRNAs (miRNAs) have emerged as promising disease biomarkers, we sought to establish an miRNA signature in urinary cell pellets comparing kidney transplant patients diagnosed with chronic allograft dysfunction (CAD) with interstitial fibrosis and tubular atrophy and those recipients with normal graft function. Overall, we evaluated 191 samples from 125 deceased donor primary kidney transplant recipients in the discovery, initial validation, and the longitudinal validation studies for noninvasive monitoring of graft function. Of 1733 mature miRNAs studied using microarrays, 22 were found to be differentially expressed between groups. Ontology and pathway analyses showed inflammation as the principal biological function associated with these miRNAs. Twelve selected miRNAs were longitudinally evaluated in urine samples of an independent set of 66 patients, at two time points after kidney transplant. A subset of these miRNAs was found to be differentially expressed between groups early after kidney transplant before histological allograft injury was evident. Thus, a panel of urine miRNAs was identified as potential biomarkers for monitoring graft function and anticipating progression to CAD in kidney transplant patients.
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Affiliation(s)
- Daniel G Maluf
- University of Virginia, Department of Surgery, PO Box 800679, Charlottesville, VA 22908-0679
| | - Catherine I Dumur
- Virginia Commonwealth University, Department of Pathology, PO Box 980662, VA 23298-0662
| | - Jihee L Suh
- University of Virginia, Department of Surgery, PO Box 800679, Charlottesville, VA 22908-0679
| | - Mariano J Scian
- University of Virginia, Department of Surgery, PO Box 800679, Charlottesville, VA 22908-0679
| | - Anne L King
- Virginia Commonwealth University, Division of Transplant, PO Box 980645, VA 23219-0645
| | - Helen Cathro
- Virginia Commonwealth University, Department of Pathology, PO Box 980662, VA 23298-0662
| | - Jae K Lee
- University of Virginia, Division of Biostatistics, Department of Public Health Sciences, PO Box 800717, VA 22908-0717
| | - Ricardo C Gehrau
- University of Virginia, Department of Surgery, PO Box 800679, Charlottesville, VA 22908-0679
| | - Kenneth L Brayman
- University of Virginia, Department of Surgery, PO Box 800679, Charlottesville, VA 22908-0679
| | - Lorenzo Gallon
- Northwestern University, Division of Nephrology, Department of Internal Medicine, Comprehensive Transplant Center, Chicago, IL 60611
| | - Valeria R Mas
- University of Virginia, Department of Surgery, PO Box 800679, Charlottesville, VA 22908-0679
- Corresponding author: Valeria Mas, Ph.D., Associate Professor Research Surgery, Co-Director Transplant Research, Director Translational Genomics Transplant Laboratory, Transplant Division, Department of Surgery, University of Virginia, Department of Surgery, PO Box 800679, Charlottesville, VA 22908-0679,
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Abstract
Large numbers of macrophage lineage cells are present in transplants undergoing ischemia-reperfusion injury and rejection, and their presence correlates with a high probability of rejection. However, the extent to which monocytes and macrophages contribute to kidney graft rejection is poorly understood. The heterogeneity of the monocyte/macrophage lineage cells could be one of the reasons why these cells have been neglected up to now. Circulating monocytes can be divided into various subsets, which are able to give rise to tissue macrophages and dendritic cells. Macrophages are believed to be highly plastic cells that can respond to environmental signals by changing their phenotype and function. Macrophages have established roles in early and late kidney graft inflammation, tissue homeostasis, remodeling, and repair. In kidney transplantation, macrophages are believed to play a role in both damage and repair of the graft, depending on the type of macrophages involved, the environmental drive, and the time after transplantation. The heterogeneity and plasticity of monocytes and macrophages are obstacles to translating the functional relevance of this cell lineage to diagnostic and prognostic clinical parameters and to defining specific, macrophage-related, therapeutic targets. Recent evidence has indicated an immunomodulatory role for the so-called regulatory macrophages in induction of tolerance in kidney transplant recipients. In this article, we summarize current views on monocyte/macrophage immunobiology in kidney transplantation. Key issues for ongoing research are discussed.
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Scian MJ, Maluf DG, Archer KJ, Turner SD, Suh JL, David KG, King AL, Posner MP, Brayman KL, Mas VR. Identification of biomarkers to assess organ quality and predict posttransplantation outcomes. Transplantation 2012; 94:851-8. [PMID: 22992769 PMCID: PMC3927314 DOI: 10.1097/tp.0b013e318263702b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
UNLABELLED The increased disparity between organ supply and need has led to the use of extended criteria donors and donation after cardiac death donors with other comorbidities. METHODS We have examined the preimplantation transcriptome of 112 kidney transplant recipient samples from 100 deceased-donor kidneys by microarray profiling. Subject groups were segregated based on estimated glomerular filtration rate (eGFR) at 1 month after transplantation: the GFR-high group (n=74) included patients with eGFR 45 mL/min per 1.73 m(2), whereas the GFR-low group (n=35) included patients with eGFR 45 mL/min or less per 1.73 m(2). RESULTS Gene expression profiling identified higher expression of 160 probe sets (140 genes) in the GFR-low group, whereas expression of 37 probe sets (33 genes) was higher in the GFR-high group (P<0.01, false discovery rate <0.2). Four genes (CCL5, CXCR4, ITGB2, and EGF) were selected based on fold change and P value and further validated using an independent set of samples. A random forest analysis identified three of these genes (CCL5, CXCR4, and ITGB2) as important predictors of graft function after transplantation. CONCLUSIONS Inclusion of pretransplantation molecular gene expression profiles in donor quality assessment systems may provide the necessary information for better donor organ selection and function prediction. These biomarkers would further allow a more objective and complete assessment of procured renal allografts at pretransplantation time.
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Affiliation(s)
- Mariano J Scian
- Division of Transplantation, Department of Surgery, University of Virginia School of Medicine, Charlottesville, VA 22908-0679, USA
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19
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Microarray gene expression profiling of chronic allograft nephropathy in the rat kidney transplant model. Transpl Immunol 2012; 27:75-82. [DOI: 10.1016/j.trim.2012.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 06/12/2012] [Accepted: 06/13/2012] [Indexed: 11/20/2022]
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Abstract
PURPOSE OF REVIEW Tubulointerstitial injury in the kidney is complex, involving a number of independent and overlapping cellular and molecular pathways, with renal interstitial fibrosis and tubular atrophy (IFTA) as the final common pathway. Furthermore, there are multiple ways to assess IFTA. RECENT FINDINGS Cells involved include tubular epithelial cells, fibroblasts, fibrocytes, myofibroblasts, monocyte/macrophages, and mast cells with complex and still incompletely characterized cell-molecular interactions. Molecular mediators involved are numerous and involve pathways such as transforming growth factor (TGF)-β, bone morphogenic protein (BMP), platelet-derived growth factor (PDGF), and hepatocyte growth factor (HGF). Recent genomic approaches have shed insight into some of these cellular and molecular pathways. Pathologic evaluation of IFTA is central in assessing the severity of chronic disease; however, there are a variety of methods used to assess IFTA. Most assessment of IFTA relies on pathologist assessment of special stains such as trichrome, Sirius Red, and collagen III immunohistochemistry. Visual pathologist assessment can be prone to intra and interobserver variability, but some methods employ computerized morphometery, without a clear consensus as to the best method. SUMMARY IFTA results from on orchestration of cell types and molecular pathways. Opinions vary on the optimal qualitative and quantitative assessment of IFTA.
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Affiliation(s)
- Alton B Farris
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia 30322, USA.
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Danger R, Pallier A, Giral M, Martínez-Llordella M, Lozano JJ, Degauque N, Sanchez-Fueyo A, Soulillou JP, Brouard S. Upregulation of miR-142-3p in peripheral blood mononuclear cells of operationally tolerant patients with a renal transplant. J Am Soc Nephrol 2012; 23:597-606. [PMID: 22282590 DOI: 10.1681/asn.2011060543] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Achieving drug-free tolerance or successfully using only small doses of immunosuppression is a major goal in organ transplantation. To investigate the potential mechanisms by which some kidney transplant recipients can achieve operational tolerance, we compared the expression profiles of microRNA in peripheral blood mononuclear cells of operationally tolerant patients with those of stable patients treated with conventional immunosuppression. B cells from operationally tolerant patients overexpressed miR-142-3p. The expression of miR-142-3p was stable over time and was not modulated by immunosuppression. In Raji B cells, overexpression of miR-142-3p modulated nearly 1000 genes related to the immune response of B cells, including potential miR-142-3p targets and molecules previously identified in the blood of operationally tolerant patients. Furthermore, our results suggested that a negative feedback loop involving TGF-β signaling and miR-142-3p expression in B cells may contribute to the maintenance of tolerance. In summary, miR-142-3p expression in peripheral blood mononuclear cells correlates with operational tolerance. Whether upregulation of miR-142-3p modulates inflammatory responses to promote tolerance or is a result of this tolerance state requires further study.
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Affiliation(s)
- Richard Danger
- Institut National de la Santé Et de la Recherche Médicale UMR643 and Institut de Transplantation Urologie, Néphrologie, Nantes, France
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Scian MJ, Maluf DG, David KG, Archer KJ, Suh JL, Wolen AR, Mba MU, Massey HD, King AL, Gehr T, Cotterell A, Posner M, Mas V. MicroRNA profiles in allograft tissues and paired urines associate with chronic allograft dysfunction with IF/TA. Am J Transplant 2011; 11:2110-22. [PMID: 21794090 PMCID: PMC3184368 DOI: 10.1111/j.1600-6143.2011.03666.x] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Despite the advances in immunosuppression, renal allograft attrition over time remains unabated due to chronic allograft dysfunction (CAD) with interstitial fibrosis (IF) and tubular atrophy (TA). We aimed to evaluate microRNA (miRNA) signatures in CAD with IF/TA and appraise correlation with paired urine samples and potential utility in prospective evaluation of graft function. MiRNA signatures were established between CAD with IF/TA versus normal allografts by microarray. Validation of the microarray results and prospective evaluation of urine samples was performed using real-time quantitative-PCR (RT-qPCR). Fifty-six miRNAs were identified in samples with CAD-IF/TA. Five miRNAs were selected for further validation based on array fold change, p-value and in silico predicted mRNA targets. We confirmed the differential expression of these five miRNAs by RT-qPCR using an independent set of samples. Differential expression was detected for miR-142-3p, miR-204, miR-107 and miR-211 (p < 0.001) and miR-32 (p < 0.05). Furthermore, differential expression of miR-142-3p (p < 0.01), miR-204 (p < 0.01) and miR-211 (p < 0.05) was also observed between patient groups in urine samples. A characteristic miRNA signature for IF/TA that correlates with paired urine samples was identified. These results support the potential use of miRNAs as noninvasive markers of IF/TA and for monitoring graft function.
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Affiliation(s)
- MJ Scian
- Virginia Commonwealth University, Department of Surgery P.O. Box 980645, 1200 E. Broad Street, Richmond, VA 23219-0645
| | - DG Maluf
- Virginia Commonwealth University, Department of Surgery P.O. Box 980645, 1200 E. Broad Street, Richmond, VA 23219-0645
| | - KG David
- Virginia Commonwealth University, Department of Surgery P.O. Box 980645, 1200 E. Broad Street, Richmond, VA 23219-0645
| | - KJ Archer
- Virginia Commonwealth University, Department of Surgery P.O. Box 980645, 1200 E. Broad Street, Richmond, VA 23219-0645,
Virginia Commonwealth University, Department of Biostatistics P.O. Box 980032, 730 East Broad Street, Room 3006, Richmond, VA 23298-0032
| | - JL Suh
- Virginia Commonwealth University, Department of Surgery P.O. Box 980645, 1200 E. Broad Street, Richmond, VA 23219-0645
| | - AR Wolen
- Virginia Commonwealth University, Department of Human and Molecular Genetics P.O. Box 980033, 1101 East Marshall Street, Richmond, Virginia 23298-0033
| | - MU Mba
- Virginia Commonwealth University, Department of Surgery P.O. Box 980645, 1200 E. Broad Street, Richmond, VA 23219-0645
| | - HD Massey
- Virginia Commonwealth University, Department of Surgery P.O. Box 980645, 1200 E. Broad Street, Richmond, VA 23219-0645
| | - AL King
- Virginia Commonwealth University, Department of Surgery P.O. Box 980645, 1200 E. Broad Street, Richmond, VA 23219-0645
| | - T Gehr
- Virginia Commonwealth University, Department of Surgery P.O. Box 980645, 1200 E. Broad Street, Richmond, VA 23219-0645
| | - A Cotterell
- Virginia Commonwealth University, Department of Surgery P.O. Box 980645, 1200 E. Broad Street, Richmond, VA 23219-0645
| | - M Posner
- Virginia Commonwealth University, Department of Surgery P.O. Box 980645, 1200 E. Broad Street, Richmond, VA 23219-0645
| | - V Mas
- Virginia Commonwealth University, Department of Surgery P.O. Box 980645, 1200 E. Broad Street, Richmond, VA 23219-0645,
Virginia Commonwealth University, Department of Pathology PO Box 980662, 1101 E. Marshall Street, Richmond, VA 23298-0662,Corresponding author: Virginia Commonwealth University, Department of Surgery P.O. Box 980645 1200 E. Broad Street, Richmond VA 23219-0645
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Naesens M, Khatri P, Li L, Sigdel TK, Vitalone MJ, Chen R, Butte AJ, Salvatierra O, Sarwal MM. Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes. Kidney Int 2011; 80:1364-76. [PMID: 21881554 DOI: 10.1038/ki.2011.245] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The degree of progressive chronic histological damage is associated with long-term renal allograft survival. In order to identify promising molecular targets for timely intervention, we examined renal allograft protocol and indication biopsies from 120 low-risk pediatric and adolescent recipients by whole-genome microarray expression profiling. In data-driven analysis, we found a highly regulated pattern of adaptive and innate immune gene expression that correlated with established or ongoing histological chronic injury, and also with development of future chronic histological damage, even in histologically pristine kidneys. Hence, histologically unrecognized immunological injury at a molecular level sets the stage for the development of chronic tissue injury, while the same molecular response is accentuated during established and worsening chronic allograft damage. Irrespective of the hypothesized immune or nonimmune trigger for chronic allograft injury, a highly orchestrated regulation of innate and adaptive immune responses was found in the graft at the molecular level. This occurred months before histologic lesions appear, and quantitatively below the diagnostic threshold of classic T-cell or antibody-mediated rejection. Thus, measurement of specific immune gene expression in protocol biopsies may be warranted to predict the development of subsequent chronic injury in histologically quiescent grafts and as a means to titrate immunosuppressive therapy.
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Affiliation(s)
- Maarten Naesens
- Division of Nephrology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
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