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Rroji M, Figurek A, Spasovski G. Advancing kidney transplant outcomes: the role of urinary proteomics in graft function monitoring and rejection detection. Expert Rev Proteomics 2024. [PMID: 39133121 DOI: 10.1080/14789450.2024.2389829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/15/2024] [Accepted: 07/30/2024] [Indexed: 08/13/2024]
Abstract
INTRODUCTION Kidney transplantation significantly improves the lives of those with end-stage kidney disease, offering best alternative to dialysis. However, transplant success is threatened by the acute and chronic rejection mechanisms due to complex immune responses against the new organ. AREAS COVERED The ongoing research into biomarkers holds promise for revolutionizing the early detection and monitoring of the graft health. Liquid biopsy techniques offer a new avenue, with several diagnostic, predictive, and prognostic biomarkers showing promise in detecting and monitoring kidney diseases and an early and chronic allograft rejection. EXPERT OPINIONS Evaluating the protein composition related to kidney transplant results could lead to identifying biomarkers that provide insights into the graft functionality. Non-invasive proteomic biomarkers can drastically enhance clinical outcomes and change the way how kidney transplants are evaluated for patients and physicians if they succeed in this transition. Hence, the advancement in proteomic technologies, leads toward a significant improvement in understanding of the protein markers and molecular mechanisms linked to the outcomes of kidney transplants. However, the road from discovery to the use of such proteins in clinical practice is long, with a need for continuous validation and beyond the singular research team with comprehensive infrastructure and across research groups collaboration.
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Affiliation(s)
- Merita Rroji
- Faculty of Medicine, University Department of Nephrology, Tirana, Albania
| | - Andreja Figurek
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Goce Spasovski
- Medical Faculty, University Department of Nephrology, Skopje, Macedonia
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Mizuno H, Murakami N. Multi-omics Approach in Kidney Transplant: Lessons Learned from COVID-19 Pandemic. CURRENT TRANSPLANTATION REPORTS 2023; 10:173-187. [PMID: 38152593 PMCID: PMC10751044 DOI: 10.1007/s40472-023-00410-8] [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] [Accepted: 08/09/2023] [Indexed: 12/29/2023]
Abstract
Purpose of Review Multi-omics approach has advanced our knowledge on transplantation-associated clinical outcomes, such as acute rejection and infection, and emerging omics data are becoming available in kidney transplant and COVID-19. Herein, we discuss updated findings of multi-omics data on kidney transplant outcomes, as well as COVID-19 and kidney transplant. Recent Findings Transcriptomics, proteomics, and metabolomics revealed various inflammation pathways associated with kidney transplantation-related outcomes and COVID-19. Although multi-omics data on kidney transplant and COVID-19 is limited, activation of innate immune pathways and suppression of adaptive immune pathways were observed in the active phase of COVID-19 in kidney transplant recipients. Summary Multi-omics analysis has led us to a deeper exploration and a more comprehensive understanding of key biological pathways in complex clinical settings, such as kidney transplantation and COVID-19. Future multi-omics analysis leveraging multi-center biobank collaborative will further advance our knowledge on the precise immunological responses to allograft and emerging pathogens.
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Affiliation(s)
- Hiroki Mizuno
- Transplant Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 305, Boston, MA 02115, USA
- Dvision of Nephrology and Rheumatology, Toranomon Hospital, Tokyo, Japan
| | - Naoka Murakami
- Transplant Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 305, Boston, MA 02115, USA
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Farkona S, Pastrello C, Konvalinka A. Proteomics: Its Promise and Pitfalls in Shaping Precision Medicine in Solid Organ Transplantation. Transplantation 2023; 107:2126-2142. [PMID: 36808112 DOI: 10.1097/tp.0000000000004539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Solid organ transplantation is an established treatment of choice for end-stage organ failure. However, all transplant patients are at risk of developing complications, including allograft rejection and death. Histological analysis of graft biopsy is still the gold standard for evaluation of allograft injury, but it is an invasive procedure and prone to sampling errors. The past decade has seen an increased number of efforts to develop minimally invasive procedures for monitoring allograft injury. Despite the recent progress, limitations such as the complexity of proteomics-based technology, the lack of standardization, and the heterogeneity of populations that have been included in different studies have hindered proteomic tools from reaching clinical transplantation. This review focuses on the role of proteomics-based platforms in biomarker discovery and validation in solid organ transplantation. We also emphasize the value of biomarkers that provide potential mechanistic insights into the pathophysiology of allograft injury, dysfunction, or rejection. Additionally, we forecast that the growth of publicly available data sets, combined with computational methods that effectively integrate them, will facilitate a generation of more informed hypotheses for potential subsequent evaluation in preclinical and clinical studies. Finally, we illustrate the value of combining data sets through the integration of 2 independent data sets that pinpointed hub proteins in antibody-mediated rejection.
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Affiliation(s)
- Sofia Farkona
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Ana Konvalinka
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Canadian Donation and Transplantation Research Program, Edmonton, AB, Canada
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Novacescu D, Latcu SC, Bardan R, Daminescu L, Cumpanas AA. Contemporary Biomarkers for Renal Transplantation: A Narrative Overview. J Pers Med 2023; 13:1216. [PMID: 37623466 PMCID: PMC10456039 DOI: 10.3390/jpm13081216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/18/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
Renal transplantation (RT) is the preferred treatment for end-stage renal disease. However, clinical challenges persist, i.e., early detection of graft dysfunction, timely identification of rejection episodes, personalization of immunosuppressive therapy, and prediction of long-term graft survival. Biomarkers have emerged as valuable tools to address these challenges and revolutionize RT patient care. Our review synthesizes the existing scientific literature to highlight promising biomarkers, their biological characteristics, and their potential roles in enhancing clinical decision-making and patient outcomes. Emerging non-invasive biomarkers seemingly provide valuable insights into the immunopathology of nephron injury and allograft rejection. Moreover, we analyzed biomarkers with intra-nephron specificities, i.e., glomerular vs. tubular (proximal vs. distal), which can localize an injury in different nephron areas. Additionally, this paper provides a comprehensive analysis of the potential clinical applications of biomarkers in the prediction, detection, differential diagnosis and assessment of post-RT non-surgical allograft complications. Lastly, we focus on the pursuit of immune tolerance biomarkers, which aims to reclassify transplant recipients based on immune risk thresholds, guide personalized immunosuppression strategies, and ultimately identify patients for whom immunosuppression may safely be reduced. Further research, validation, standardization, and prospective studies are necessary to fully harness the clinical utility of RT biomarkers and guide the development of targeted therapies.
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Affiliation(s)
- Dorin Novacescu
- Doctoral School, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
| | - Silviu Constantin Latcu
- Doctoral School, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
- Department of Urology, “Pius Brinzeu” Timisoara County Emergency Hospital, Liviu Rebreanu Boulevard, Nr. 156, 300723 Timisoara, Romania; (R.B.); (L.D.); (A.A.C.)
- Department XV, Discipline of Urology, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
| | - Razvan Bardan
- Department of Urology, “Pius Brinzeu” Timisoara County Emergency Hospital, Liviu Rebreanu Boulevard, Nr. 156, 300723 Timisoara, Romania; (R.B.); (L.D.); (A.A.C.)
- Department XV, Discipline of Urology, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
| | - Liviu Daminescu
- Department of Urology, “Pius Brinzeu” Timisoara County Emergency Hospital, Liviu Rebreanu Boulevard, Nr. 156, 300723 Timisoara, Romania; (R.B.); (L.D.); (A.A.C.)
| | - Alin Adrian Cumpanas
- Department of Urology, “Pius Brinzeu” Timisoara County Emergency Hospital, Liviu Rebreanu Boulevard, Nr. 156, 300723 Timisoara, Romania; (R.B.); (L.D.); (A.A.C.)
- Department XV, Discipline of Urology, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
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Johnson AC, Silva JAF, Kim SC, Larsen CP. Progress in kidney transplantation: The role for systems immunology. Front Med (Lausanne) 2022; 9:1070385. [PMID: 36590970 PMCID: PMC9800623 DOI: 10.3389/fmed.2022.1070385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
The development of systems biology represents an immense breakthrough in our ability to perform translational research and deliver personalized and precision medicine. A multidisciplinary approach in combination with use of novel techniques allows for the extraction and analysis of vast quantities of data even from the volume and source limited samples that can be obtained from human subjects. Continued advances in microfluidics, scalability and affordability of sequencing technologies, and development of data analysis tools have made the application of a multi-omics, or systems, approach more accessible for use outside of specialized centers. The study of alloimmune and protective immune responses after solid organ transplant offers innumerable opportunities for a multi-omics approach, however, transplant immunology labs are only just beginning to adopt the systems methodology. In this review, we focus on advances in biological techniques and how they are improving our understanding of the immune system and its interactions, highlighting potential applications in transplant immunology. First, we describe the techniques that are available, with emphasis on major advances that allow for increased scalability. Then, we review initial applications in the field of transplantation with a focus on topics that are nearing clinical integration. Finally, we examine major barriers to adapting these methods and discuss potential future developments.
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Lai X, Zheng X, Mathew JM, Gallon L, Leventhal JR, Zhang ZJ. Tackling Chronic Kidney Transplant Rejection: Challenges and Promises. Front Immunol 2021; 12:661643. [PMID: 34093552 PMCID: PMC8173220 DOI: 10.3389/fimmu.2021.661643] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/27/2021] [Indexed: 01/09/2023] Open
Abstract
Despite advances in post-transplant management, the long-term survival rate of kidney grafts and patients has not improved as approximately forty percent of transplants fails within ten years after transplantation. Both immunologic and non-immunologic factors contribute to late allograft loss. Chronic kidney transplant rejection (CKTR) is often clinically silent yet progressive allogeneic immune process that leads to cumulative graft injury, deterioration of graft function. Chronic active T cell mediated rejection (TCMR) and chronic active antibody-mediated rejection (ABMR) are classified as two principal subtypes of CKTR. While significant improvements have been made towards a better understanding of cellular and molecular mechanisms and diagnostic classifications of CKTR, lack of early detection, differential diagnosis and effective therapies continue to pose major challenges for long-term management. Recent development of high throughput cellular and molecular biotechnologies has allowed rapid development of new biomarkers associated with chronic renal injury, which not only provide insight into pathogenesis of chronic rejection but also allow for early detection. In parallel, several novel therapeutic strategies have emerged which may hold great promise for improvement of long-term graft and patient survival. With a brief overview of current understanding of pathogenesis, standard diagnosis and challenges in the context of CKTR, this mini-review aims to provide updates and insights into the latest development of promising novel biomarkers for diagnosis and novel therapeutic interventions to prevent and treat CKTR.
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Affiliation(s)
- Xingqiang Lai
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Organ Transplant Center, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xin Zheng
- Department of Urology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - James M. Mathew
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Lorenzo Gallon
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Medicine, Nephrology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Joseph R. Leventhal
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Zheng Jenny Zhang
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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Kamianowska M, Szczepański M, Wasilewska A. Tubular and Glomerular Biomarkers of Acute Kidney Injury in Newborns. Curr Drug Metab 2019; 20:332-349. [PMID: 30907310 DOI: 10.2174/1389200220666190321142417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 02/28/2019] [Accepted: 03/11/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Acute Kidney Injury (AKI) is a sudden decrease in kidney function. In the early period, the highest percentage of AKI occurs among newborns hospitalized in the neonatal intensive care units, especially premature neonates. The prognosis of AKI depends on the type and severity of the cause of an injury, the accuracy and the time of diagnosis and treatment. The concentration of serum creatinine is still the main diagnostic test, although it changes in the course of AKI later than glomerular filtration rate GFR. In addition, the reliability of the determination of creatinine level is limited because it depends on many factors. New studies have presented other, more useful laboratory markers of renal function that can be measured in serum and/or in urine. OBJECTIVE The aim of the work was to present the latest data about tubular and glomerular biomarkers of acute kidney injury in newborns. METHODS We undertook a structured search of bibliographic databases for peer-reviewed research literature by using focused review topics. According to the conceptual framework, the main idea of research literature has been summarized and presented in this study. RESULTS The concentrations of some novel biomarkers are higher in serum and/or urine of term and preterm newborns with AKI, especially in the course of perinatal asphyxia. CONCLUSION In this systematic review of the literature, we have highlighted the usefulness of biomarkers in predicting tubular and/or glomerular injury in newborns. However, novel biomarkers need to prove their clinical applicability, accuracy, and cost-effectiveness prior to their implementation in clinical practice.
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Affiliation(s)
- Monika Kamianowska
- Department of Neonatology and Neonatal Intensive Care, Medical University of Bialystok, Białystok, Poland
| | - Marek Szczepański
- Department of Neonatology and Neonatal Intensive Care, Medical University of Bialystok, Białystok, Poland
| | - Anna Wasilewska
- Department of Pediatrics and Nephrology, Medical University of Bialystok, Białystok, Poland
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Affiliation(s)
- Arjun Chakraborty
- Department of Surgery, University of California San Francisco, San Francisco, USA
| | - Minnie Sarwal
- Director of Precision Transplant Medicine, University of California San Francisco, San Francisco, USA
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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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10
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Validation of Biomarker Proteins Using Reverse Capture Protein Microarrays. Methods Mol Biol 2016. [PMID: 27807840 DOI: 10.1007/978-1-4939-6539-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Genomics has revolutionized large-scale and high-throughput sequencing and has led to the discovery of thousands of new proteins. Protein chip technology is emerging as a miniaturized and highly parallel platform that is suited to rapid, simultaneous screening of large numbers of proteins and the analysis of various protein-binding activities, enzyme substrate relationships, and posttranslational modifications. Specifically, reverse capture protein microarrays provide the most appropriate platform for identifying low-abundance, disease-specific biomarker proteins in a sea of high-abundance proteins from biological fluids such as blood, serum, plasma, saliva, urine, and cerebrospinal fluid as well as tissues and cells obtained by biopsy. Samples from hundreds of patients can be spotted in serial dilutions on many replicate glass slides. Each slide can then be probed with one specific antibody to the biomarker of interest. That antibody's titer can then be determined quantitatively for each patient, allowing for the statistical assessment and validation of the diagnostic or prognostic utility of that particular antigen. As the technology matures and the availability of validated, platform-compatible antibodies increases, the platform will move further into the desirable realm of discovery science for detecting and quantitating low-abundance signaling proteins. In this chapter, we describe methods for the successful application of the reverse capture protein microarray platform for which we have made substantial contributions to the development and application of this method, particularly in the use of body fluids other than serum/plasma.
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Erpicum P, Hanssen O, Weekers L, Lovinfosse P, Meunier P, Tshibanda L, Krzesinski JM, Hustinx R, Jouret F. Non-invasive approaches in the diagnosis of acute rejection in kidney transplant recipients, part II: omics analyses of urine and blood samples. Clin Kidney J 2016. [PMID: 28643819 PMCID: PMC5469577 DOI: 10.1093/ckj/sfw077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Kidney transplantation (KTx) represents the best available treatment for patients with end-stage renal disease. Still, the full benefits of KTx are undermined by acute rejection (AR). The diagnosis of AR ultimately relies on transplant needle biopsy. However, such an invasive procedure is associated with a significant risk of complications and is limited by sampling error and interobserver variability. In the present review, we summarize the current literature about non-invasive approaches for the diagnosis of AR in kidney transplant recipients (KTRs), including in vivo imaging, gene-expression profiling and omics analyses of blood and urine samples. Most imaging techniques, such as contrast-enhanced ultrasound and magnetic resonance, exploit the fact that blood flow is significantly lowered in case of AR-induced inflammation. In addition, AR-associated recruitment of activated leucocytes may be detectable by 18F-fluorodeoxyglucose positron emission tomography. In parallel, urine biomarkers, including CXCL9/CXCL10 or a three-gene signature of CD3ε, CXCL10 and 18S RNA levels, have been identified. None of these approaches has yet been adopted in the clinical follow-up of KTRs, but standardization of analysis procedures may help assess reproducibility and comparative diagnostic yield in large, prospective, multicentre trials.
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Affiliation(s)
- Pauline Erpicum
- Division of Nephrology, University of Liège Academic Hospital (ULg CHU), B-4000 Liège, Belgium.,GIGA Cardiovascular Sciences, Université de Liège, Liège, Belgium
| | - Oriane Hanssen
- Division of Nephrology, University of Liège Academic Hospital (ULg CHU), B-4000 Liège, Belgium
| | - Laurent Weekers
- Division of Nephrology, University of Liège Academic Hospital (ULg CHU), B-4000 Liège, Belgium
| | - Pierre Lovinfosse
- Division of Nuclear Medicine, University of Liège Academic Hospital (ULg CHU), Liège, Belgium
| | - Paul Meunier
- Division of Radiology, University of Liège Academic Hospital (ULg CHU), Liège, Belgium
| | - Luaba Tshibanda
- Division of Radiology, University of Liège Academic Hospital (ULg CHU), Liège, Belgium
| | - Jean-Marie Krzesinski
- Division of Nephrology, University of Liège Academic Hospital (ULg CHU), B-4000 Liège, Belgium.,GIGA Cardiovascular Sciences, Université de Liège, Liège, Belgium
| | - Roland Hustinx
- Division of Nuclear Medicine, University of Liège Academic Hospital (ULg CHU), Liège, Belgium
| | - François Jouret
- Division of Nephrology, University of Liège Academic Hospital (ULg CHU), B-4000 Liège, Belgium.,GIGA Cardiovascular Sciences, Université de Liège, Liège, Belgium
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Quantitative proteomic profiling of renal tissue in human chronic rejection biopsy samples after renal transplantation. Transplant Proc 2015; 47:323-31. [PMID: 25769567 DOI: 10.1016/j.transproceed.2014.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/29/2014] [Accepted: 10/05/2014] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Chronic rejection (CR) is the leading cause of late renal transplant failure and is characterized by a relatively slow but progressive loss of renal function in combination with proteinuria and hypertension >3 months after transplantation. To identify and quantify the protein profiles in renal tissues of CR patients, we used isotope tagging for relative and absolute quantification (iTRAQ)-based proteomic technology to perform global protein expression analyses in CR patients and control subjects. MATERIALS AND METHODS After protein extraction, quantitation, and digestion, samples were labeled with iTRAQ reagents and then separated by strong cation exchange and high-performance liquid chromatography. The fractions were further analyzed by tandem mass spectrometry. ProteinPilot version 4.0 software and the Swiss-Prot human database were applied for statistical analysis and database searching, respectively. Differentially expressed proteins were subjected to bioinformatic analysis by using the Gene Ontology database and the Kyoto Encyclopedia of Genes and Genomes database to further characterize their potential functional roles and related pathways in CR. RESULTS In total, 1857 distinct proteins (confidence >95%, ρ < .05) were identified and quantified. Using a strict cutoff value of 1.5-fold for expressed variation, 87 proteins showed significant differences in expression between the CR and control groups; 53 were up-regulated and 34 were down-regulated. The differentially expressed proteins were mainly involved in protein binding, structural molecule activity, and extracellular matrix structural constituent. Several proteins, such as the alpha-1 chain of collagen type IV and integrin alpha-1, may play roles in the pathogenesis of CR and were implicated in the extracellular matrix-receptor interaction pathway. CONCLUSIONS This study is the first to focus on iTRAQ-based quantitative proteomic characterization of renal tissue in CR. These insights may broaden our understanding of the molecular mechanisms underlying CR and provide potential biomarker candidates for future diagnostics.
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Abstract
All of life is regulated by complex and organized chemical reactions that help dictate when to grow, to move, to reproduce, and to die. When these processes go awry, or are interrupted by pathological agents, diseases such as cancer, autoimmunity, or infections can result. Cytokines, chemokines, growth factors, adipokines, and other chemical moieties make up a vast subset of these chemical reactions that are altered in disease states, and monitoring changes in these molecules could provide for the identification of disease biomarkers. From the first identification of carcinoembryonic antigen, to the discovery of prostate-specific antigen, to numerous others described within, biomarkers of disease are detectable in a plethora of sample types. The growing number of biomarkers for infection, autoimmunity, and cancer allow for increasingly early detection, to identification of novel drug targets, to prognostic indicators of disease outcome. However, more and more studies are finding that a single cytokine or growth factor is insufficient as a true disease biomarker and that a more global perspective is needed to understand true disease biology. Such a broad view requires a multiplexed platform for chemical detection, and antibody arrays meet and exceed this need by performing this detection in a high-throughput fashion. Herein, we will discuss how antibody arrays have evolved, and how they have helped direct new drug target design, helped identify therapeutic disease markers, and helped in earlier disease detection. From asthma to renal disease, and neurological dysfunction to immunologic disorders, antibody arrays afford a bright future for new biomarkers discovery.
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Srivastava M, Torosyan Y, Eidelman O, Jozwik C, Pollard HB, Mannon R. Reduced PARP1 as a Serum Biomarker for Graft Rejection in Kidney Transplantation. ACTA ACUST UNITED AC 2015; 8:031-38. [PMID: 26962294 PMCID: PMC4780413 DOI: 10.4172/jpb.1000350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A serum proteomics platform enabling expression Profiling in transplantation-associated clinical subsets gives an opportunity to identify non-invasive biomarkers that can accurately predict transplant outcome. In this study, we attempted to identify candidate serum biomarkers that could predict kidney allograft rejection/injury, regardless of its etiological and therapeutic heterogeneity. Using serum samples collected from kidney transplantation patients and healthy controls, we first employed Clontech-500 Ab microarrays to Profile acute rejection (AR) and chronic graft injury (CGI) versus stable graft function (SF) and normal kidneys (NK). Using GenePattern analysis of duplicate arrays on pooled samples, we identified gender-independent biomarkers PARP1, MAPK1, SRP54, DP1, and p57 (FDR ≈ 25%), the concordant downregulation of which represented a detrimental Profile common for both rejection/ injury types (AR-CGI). The reverse phase arrays qualified a 2-fold upregulation of PARP1 with an ROC of 0.87 in individual samples from patients with SF vs. AR-CGI rendering serum PARP1 as a biomarker for early prognosis. Ingenuity Pathways Analysis (IPA) connected PARP1 to some other markers (MAPK1), elucidating their possible interactions and connections to the immune response and graft-versus-host disease signaling. The downregulation of serum PARP1 in the damaged graft tissues, represents a perspective non-invasive marker, predicting the failing kidney graft, regardless of rejection/injury causes or gender. Thus, the successful identification of PARP1 as a bio-marker in limited patient cohorts demonstrates that serum proteomics platform empowered by the GenePattern- and IPA-based Bioinformatics algorithm can guarantee a successful development of the clinically applicable prognostic biomarker panel.
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Affiliation(s)
- Meera Srivastava
- Department of Anatomy, Physiology and Genetics, and Institute for Molecular Medicine, Uniformed Services University School of Medicine (USUHS), Bethesda, MD, USA
| | - Yelizaveta Torosyan
- Department of Anatomy, Physiology and Genetics, and Institute for Molecular Medicine, Uniformed Services University School of Medicine (USUHS), Bethesda, MD, USA
| | - Ofer Eidelman
- Department of Anatomy, Physiology and Genetics, and Institute for Molecular Medicine, Uniformed Services University School of Medicine (USUHS), Bethesda, MD, USA
| | - Catherine Jozwik
- Department of Anatomy, Physiology and Genetics, and Institute for Molecular Medicine, Uniformed Services University School of Medicine (USUHS), Bethesda, MD, USA
| | - Harvey B Pollard
- Department of Anatomy, Physiology and Genetics, and Institute for Molecular Medicine, Uniformed Services University School of Medicine (USUHS), Bethesda, MD, USA
| | - Rosyln Mannon
- Division of Nephrology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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15
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Ong S, Mannon RB. Genomic and proteomic fingerprints of acute rejection in peripheral blood and urine. Transplant Rev (Orlando) 2014; 29:60-7. [PMID: 25542607 DOI: 10.1016/j.trre.2014.12.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 12/06/2014] [Indexed: 12/13/2022]
Abstract
Acute dysfunction of a kidney transplant can be the result of many different etiologies and an allograft biopsy is frequently necessary to diagnose acute rejection. This invasive procedure, while generally safe, is time consuming, costly and inconvenient. We summarize recent advances in genomic and proteomic techniques using peripheral blood and urine for the diagnosis of acute rejection. While much progress has been made, validation of these new molecular tests in the clinical setting is still required.
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Affiliation(s)
- Song Ong
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Roslyn B Mannon
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA; Division of Transplantation, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA.
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Masuda M, Yamada T. Signaling pathway profiling by reverse-phase protein array for personalized cancer medicine. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:651-7. [PMID: 25448010 DOI: 10.1016/j.bbapap.2014.10.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/01/2014] [Accepted: 10/20/2014] [Indexed: 11/28/2022]
Abstract
Deregulation of intracellular signaling through accumulation of genetic alterations is a hallmark of cancer. In the past few decades, concerted and systematic efforts have been made to identify key genetic alterations and to develop therapeutic agents targeting active signaling molecules. However, the efficacy of molecular therapeutics often varies among individuals, and precise mapping of active molecules in individual patients is now considered an essential for therapy optimization. Reverse-phase protein array or microarray (RPPA or RPPM) is an emerging antibody-based highly quantitative proteomic technology, especially suitable for profiling of expression and modification of signaling proteins in low abundance. Because the supply of clinical materials is often limited, RPPA technology is highly advantageous for clinical proteomics in view of its high sensitivity as well as accurate quantification. RPPA has now begun to be incorporated into various clinical trials employing molecular-targeted therapeutics. In this article we review and discuss the application of RPPA technology in the fields of basic, preclinical, and clinical research. The RPPA Global Workshop was recently launched to accelerate the exchange of rapidly expanding knowledge of this fascinating technology among academic laboratories and industries worldwide. This article is part of a Special Issue entitled: Medical Proteomics.
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Affiliation(s)
- Mari Masuda
- Division of Chemotherapy and Clinical Research, Translational Research Group, National Cancer Center Research Institute, Tokyo, Japan
| | - Tesshi Yamada
- Division of Chemotherapy and Clinical Research, Translational Research Group, National Cancer Center Research Institute, Tokyo, Japan.
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Akbani R, Becker KF, Carragher N, Goldstein T, de Koning L, Korf U, Liotta L, Mills GB, Nishizuka SS, Pawlak M, Petricoin EF, Pollard HB, Serrels B, Zhu J. Realizing the promise of reverse phase protein arrays for clinical, translational, and basic research: a workshop report: the RPPA (Reverse Phase Protein Array) society. Mol Cell Proteomics 2014; 13:1625-43. [PMID: 24777629 DOI: 10.1074/mcp.o113.034918] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Reverse phase protein array (RPPA) technology introduced a miniaturized "antigen-down" or "dot-blot" immunoassay suitable for quantifying the relative, semi-quantitative or quantitative (if a well-accepted reference standard exists) abundance of total protein levels and post-translational modifications across a variety of biological samples including cultured cells, tissues, and body fluids. The recent evolution of RPPA combined with more sophisticated sample handling, optical detection, quality control, and better quality affinity reagents provides exquisite sensitivity and high sample throughput at a reasonable cost per sample. This facilitates large-scale multiplex analysis of multiple post-translational markers across samples from in vitro, preclinical, or clinical samples. The technical power of RPPA is stimulating the application and widespread adoption of RPPA methods within academic, clinical, and industrial research laboratories. Advances in RPPA technology now offer scientists the opportunity to quantify protein analytes with high precision, sensitivity, throughput, and robustness. As a result, adopters of RPPA technology have recognized critical success factors for useful and maximum exploitation of RPPA technologies, including the following: preservation and optimization of pre-analytical sample quality, application of validated high-affinity and specific antibody (or other protein affinity) detection reagents, dedicated informatics solutions to ensure accurate and robust quantification of protein analytes, and quality-assured procedures and data analysis workflows compatible with application within regulated clinical environments. In 2011, 2012, and 2013, the first three Global RPPA workshops were held in the United States, Europe, and Japan, respectively. These workshops provided an opportunity for RPPA laboratories, vendors, and users to share and discuss results, the latest technology platforms, best practices, and future challenges and opportunities. The outcomes of the workshops included a number of key opportunities to advance the RPPA field and provide added benefit to existing and future participants in the RPPA research community. The purpose of this report is to share and disseminate, as a community, current knowledge and future directions of the RPPA technology.
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Affiliation(s)
- Rehan Akbani
- From the *University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Neil Carragher
- §Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Ted Goldstein
- ¶Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California
| | | | - Ulrike Korf
- **German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Gordon B Mills
- From the *University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Michael Pawlak
- §§§The Natural and Medical Sciences Institute, Reutlingen, Germany
| | | | - Harvey B Pollard
- ¶¶Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Bryan Serrels
- §Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Jingchun Zhu
- ¶Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California
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Akiyama M. Identification of UACA, EXOSC9, and ΤΜX2 in bovine periosteal cells by mass spectrometry and immunohistochemistry. Anal Bioanal Chem 2014; 406:5805-13. [PMID: 24696107 DOI: 10.1007/s00216-014-7673-3] [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] [Received: 10/29/2013] [Revised: 12/07/2013] [Accepted: 01/28/2014] [Indexed: 10/25/2022]
Abstract
Inspection of patient-derived cells used in transplantation is non-invasive. Therefore, proteomics analysis using supernatants of cells cultured before transplantation is informative. In order to investigate the cell niche of bovine periosteal cells, supernatants of these cultured cells were subjected to 2-D electrophoresis followed by mass spectrometry, which identified type 1 collagen and the C-terminus of type 3 collagen. Only the C-terminal peptide from type 3 collagen was found in supernatants. It is known that type 3 collagen may be expressed intra- or extra-cellularly. Paraffin sections of the cultured cells were next examined by immunohistochemistry, which revealed that type 3 collagen regions besides the C-terminal peptide were present around the bovine periosteal cells but were not found in supernatants. Full-length type 3 collagen was closely associated with the cells, and only the C-terminal peptide was detectable in culture supernatants. Mass spectrometry analysis of partial peptide data combined with immunohistochemistry also indicated that uveal autoantigen with coiled coil domains and ankyrin repeats (UACA), exosome complex component RRP45 (EXOSC9), and thioredoxin-related transmembrane protein 2 (TMX2) were expressed in bovine periosteal cells. Results of this study indicate that analysis of culture supernatants before cell transplantation can provide useful biomarkers indicating the niche of cells used for transplantation.
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Affiliation(s)
- Mari Akiyama
- Department of Biomaterials, Osaka Dental University, 8-1, Kuzuhahanazono-cho, Hirakata-shi, Osaka, 573-1121, Japan,
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High-Throughput Proteomic Approaches to the Elucidation of Potential Biomarkers of Chronic Allograft Injury (CAI). Proteomes 2013; 1:159-179. [PMID: 28250402 PMCID: PMC5302743 DOI: 10.3390/proteomes1020159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/06/2013] [Accepted: 09/09/2013] [Indexed: 12/12/2022] Open
Abstract
This review focuses on the role of OMICs technologies, concentrating in particular on proteomics, in biomarker discovery in chronic allograft injury (CAI). CAI is the second most prevalent cause of allograft dysfunction and loss in the first decade post-transplantation, after death with functioning graft (DWFG). The term CAI, sometimes referred to as chronic allograft nephropathy (CAN), describes the deterioration of renal allograft function and structure as a result of immunological processes (chronic antibody-mediated rejection), and other non-immunological factors such as calcineurin inhibitor (CNI) induced nephrotoxicity, hypertension and infection. Current methods for assessing allograft function are costly, insensitive and invasive; traditional kidney function measurements such as serum creatinine and glomerular filtration rate (GFR) display poor predictive abilities, while the current “gold-standard” involving histological diagnosis with a renal biopsy presents its own inherent risks to the overall health of the allograft. As early as two years post-transplantation, protocol biopsies have shown more than 50% of allograft recipients have mild CAN; ten years post-transplantation more than 50% of the allograft recipients have progressed to severe CAN which is associated with diminishing graft function. Thus, there is a growing medical requirement for minimally invasive biomarkers capable of identifying the early stages of the disease which would allow for timely intervention. Proteomics involves the study of the expression, localization, function and interaction of the proteome. Proteomic technologies may be powerful tools used to identify novel biomarkers which would predict CAI in susceptible individuals. In this paper we will review the use of proteomics in the elucidation of novel predictive biomarkers of CAI in clinical, animal and in vitro studies.
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Abstract
BACKGROUND Increasing evidence accumulates on the central involvement of microRNAs (miRNAs) in disease pathophysiology. We identified distinctly deregulated miRNAs in human renal allograft biopsies from patients undergoing acute cellular rejection, antibody-mediated rejection (ABMR), and delayed graft function (DGF). METHODS Sixty-five posttransplantation kidney biopsy samples covering 41 cases with acute rejection (15 vascular rejection, 15 interstitial rejection, and 11 ABMR), 14 DGF cases, and 10 protocol biopsies serving as controls were analyzed using the Affymetrix GeneChip miRNA Array. Differentially regulated miRNAs were identified by Student's t test and Bonferroni correction. Target genes for the set of miRNAs were retrieved from miRTarBase (experimentally verified targets) as well as by applying the target prediction routines DIANAmT, miRanda, and Targetscan. RESULTS Patients with acute cellular rejection, ABMR, and DGF discriminate from the control group (protocol biopsies) in unsupervised clustering of miRNA profiles, clearly identifying deregulated miRNAs in rejection and DGF. Angiogenesis, apoptosis, and transforming growth factor-β signaling were identified as relevant pathways in ischemic response following an integrative analysis of miRNA targets and mRNA expression profiles. Inflammation by chemokine and cytokine signaling, T-cell activation, and B-cell activation were identified as relevant in acute rejection accordingly. CONCLUSION These data suggest that distinct miRNA signatures playing a role in specific biological pathways discriminate acute cellular and humoral rejection and DGF. This finding serves as valuable tool for a rational selection of diagnostic, prognostic, and potentially therapeutic molecular targets of posttransplantation events.
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Bohra R, Klepacki J, Klawitter J, Klawitter J, Thurman J, Christians U. Proteomics and metabolomics in renal transplantation-quo vadis? Transpl Int 2013; 26:225-41. [PMID: 23350848 PMCID: PMC4006577 DOI: 10.1111/tri.12003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 05/07/2012] [Accepted: 10/07/2012] [Indexed: 12/13/2022]
Abstract
The improvement of long-term transplant organ and patient survival remains a critical challenge following kidney transplantation. Proteomics and biochemical profiling (metabolomics) may allow for the detection of early changes in cell signal transduction regulation and biochemistry with high sensitivity and specificity. Hence, these analytical strategies hold the promise to detect and monitor disease processes and drug effects before histopathological and pathophysiological changes occur. In addition, they will identify enriched populations and enable individualized drug therapy. However, proteomics and metabolomics have not yet lived up to such high expectations. Renal transplant patients are highly complex, making it difficult to establish cause-effect relationships between surrogate markers and disease processes. Appropriate study design, adequate sample handling, storage and processing, quality and reproducibility of bioanalytical multi-analyte assays, data analysis and interpretation, mechanistic verification, and clinical qualification (=establishment of sensitivity and specificity in adequately powered prospective clinical trials) are important factors for the success of molecular marker discovery and development in renal transplantation. However, a newly developed and appropriately qualified molecular marker can only be successful if it is realistic that it can be implemented in a clinical setting. The development of combinatorial markers with supporting software tools is an attractive goal.
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Affiliation(s)
- Rahul Bohra
- iC42 Clinical Research & Development, Department of Anesthesiology, University of Colorado Denver, Aurora, Colorado, USA
| | - Jacek Klepacki
- iC42 Clinical Research & Development, Department of Anesthesiology, University of Colorado Denver, Aurora, Colorado, USA
| | - Jelena Klawitter
- iC42 Clinical Research & Development, Department of Anesthesiology, University of Colorado Denver, Aurora, Colorado, USA
- Renal Medicine, University of Colorado Denver, Aurora, USA
| | - Jost Klawitter
- iC42 Clinical Research & Development, Department of Anesthesiology, University of Colorado Denver, Aurora, Colorado, USA
| | - Joshua Thurman
- Renal Medicine, University of Colorado Denver, Aurora, USA
| | - Uwe Christians
- iC42 Clinical Research & Development, Department of Anesthesiology, University of Colorado Denver, Aurora, Colorado, USA
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Pollard JR, Eidelman O, Mueller GP, Dalgard CL, Crino PB, Anderson CT, Brand EJ, Burakgazi E, Ivaturi SK, Pollard HB. The TARC/sICAM5 Ratio in Patient Plasma is a Candidate Biomarker for Drug Resistant Epilepsy. Front Neurol 2013; 3:181. [PMID: 23293627 PMCID: PMC3535822 DOI: 10.3389/fneur.2012.00181] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 12/09/2012] [Indexed: 12/14/2022] Open
Abstract
Epilepsy is a common affliction that involves inflammatory processes. There are currently no definitive chemical diagnostic biomarkers in the blood, so diagnosis is based on a sometimes expensive synthesis of clinical observation, radiology, neuro-psychological testing, and interictal and ictal EEG studies. Soluble ICAM5 (sICAM5), also known as telencephalin, is an anti-inflammatory protein of strictly central nervous system tissue origin that is also found in blood. Here we have tested the hypothesis that plasma concentrations of select inflammatory cytokines, including sICAM5, might serve as biomarkers for epilepsy diagnosis. To test this hypothesis, we developed a highly sensitive and accurate electrochemiluminescent ELISA assay to measure sICAM5 levels, and measured levels of sICAM5 and 18 other inflammatory mediators in epilepsy patient plasma and controls. Patient samples were drawn from in-patients undergoing video-EEG monitoring, without regard to timing of seizures. Differences were defined by t-test, and Receiver Operating Condition (ROC) curves determined the ability of these tests to distinguish between the two populations. In epilepsy patient plasmas, we found that concentrations of anti-inflammatory sICAM5 are reduced (p = 0.002) and pro-inflammatory IL-1β, IL-2, and IL-8 are elevated. TARC (thymus and activation regulated chemokine, CCL17) concentrations trend high. In contrast, levels of BDNF and a variety of other pro-inflammatory mediators are not altered. Based on p-value and ROC analysis, we find that the ratio of TARC/sICAM5 discriminates accurately between patients and controls, with an ROC Area Under the Curve (AUC) of 1.0 (p = 0.034). In conclusion, we find that the ratio of TARC to sICAM5 accurately distinguishes between the two populations and provides a statistically and mechanistically compelling candidate blood biomarker for drug resistant epilepsy.
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Affiliation(s)
- John R Pollard
- Penn Epilepsy Center, Department of Neurology, University of Pennsylvania Philadelphia, PA, USA
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Sigdel TK, Gao X, Sarwal MM. Protein and peptide biomarkers in organ transplantation. Biomark Med 2012; 6:259-71. [PMID: 22731899 DOI: 10.2217/bmm.12.29] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Organ transplantation is the optimal treatment choice for end-stage organ failure in pediatric patients. The ideal maintenance of a transplanted organ requires efficient monitoring tools and an effective individualized post-transplant treatment plan. Currently available post-transplant monitoring options are not ideal because of their invasiveness or their lack of sensitivity and specificity when providing an accurate assessment of transplant injury. Current research on proteins and peptides, including mass spectrometry-based proteomics, can identify novel surrogate protein and peptide biomarkers that can assist in monitoring the graft in order to correctly assess the status of the transplanted organ. In this article, we have critically reviewed current relevant literature to highlight the importance of protein and peptide biomarkers in the field of pediatric organ transplantation, the status of research findings in the field of protein and peptide biomarkers in different organ transplantation and factors that impact and inhibit the progression of protein biomarker discovery in the field of solid-organ transplantation in pediatrics.
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Affiliation(s)
- Tara K Sigdel
- California Pacific Medical Center - Research Institute, San Francisco, USA.
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Pisitkun T, Gandolfo MT, Das S, Knepper MA, Bagnasco SM. Application of systems biology principles to protein biomarker discovery: urinary exosomal proteome in renal transplantation. Proteomics Clin Appl 2012; 6:268-78. [PMID: 22641613 DOI: 10.1002/prca.201100108] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE In mass spectrometry (MS)-based studies to discover urinary protein biomarkers, an important question is how to analyze the data to find the most promising potential biomarkers to be advanced to large-scale validation studies. Here, we describe a "systems biology-based" approach to address this question. EXPERIMENTAL DESIGN We analyzed large-scale liquid chromatography-tandem mass spectrometry (LC-MS/MS) data of urinary exosomes from renal allograft recipients with biopsy-proven evidence of immunological rejection or tubular injury (TI). We asked whether bioinformatic analysis of urinary exosomal proteins can identify biological-process based protein groups that correlate with biopsy findings and whether the protein groups fit with general knowledge of the pathophysiological mechanisms involved. RESULTS LC-MS/MS analysis of urinary exosomal proteomes identified more than 1000 proteins in each pathologic group. These protein lists were analyzed computationally to identify the Biological Process and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway terms that are significantly associated with each pathological group. Among the most informative terms for each group were: "sodium ion transport" for TI; "immune response" for all rejection; "epithelial cell differentiation" for cell-mediated rejection; and "acute inflammatory response" for antibody-mediated rejection. Based on these terms, candidate biomarkers were identified using a novel strategy to allow a dichotomous classification between different pathologic categories. CONCLUSIONS AND CLINICAL RELEVANCE The terms and candidate biomarkers identified make rational connections to pathophysiological mechanisms, suggesting that the described bioinformatic approach will be useful in advancing large-scale biomarker identification studies toward a validation phase.
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Affiliation(s)
| | - Maria T Gandolfo
- Department of Pathology, Johns Hopkins University, Baltimore, MD
| | - Samarjit Das
- Department of Pathology, Johns Hopkins University, Baltimore, MD
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, NHLBI, NIH, Bethesda, MD
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Zitzner JR, Tambur AR. Role of ELISPOT Assays in Risk Assessment Pre- and Post-Kidney Transplantation. Cells 2012; 1:100-10. [PMID: 24710417 PMCID: PMC3901086 DOI: 10.3390/cells1020100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/30/2012] [Accepted: 05/07/2012] [Indexed: 12/31/2022] Open
Abstract
Immunologic risk in kidney transplantation is typically minimized by avoiding, or at least limiting, the potential of donor specific humoral responses by testing for the presence of donor-specific antibodies (DSA). Additionally, selecting donor and recipient pairs with the least number of human leukocyte antigen (HLA) mismatches has been shown to play a role in transplant outcome. However, numerous other factors may play a role in the success of transplant outcome and patient health. Specifically, the use of T-cell allospecific ELISPOT assays have helped elucidate the role of pre-formed cellular responses as additional factors in post-transplant outcome. In this review, we will evaluate numerous uses of ELISPOT assays to assess the pre- and post-transplant immunologic risk of rejection episodes, graft survival and even viral susceptibility as well as the utility of ELISPOT assays in monitoring tolerance and withdrawal of immunosuppressive medications following kidney transplantation.
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Affiliation(s)
- Jennifer R Zitzner
- Comprehensive Transplant Center Feinberg School of Medicine, Northwestern University, 303 E Chicago Ave., Tarry Building Suite 11-703, Chicago, IL 60611-3008, USA.
| | - Anat R Tambur
- Comprehensive Transplant Center Feinberg School of Medicine, Northwestern University, 303 E Chicago Ave., Tarry Building Suite 11-703, Chicago, IL 60611-3008, USA.
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Roshdy A, El-Khatib MM, Rizk MN, El-shehaby AM. CRP and acute renal rejection: a marker to the point. Int Urol Nephrol 2012; 44:1251-5. [DOI: 10.1007/s11255-011-0098-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 11/21/2011] [Indexed: 10/14/2022]
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