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Katsiki AD, Karatzas PE, De Lastic HX, Georgakilas AG, Tsitsilonis O, Vorgias CE. DExplore: An Online Tool for Detecting Differentially Expressed Genes from mRNA Microarray Experiments. BIOLOGY 2024; 13:351. [PMID: 38785833 PMCID: PMC11117493 DOI: 10.3390/biology13050351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Microarray experiments, a mainstay in gene expression analysis for nearly two decades, pose challenges due to their complexity. To address this, we introduce DExplore, a user-friendly web application enabling researchers to detect differentially expressed genes using data from NCBI's GEO. Developed with R, Shiny, and Bioconductor, DExplore integrates WebGestalt for functional enrichment analysis. It also provides visualization plots for enhanced result interpretation. With a Docker image for local execution, DExplore accommodates unpublished data. To illustrate its utility, we showcase two case studies on cancer cells treated with chemotherapeutic drugs. DExplore streamlines microarray data analysis, empowering molecular biologists to focus on genes of biological significance.
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Affiliation(s)
- Anna D. Katsiki
- Department of Biology, School of Science, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Pantelis E. Karatzas
- Unit of Process Control and Informatics, Department of Process Analysis and Plant Design, School of Chemical Engineering, National Technical University of Athens (NTUA), Zografou Campus, 15780 Athens, Greece
| | - Hector-Xavier De Lastic
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou Campus, 15780 Athens, Greece
| | - Alexandros G. Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou Campus, 15780 Athens, Greece
| | - Ourania Tsitsilonis
- Department of Biology, School of Science, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Constantinos E. Vorgias
- Department of Biology, School of Science, National and Kapodistrian University of Athens, 15784 Athens, Greece
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2
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Advances and New Insights in Post-Transplant Care: From Sequencing to Imaging. CURRENT TREATMENT OPTIONS IN CARDIOVASCULAR MEDICINE 2020. [DOI: 10.1007/s11936-020-00828-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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3
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The Use of Genomics and Pathway Analysis in Our Understanding and Prediction of Clinical Renal Transplant Injury. Transplantation 2017; 100:1405-14. [PMID: 26447506 DOI: 10.1097/tp.0000000000000943] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The development and application of high-throughput molecular profiling have transformed the study of human diseases. The problem of handling large, complex data sets has been facilitated by advances in complex computational analysis. In this review, the recent literature regarding the application of transcriptional genomic information to renal transplantation, with specific reference to acute rejection, acute kidney injury in allografts, chronic allograft injury, and tolerance is discussed, as is the current published data regarding other "omics" strategies-proteomics, metabolomics, and the microRNA transcriptome. These data have shed new light on our understanding of the pathogenesis of specific disease conditions after renal transplantation, but their utility as a biomarker of disease has been hampered by study design and sample size. This review aims to highlight the opportunities and obstacles that exist with genomics and other related technologies to better understand and predict renal allograft outcome.
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4
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Menon MC, Murphy B, Heeger PS. Moving Biomarkers toward Clinical Implementation in Kidney Transplantation. J Am Soc Nephrol 2017; 28:735-747. [PMID: 28062570 DOI: 10.1681/asn.2016080858] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Long-term kidney transplant outcomes remain suboptimal, delineating an unmet medical need. Although current immunosuppressive therapy in kidney transplant recipients is effective, dosing is conventionally adjusted empirically on the basis of time after transplant or altered in response to detection of kidney dysfunction, histologic evidence of allograft damage, or infection. Such strategies tend to detect allograft rejection after significant injury has already occurred, fail to detect chronic subclinical inflammation that can negatively affect graft survival, and ignore specific risks and immune mechanisms that differentially contribute to allograft damage among transplant recipients. Assays and biomarkers that reliably quantify and/or predict the risk of allograft injury have the potential to overcome these deficits and thereby, aid clinicians in optimizing immunosuppressive regimens. Herein, we review the data on candidate biomarkers that we contend have the highest potential to become clinically useful surrogates in kidney transplant recipients, including functional T cell assays, urinary gene and protein assays, peripheral blood cell gene expression profiles, and allograft gene expression profiles. We identify barriers to clinical biomarker adoption in the transplant field and suggest strategies for moving biomarker-based individualization of transplant care from a research hypothesis to clinical implementation.
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Affiliation(s)
- Madhav C Menon
- Renal Division, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Barbara Murphy
- Renal Division, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Peter S Heeger
- Renal Division, Department of Medicine, Translational Transplant Research Center, Icahn School of Medicine at Mount Sinai, New York, New York
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5
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Crescioli C. Chemokines and transplant outcome. Clin Biochem 2016; 49:355-62. [DOI: 10.1016/j.clinbiochem.2015.07.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/10/2015] [Accepted: 07/20/2015] [Indexed: 12/26/2022]
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6
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Menon MC, Chuang PY, Li Z, Wei C, Zhang W, Luan Y, Yi Z, Xiong H, Woytovich C, Greene I, Overbey J, Rosales I, Bagiella E, Chen R, Ma M, Li L, Ding W, Djamali A, Saminego M, O'Connell PJ, Gallon L, Colvin R, Schroppel B, He JC, Murphy B. Intronic locus determines SHROOM3 expression and potentiates renal allograft fibrosis. J Clin Invest 2014; 125:208-21. [PMID: 25437874 DOI: 10.1172/jci76902] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 10/31/2014] [Indexed: 01/01/2023] Open
Abstract
Fibrosis underlies the loss of renal function in patients with chronic kidney disease (CKD) and in kidney transplant recipients with chronic allograft nephropathy (CAN). Here, we studied the effect of an intronic SNP in SHROOM3, which has previously been linked to CKD, on the development of CAN in a prospective cohort of renal allograft recipients. The presence of the rs17319721 allele at the SHROOM3 locus in the donor correlated with increased SHROOM3 expression in the allograft. In vitro, we determined that the sequence containing the risk allele at rs17319721 is a transcription factor 7-like 2-dependent (TCF7L2-dependent) enhancer element that functions to increase SHROOM3 transcription. In renal tubular cells, TGF-β1 administration upregulated SHROOM3 expression in a β-catenin/TCF7L2-mediated manner, while SHROOM3 in turn facilitated canonical TGF-β1 signaling and increased α1 collagen (COL1A1) expression. Inducible and tubular cell-specific knockdown of Shroom3 markedly abrogated interstitial fibrosis in mice with unilateral ureteric obstruction. Moreover, SHROOM3 expression in allografts at 3 months after transplant and the presence of the SHROOM3 risk allele in the donor correlated with increased allograft fibrosis and with reduced estimated glomerular filtration rate at 12 months after transplant. Our findings suggest that rs17319721 functions as a cis-acting expression quantitative trait locus of SHROOM3 that facilitates TGF-β1 signaling and contributes to allograft injury.
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Abstract
Transcriptional profiling of organ transplants is increasingly defining the biological pathways responsible for graft rejection at the molecular level and identifying gene transcripts that diagnose or predict rejection. These advances hold significant promise for the treatment of organ rejection and for improving clinical outcomes after transplantation, but hurdles remain.
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Affiliation(s)
- Fadi G Lakkis
- the Department of Surgery University of Pittsburgh School of Medicine, Pittsburgh, PA 15261. F.G. Lakkis is at the Thomas E. Starzl Transplantation Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
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8
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Volk HD, Sawitzki B, Reinke P. Molecular analysis of renal allograft biopsies--more than a nice toy for researchers? Am J Transplant 2013; 13:539-40. [PMID: 23437880 DOI: 10.1111/ajt.12081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 11/28/2012] [Accepted: 11/29/2012] [Indexed: 01/25/2023]
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9
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Zarrinpar A, Busuttil RW. Immunomodulating options for liver transplant patients. Expert Rev Clin Immunol 2013; 8:565-78; quiz 578. [PMID: 22992151 DOI: 10.1586/eci.12.47] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Much has changed since the early years of liver transplantation. Improvements in post-transplant survival are largely due to more selective and less toxic immunosuppression regimens and advances in operative and perioperative care. This has allowed liver transplantation to become an extremely successful treatment option for patients with endstage liver disease. Beginning with cyclosporine, a cyclic endecapeptide of fungal origin and the first of the calcineurin inhibitors to find widespread use, immunosuppressive regimens have evolved to include additional calcineurin inhibitors, steroids, mTOR inhibitors, antimetabolites and antibodies, mostly targeting T-cell activation. This review will present currently available immunosuppressive agents used in the perioperative period of liver transplantation, as well as maintenance treatments, tailoring therapeutic strategies for specific populations, and advances in immune monitoring and tolerance.
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Affiliation(s)
- Ali Zarrinpar
- Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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Scherer A, Dai M, Meng F. Impact of experimental noise and annotation imprecision on data quality in microarray experiments. Methods Mol Biol 2013; 972:155-76. [PMID: 23385537 DOI: 10.1007/978-1-60327-337-4_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Data quality is intrinsically influenced by design, technical, and analytical parameters. Quality parameters have not yet been well defined for gene expression analysis by microarrays, though ad interim, following recommended good experimental practice guidelines should ensure generation of reliable and reproducible data. Here we summarize essential practical recommendations for experimental design, technical considerations, feature annotation issues, and standardization efforts.
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Affiliation(s)
- Andreas Scherer
- Genomics, Biomarker Development, Spheromics, Kontiolahti, Joensuu, Finland.
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11
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Chauhan V, Howland M, Mendenhall A, O'Hara S, Stocki TJ, McNamee JP, Wilkins RC. Effects of alpha particle radiation on gene expression in human pulmonary epithelial cells. Int J Hyg Environ Health 2012; 215:522-35. [PMID: 22608759 DOI: 10.1016/j.ijheh.2012.04.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 03/27/2012] [Accepted: 04/15/2012] [Indexed: 01/11/2023]
Abstract
The general public receives approximately half of its exposure to natural radiation through alpha (α)-particles from radon ((222)Rn) gas and its decay progeny. Epidemiological studies have found a positive correlation between exposure to (222)Rn and lung carcinogenesis. An understanding of the transcriptional responses involved in these effects remains limited. In this study, genomic technology was employed to mine for subtle changes in gene expression that may be representative of an altered physiological state. Human lung epithelial cells were exposed to 0, 0.03, 0.3 and 0.9Gy of α-particle radiation. Microarray analysis was employed to determine transcript expression levels 4h and 24h after exposure. A total of 590 genes were shown to be differentially expressed in the α-particle radiated samples (false discovery rate (FDR)≤0.05). Sub-set of these transcripts were time-responsive, dose-responsive and both time- and dose-responsive. Pathway analysis showed functions related to cell cycle arrest, and DNA replication, recombination and repair (FDR≤0.05). The canonical pathways associated with these genes were in relation to pyrimidine metabolism, G2/M damage checkpoint regulation and p53 signaling (FDR≤0.05). Overall, this gene expression profile suggests that α-particle radiation inhibits DNA synthesis and subsequent mitosis, and causes cell cycle arrest.
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Affiliation(s)
- Vinita Chauhan
- Environmental and Radiation Health Sciences Directorate, Health Canada, Ottawa, Ontario, Canada K1A 0K9. Vinita
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12
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Romagnani P, Crescioli C. CXCL10: a candidate biomarker in transplantation. Clin Chim Acta 2012; 413:1364-73. [PMID: 22366165 DOI: 10.1016/j.cca.2012.02.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Revised: 02/10/2012] [Accepted: 02/10/2012] [Indexed: 10/28/2022]
Abstract
Interferon (IFN) γ-induced protein 10 kDa (IP-10) or C-X-C motif chemokine 10 (CXCL10) is a small cytokine belonging to the CXC chemokine family. This family of signaling molecules is known to control several biological functions and to also play pivotal roles in disease initiation and progression. By binding to its specific cognate receptor CXCR3, CXCL10 critically regulates chemotaxis during several immune-inflammatory processes. In particular, this chemokine controls chemotaxis during the inflammatory response resulting from allograft rejection after transplantation. Interestingly, a strong association has been described between CXCL10 production, immune response and the fate of the graft following allotransplantation. Enhanced CXCL10 production has been observed in recipients of transplants of different organs. This enhanced production likely comes from either the graft or the immune cells and is correlated with an increase in the concentration of circulating CXCL10. Because CXCL10 can be easily measured in the serum and plasma from a patient, the detection and quantitation of circulating CXCL10 could be used to reveal a transplant recipient's immune status. The purpose of this review is to examine the critical role of CXCL10 in the pathogenesis of allograft rejection following organ transplantation. This important role highlights the potential utilization of CXCL10 not only as a therapeutic target but also as a biomarker to predict the severity of rejection, to monitor the inflammatory status of organ recipients and, hopefully, to fine-tune patient therapy in transplantation.
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Affiliation(s)
- Paola Romagnani
- Excellence Center for Research, Transfer and High Education (DENOthe), University of Florence, 50139 Florence, Italy
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Zarkhin V, Sarwal MM. The coin toss of B cells in rejection and tolerance: danger versus defense. Semin Immunol 2011; 24:86-91. [PMID: 22035649 DOI: 10.1016/j.smim.2011.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 09/30/2011] [Indexed: 01/27/2023]
Abstract
Transplantation is the preferred therapy for the end stage organ disease. Since the introduction of organ transplantation into medical practice in 1953 [1], significant progress has been achieved in patient and graft survival rates due to improvements in surgical techniques and more targeted immunosuppressive medications [2]. Nevertheless, current gaps in the management of the transplant patient stem from an incomplete understanding about the heterogeneity of the injury response in organ transplantation, at different rates and different time points after transplantation, as well as our inability to monitor the immunologic threshold of risk versus safety in each individual patient. Recent advances in immunology/transplantation biology with the advent of high throughput "omic" assays such as gene microarrays, proteomics, metabolomics, antibiomics, chemical genomics and functional imaging with nanoparticles, offers us unique methods to interrogate and decipher the variability and unpredictability of the immune response in organ transplantation (Fig. 1) [3]. Recent studies using these applications [3-8] have uncovered a critical and pivotal role for specific B cell lineages in organ injury [9] and organ acceptance [10,11] (Fig. 2). The availability of specific therapies against some of these defined B cell populations provides for an exciting new field of B cell targeted manipulation that can both abrogate the allospecific injury response, as well as promote allospecific graft accommodation and health.
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Affiliation(s)
- Valeriya Zarkhin
- Department of Pediatrics, Stanford University, Stanford, CA, USA
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Pallet N, Djamali A, Legendre C. Challenges in diagnosing acute calcineurin-inhibitor induced nephrotoxicity: From toxicogenomics to emerging biomarkers. Pharmacol Res 2011; 64:25-30. [DOI: 10.1016/j.phrs.2011.03.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/21/2011] [Accepted: 03/27/2011] [Indexed: 10/18/2022]
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Mas VR, Mueller TF, Archer KJ, Maluf DG. Identifying biomarkers as diagnostic tools in kidney transplantation. Expert Rev Mol Diagn 2011; 11:183-96. [PMID: 21405969 DOI: 10.1586/erm.10.119] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is a critical need for biomarkers for early diagnosis, treatment response, and surrogate end point and outcome prediction in organ transplantation, leading to a tailored and individualized treatment. Genomic and proteomic platforms have provided multiple promising new biomarkers during the last few years. However, there is still no routine application of any of these markers in clinical transplantation. This article will discuss the existing gap between biomarker discovery and clinical application in the kidney transplant setting. Approaches to implementing biomarker monitoring into clinical practice will also be discussed.
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Affiliation(s)
- Valeria R Mas
- Molecular Transplant Research Laboratory, Transplant Division, Department of Surgery, Molecular Medicine Research Building, Virginia Commonwealth University, 1220 East Broad Street, Richmond, VA 23298, USA.
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Roedder S, Vitalone M, Khatri P, Sarwal MM. Biomarkers in solid organ transplantation: establishing personalized transplantation medicine. Genome Med 2011; 3:37. [PMID: 21658299 PMCID: PMC3218811 DOI: 10.1186/gm253] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Technological advances in molecular and in silico research have enabled significant progress towards personalized transplantation medicine. It is now possible to conduct comprehensive biomarker development studies of transplant organ pathologies, correlating genomic, transcriptomic and proteomic information from donor and recipient with clinical and histological phenotypes. Translation of these advances to the clinical setting will allow assessment of an individual patient's risk of allograft damage or accommodation. Transplantation biomarkers are needed for active monitoring of immunosuppression, to reduce patient morbidity, and to improve long-term allograft function and life expectancy. Here, we highlight recent pre- and post-transplantation biomarkers of acute and chronic allograft damage or adaptation, focusing on peripheral blood-based methodologies for non-invasive application. We then critically discuss current findings with respect to their future application in routine clinical transplantation medicine. Complement-system-associated SNPs present potential biomarkers that may be used to indicate the baseline risk for allograft damage prior to transplantation. The detection of antibodies against novel, non-HLA, MICA antigens, and the expression of cytokine genes and proteins and cytotoxicity-related genes have been correlated with allograft damage and are potential post-transplantation biomarkers indicating allograft damage at the molecular level, although these do not have clinical relevance yet. Several multi-gene expression-based biomarker panels have been identified that accurately predicted graft accommodation in liver transplant recipients and may be developed into a predictive biomarker assay.
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Affiliation(s)
- Silke Roedder
- Department of Pediatrics and Immunology, Stanford University, G306 300 Pasteur Drive, Palo Alto, CA 94304, USA.
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Mueller TF, Solez K, Mas V. Assessment of kidney organ quality and prediction of outcome at time of transplantation. Semin Immunopathol 2011; 33:185-99. [PMID: 21274534 DOI: 10.1007/s00281-011-0248-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 01/13/2011] [Indexed: 12/13/2022]
Abstract
The critical importance of donor organ quality, i.e., number of surviving nephrons, ability to withstand injury, and capacity for repair in determining short- and long-term outcomes is becoming increasingly clear. This review provides an overview of studies to assess donor kidney quality and subsequent transplant outcomes based on clinical pathology and transcriptome-based variables available at time of transplantation. Prediction scores using clinical variables function when applied to large data sets but perform poorly for the individual patient. Histopathology findings in pre-implantation or post-reperfusion biopsies help to assess structural integrity of the donor kidney, provide information on pre-existing donor disease, and can serve as a baseline for tracking changes over time. However, more validated approaches of analysis and prospective studies are needed to reduce the number of discarded organs, improve allocation, and allow prediction of outcomes. Molecular profiling detects changes not seen by morphology or captured by clinical markers. In particular, molecular profiles provide a quantitative measurement of inflammatory burden or immune activation and reflect coordinated changes in pathways associated with injury and repair. However, description of transcriptome patterns is not an end in itself. The identification of predictive gene sets and the application to an individualized patient management needs the integration of clinical and pathology-based variables, as well as more objective reference markers of transplant function, post-transplant events, and long-term outcomes.
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Affiliation(s)
- Thomas F Mueller
- Division of Nephrology and Immunology, Department of Medicine, University of Alberta, Edmonton, AB, Canada.
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Distinctive gene expression profiles characterize donor biopsies from HCV-positive kidney donors. Transplantation 2011; 90:1172-9. [PMID: 20935597 DOI: 10.1097/tp.0b013e3181f9ca6c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Because of the shortage of organs for transplantation, procurement of kidneys from extended criteria donors is inevitable. Frequently, donors infected with hepatitis C virus (HCV) are used. To elucidate an initial compromise of molecular pathways in HCV graft, gene expression profiles were evaluated. METHODS Twenty-four donor allograft biopsies (n=12 HCV positive (+) and n=12 HCV negative (-)) were collected at preimplantation time and profiled using microarrays. Donors were age, race, gender, and cold and warm ischemia time matched between groups. Probe level data were read into the R programming environment using the affy Bioconductor package, and the robust multiarray average method was used to obtain probe set expression summaries. To identify probe sets exhibiting differential expression, a two sample t test was performed. Molecular and biologic functions were analyzed using Interaction Networks and Functional Analysis. RESULTS Fifty-eight probe sets were differentially expressed between HCV (+) versus HCV (-) donors (P<0.001). The molecular functions associated with the two top scored networks from the analysis of the differentially expressed genes were connective tissue development and function and tissue morphology (score 34), cell death, cell signaling, cellular assembly, and organization (score 32). Among the differentially affected top canonical pathways, we found the role of RIG1-like receptors in antiviral innate immunity (P<0.001), natural killer cell signaling (P=0.007), interleukin-8 signaling (P=0.048), interferon signaling (P=0.0 11; INFA21, INFGR1, and MED14), ILK signaling (P=0.001), and apoptosis signaling. CONCLUSIONS A unique gene expression pattern was identified in HCV (+) kidney grafts. Innate immune system and inflammatory pathways were the most affected.
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Selzner N, Grant DR, Shalev I, Levy GA. The immunosuppressive pipeline: meeting unmet needs in liver transplantation. Liver Transpl 2010; 16:1359-72. [PMID: 21117245 DOI: 10.1002/lt.22193] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Liver transplantation is now recognized as the treatment of choice for end-stage liver failure. Its success can be attributed largely to the generation of selective immunosuppressive agents, which have resulted in a dramatic reduction in the incidence of acute rejection and improvements in the short- and long-term outcomes of patients. However, the unresolved limitation of current immunosuppressive agents is long-term toxicity, which results in increases in the incidence and severity of cardiovascular, neurological, and renal diseases. Our recent understanding of the pathways of cell activation has resulted in the development of a new generation of immunosuppressive agents that may address the challenges facing transplantation today and allow the minimization or substitution of existing agents. Furthermore, advances in our understanding of the mechanisms of tolerance and the identification of biomarker signatures hold the promise that in some patients transplantation may be able to be performed without the need for long-term immunosuppression (tolerance).
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Affiliation(s)
- Nazia Selzner
- Multiorgan Transplant Program, University Health Network, University of Toronto, Toronto, Canada
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Abstract
The past few decades are characterized by an explosive evolution of genetics and molecular cell biology. Advances in chemistry and engineering have enabled increased data throughput, permitting the study of complete sets of molecules with increasing speed and accuracy using techniques such as genomics, transcriptomics, proteomics, and metabolomics. Prediction of long-term outcomes in transplantation is hampered by the absence of sufficiently robust biomarkers and a lack of adequate insight into the mechanisms of acute and chronic alloimmune injury and the adaptive mechanisms of immunological quiescence that may support transplantation tolerance. Here, we discuss some of the great opportunities that molecular diagnostic tools have to offer both basic scientists and translational researchers for bench-to-bedside clinical application in transplantation medicine, with special focus on genomics and genome-wide association studies, epigenetics (DNA methylation and histone modifications), gene expression studies and transcriptomics (including microRNA and small interfering RNA studies), proteomics and peptidomics, antibodyomics, metabolomics, chemical genomics and functional imaging with nanoparticles. We address the challenges and opportunities associated with the newer high-throughput sequencing technologies, especially in the field of bioinformatics and biostatistics, and demonstrate the importance of integrative approaches. Although this Review focuses on transplantation research and clinical transplantation, the concepts addressed are valid for all translational research.
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Maluf DG, Archer KJ, Villamil F, Stravitz RT, Mas V. Hepatitis C virus recurrence after liver transplantation: biomarkers of disease and fibrosis progression. Expert Rev Gastroenterol Hepatol 2010; 4:445-58. [PMID: 20678018 DOI: 10.1586/egh.10.39] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
End-stage liver disease due to hepatitis C virus infection (HCV) is the principal indication for liver transplantation. In the USA, over a third of available liver allografts are transplanted into recipients with chronic HCV infection. Reinfection of the graft is universal, but the impact of reinfection on short- and long-term liver function is highly variable. HCV infection in liver transplantation recipients is characterized by an accelerated fibrogenesis, with approximately a third of patients developing cirrhosis within 5 years of follow-up. HCV is associated with decreased patient and graft survival when compared with other indications of orthotopic liver transplantation. The mechanisms responsible for the accelerated liver damage in HCV-infected orthotopic liver transplantation recipients remain largely unknown.
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Affiliation(s)
- Daniel G Maluf
- Transplant Division, Virginia Commonwealth University Medical Center, Medical College of Virginia Hospitals, 1200 East Broad Street, West Hospital, 9th Fl, South Wing, PO Box 980254, Richmond, VA 23298, USA.
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Mas VR, Archer KJ, Scian M, Maluf DG. Molecular pathways involved in loss of graft function in kidney transplant recipients. Expert Rev Mol Diagn 2010; 10:269-84. [PMID: 20370585 PMCID: PMC6846360 DOI: 10.1586/erm.10.6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Interstitial fibrosis (IF) and tubular atrophy (TA) are integral parts of chronic allograft dysfunction and represent in the new classification a separate entity with or without the identification of a specific etiology. Loss of kidney graft function with IF/TA is one of the causes of most kidney allograft losses. Despite progress in immunosuppression, chronic allograft dysfunction remains the main clinical challenge for improving long-term graft survival. The sustained damage to the allograft does not represent a single entity but the summated effects of tissue injury from several pathogenic insults, as well as the kidney's healing response, modified by alloimmunity and immunosuppression. A major challenge in the future of kidney transplantation includes the study of chronic allograft dysfunction pathogenesis to identify early markers of disease progression, as well as potential therapeutics pathways.
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Affiliation(s)
- Valeria R Mas
- Molecular Transplant Research Laboratory, Transplant Division, Department of Surgery, Molecular Medicine Research Building, Virginia Commonwealth University, Richmond, VA 23298, USA.
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Abstract
PURPOSE OF REVIEW The desire for biomarkers for diagnosis and prognosis of diseases has never been greater. With the availability of genome data and an increased availability of proteome data, the discovery of biomarkers has become increasingly feasible. This article reviews some recent applications of the many evolving 'omic technologies to organ transplantation. RECENT FINDINGS With the advancement of many high-throughput 'omic techniques such as genomics, metabolomics, antibiomics, peptidomics, and proteomics, efforts have been made to understand potential mechanisms of specific graft injuries and develop novel biomarkers for acute rejection, chronic rejection, and operational tolerance. SUMMARY The translation of potential biomarkers from the laboratory bench to the clinical bedside is not an easy task and will require the concerted effort of the immunologists, molecular biologists, transplantation specialists, geneticists, and experts in bioinformatics. Rigorous prospective validation studies will be needed using large sets of independent patient samples. The appropriate and timely exploitation of evolving 'omic technologies will lay the cornerstone for a new age of translational research for organ transplant monitoring.
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Abstract
The explosion of new discoveries in the field of immunology has provided new insights into mechanisms that promote an immune response directed against a transplanted organ. Central to the allograft response are T lymphocytes. This review summarizes the current literature on allorecognition, costimulation, memory T cells, T cell migration, and their role in both acute and chronic graft destruction. An in depth understanding of the cellular mechanisms that result in both acute and chronic allograft rejection will provide new strategies and targeted therapeutics capable of inducing long-lasting, allograft-specific tolerance.
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Affiliation(s)
- Elizabeth Ingulli
- Department of Pediatrics, University of California, San Diego, CA 92093, USA.
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Mak RH. Recent advances in chronic dialysis and renal transplantation in children. Pediatr Nephrol 2009; 24:459-61. [PMID: 19153772 DOI: 10.1007/s00467-008-1102-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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27
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Abstract
The desire for biomarkers for diagnosis and prognosis of diseases has never been greater. With the availability of genome data and an increased availability of proteome data, the discovery of biomarkers has become increasingly feasible. However, the task is daunting and requires collaborations among researchers working in the fields of transplantation, immunology, genetics, molecular biology, biostatistics and bioinformatics. With the advancement of high throughput omic techniques such as genomics and proteomics (collectively known as proteogenomics), efforts have been made to develop diagnostic tools from new and to-be discovered biomarkers. Yet biomarker validation, particularly in organ transplantation, remains challenging because of the lack of a true gold standard for diagnostic categories and analytical bottlenecks that face high-throughput data deconvolution. Even though microarray technique is relatively mature, proteomics is still growing with regards to data normalization and analysis methods. Study design, sample selection and rigorous data analysis are the critical issues for biomarker discovery using high-throughput proteogenomic technologies that combine the use and strengths of both genomics and proteomics. In this review, we look into the current status and latest developments in the field of biomarker discovery using genomics and proteomics related to organ transplantation, with an emphasis on the evolution of proteomic technologies.
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Affiliation(s)
- Tara K Sigdel
- Department of Pediatrics-Nephrology, Stanford University Medical School, Stanford University, Stanford, CA 94305, USA
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