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Rikos D, Siokas V, Burykina TI, Drakoulis N, Dardiotis E, Zintzaras E. Replication of chromosomal loci involved in Parkinson's disease: A quantitative synthesis of GWAS. Toxicol Rep 2021; 8:1762-1768. [PMID: 34712594 PMCID: PMC8528647 DOI: 10.1016/j.toxrep.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/15/2021] [Accepted: 10/09/2021] [Indexed: 11/16/2022] Open
Abstract
The first quantitative synthesis of GWAS regarding Parkinson’s Disease. Fifteen Parkinson’s Disease GWASs with 191.397 available SNPs pooled. User friendly software (METRADISC-XL) implemented. Seven chromosomal regions (bins) were replicated as associated with the Parkinson’s Disease trait.
Introduction Parkinson’s disease is a neurodegenerative disorder with a complex etiology coming from interactions between genetic and environmental factors. Research on Parkinson’s disease genetics has been an effortful struggle, while new technologies and novel study designs served as indispensable boosters. Until now, 90 loci and 20 disease-causing gene mutations have been identified. In this study we describe a novel non-parametric approach to GWAS meta-analysis and its application in PD genetics. Methods A literature search was conducted to identify Genome-Wide Association Studies (GWAS) regarding Parkinson’s disease. We applied predefined inclusion criteria and extracted the reported SNPs and their respective position and statistical significance. We divided all chromosomes in approximately equal genetic distance segments called bins and recorded the most significant SNP from each bin and each study and ranked them in terms of their p-value. Ranks from each bin were summed, averaged and added in a heterogeneity-based analysis using the METRADISC-XL software. Weighted and unweighted analysis was performed. Results Five-hundred and forty-three SNPs and their respective p-values from 15 studies were matched in their corresponding bins. The METRADISC-XL analysis resulted in 7 bins with a significant p-value. A bin on chromosome 4 where the SNCA gene is located found with genome-wide significant association with Parkinson’s Disease. Conclusion This is the first time a non-parametric method is applied in GWAS meta-analysis. The results add some insight on the overall understanding of Parkinson’s disease genetics and serve as a first step of further convergent analysis with Genome-wide linkage studies.
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Affiliation(s)
- Dimitrios Rikos
- Department of Neurology, University Hospital of Larissa, Faculty of Medicine, University of Thessaly, Larissa, Greece.,Department of Biomathematics, Faculty of Medicine, University of Thessaly Larissa, Greece
| | - Vasileios Siokas
- Department of Neurology, University Hospital of Larissa, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Tatyana I Burykina
- Department of Analytical and Forensic Medical Toxicology, Sechenov University, 119048 Moscow, Russian Federation
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 17551 Athens, Greece
| | - Efthimios Dardiotis
- Department of Neurology, University Hospital of Larissa, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Elias Zintzaras
- Department of Biomathematics, Faculty of Medicine, University of Thessaly Larissa, Greece.,The Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, United States
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Jia X, Han Q, Lu Z. Analyzing the similarity of samples and genes by MG-PCC algorithm, t-SNE-SS and t-SNE-SG maps. BMC Bioinformatics 2018; 19:512. [PMID: 30558536 PMCID: PMC6296107 DOI: 10.1186/s12859-018-2495-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 11/16/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND For analyzing these gene expression data sets under different samples, clustering and visualizing samples and genes are important methods. However, it is difficult to integrate clustering and visualizing techniques when the similarities of samples and genes are defined by PCC(Person correlation coefficient) measure. RESULTS Here, for rare samples of gene expression data sets, we use MG-PCC (mini-groups that are defined by PCC) algorithm to divide them into mini-groups, and use t-SNE-SSP maps to display these mini-groups, where the idea of MG-PCC algorithm is that the nearest neighbors should be in the same mini-groups, t-SNE-SSP map is selected from a series of t-SNE(t-statistic Stochastic Neighbor Embedding) maps of standardized samples, and these t-SNE maps have different perplexity parameter. Moreover, for PCC clusters of mass genes, they are displayed by t-SNE-SGI map, where t-SNE-SGI map is selected from a series of t-SNE maps of standardized genes, and these t-SNE maps have different initialization dimensions. Here, t-SNE-SSP and t-SNE-SGI maps are selected by A-value, where A-value is modeled from areas of clustering projections, and t-SNE-SSP and t-SNE-SGI maps are such t-SNE map that has the smallest A-value. CONCLUSIONS From the analysis of cancer gene expression data sets, we demonstrate that MG-PCC algorithm is able to put tumor and normal samples into their respective mini-groups, and t-SNE-SSP(or t-SNE-SGI) maps are able to display the relationships between mini-groups(or PCC clusters) clearly. Furthermore, t-SNE-SS(m)(or t-SNE-SG(n)) maps are able to construct independent tree diagrams of the nearest sample(or gene) neighbors, where each tree diagram is corresponding to a mini-group of samples(or genes).
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Affiliation(s)
- Xingang Jia
- School of Mathematics, Southeast University, Nanjing, 210096, People's Republic of China.
| | - Qiuhong Han
- Department of Mathematics, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, People's Republic of China
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Nariman‐Saleh‐Fam Z, Bastami M, Ardalan M, Sharifi S, Hosseinian Khatib SM, Zununi Vahed S. Cell‐free microRNA‐148a is associated with renal allograft dysfunction: Implication for biomarker discovery. J Cell Biochem 2018; 120:5737-5746. [DOI: 10.1002/jcb.27860] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/19/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Ziba Nariman‐Saleh‐Fam
- Women’s Reproductive Health Research Center, Tabriz University of Medical Sciences Tabriz Iran
| | - Milad Bastami
- Department of Medical Genetics Faculty of Medicine, Tabriz University of Medical Sciences Tabriz Iran
| | | | - Simin Sharifi
- Dental and Periodontal Research Center, Tabriz University of Medical Sciences Tabriz Iran
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Siangphoe U, Archer KJ. Estimation of random effects and identifying heterogeneous genes in meta-analysis of gene expression studies. Brief Bioinform 2017; 18:602-618. [PMID: 27345525 DOI: 10.1093/bib/bbw050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/12/2022] Open
Abstract
Combining effect sizes from individual studies using random-effects meta-analysis models are commonly applied in high-dimensional gene expression data. However, unknown study heterogeneity can arise from inconsistencies in sample quality and experimental conditions. High heterogeneity of effect sizes can reduce statistical power of the models. In this study, we describe three hypothesis-testing frameworks for meta-analysis of microarray data, and review several existing meta-analytic techniques that have been used in the genomic setting. These include P-value-based methods, rank-based methods and effect-size-based methods. We then discuss limitations of some of these methods and describe random-effects-based methods in detail. We introduce two methods for estimating the inter-study variance in random-effects meta-analytic models and another method for identifying heterogeneous genes for gene expression data. We compared various methods with the standard and existing meta-analytic techniques in the genomic framework. We demonstrate our results through a series of simulations and application in Alzheimer's gene expression data.
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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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Cumming TB, Churilov L, Sena ES. The Missing Medians: Exclusion of Ordinal Data from Meta-Analyses. PLoS One 2015; 10:e0145580. [PMID: 26697876 PMCID: PMC4689383 DOI: 10.1371/journal.pone.0145580] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/04/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Meta-analyses are considered the gold standard of evidence-based health care, and are used to guide clinical decisions and health policy. A major limitation of current meta-analysis techniques is their inability to pool ordinal data. Our objectives were to determine the extent of this problem in the context of neurological rating scales and to provide a solution. METHODS Using an existing database of clinical trials of oral neuroprotective therapies, we identified the 6 most commonly used clinical rating scales and recorded how data from these scales were reported and analysed. We then identified systematic reviews of studies that used these scales (via the Cochrane database) and recorded the meta-analytic techniques used. Finally, we identified a statistical technique for calculating a common language effect size measure for ordinal data. RESULTS We identified 103 studies, with 128 instances of the 6 clinical scales being reported. The majority- 80%-reported means alone for central tendency, with only 13% reporting medians. In analysis, 40% of studies used parametric statistics alone, 34% of studies employed non-parametric analysis, and 26% did not include or specify analysis. Of the 60 systematic reviews identified that included meta-analysis, 88% used mean difference and 22% employed difference in proportions; none included rank-based analysis. We propose the use of a rank-based generalised odds ratio (WMW GenOR) as an assumption-free effect size measure that is easy to compute and can be readily combined in meta-analysis. CONCLUSION There is wide scope for improvement in the reporting and analysis of ordinal data in the literature. We hope that adoption of the WMW GenOR will have the dual effect of improving the reporting of data in individual studies while also increasing the inclusivity (and therefore validity) of meta-analyses.
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Affiliation(s)
- Toby B. Cumming
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Australia
| | - Leonid Churilov
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Australia
| | - Emily S. Sena
- Centre for Clinical Brain Sciences, School of Clinical Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Gonzalez GH, Tahsin T, Goodale BC, Greene AC, Greene CS. Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. Brief Bioinform 2015; 17:33-42. [PMID: 26420781 PMCID: PMC4719073 DOI: 10.1093/bib/bbv087] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Indexed: 02/06/2023] Open
Abstract
Precision medicine will revolutionize the way we treat and prevent disease. A major barrier to the implementation of precision medicine that clinicians and translational scientists face is understanding the underlying mechanisms of disease. We are starting to address this challenge through automatic approaches for information extraction, representation and analysis. Recent advances in text and data mining have been applied to a broad spectrum of key biomedical questions in genomics, pharmacogenomics and other fields. We present an overview of the fundamental methods for text and data mining, as well as recent advances and emerging applications toward precision medicine.
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Winkler JM, Fox HS. Transcriptome meta-analysis reveals a central role for sex steroids in the degeneration of hippocampal neurons in Alzheimer's disease. BMC SYSTEMS BIOLOGY 2013; 7:51. [PMID: 23803348 PMCID: PMC3702487 DOI: 10.1186/1752-0509-7-51] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 06/19/2013] [Indexed: 11/12/2022]
Abstract
Background Alzheimer’s disease is the most prevalent form of dementia. While a number of transcriptomic studies have been performed on the brains of Alzheimer’s specimens, no clear picture has emerged on the basis of neuronal transcriptional alterations linked to the disease. Therefore we performed a meta-analysis of studies comparing hippocampal neurons in Alzheimer’s disease to controls. Results Homeostatic processes, encompassing control of gene expression, apoptosis, and protein synthesis, were identified as disrupted during Alzheimer’s disease. Focusing on the genes carrying out these functions, a protein-protein interaction network was produced for graph theory and cluster exploration. This approach identified the androgen and estrogen receptors as key components and regulators of the disrupted homeostatic processes. Conclusions Our systems biology approach was able to identify the importance of the androgen and estrogen receptors in not only homeostatic cellular processes but also the role of other highly central genes in Alzheimer’s neuronal dysfunction. This is important due to the controversies and current work concerning hormone replacement therapy in postmenopausal women, and possibly men, as preventative approaches to ward off this neurodegenerative disorder.
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Affiliation(s)
- Jessica M Winkler
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Dosanjh A, Robison E, Mondala T, Head SR, Salomon DR, Kurian SM. Genomic meta-analysis of growth factor and integrin pathways in chronic kidney transplant injury. BMC Genomics 2013; 14:275. [PMID: 23617750 PMCID: PMC3644490 DOI: 10.1186/1471-2164-14-275] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 04/18/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Chronic Allograft Nephropathy (CAN) is a clinical entity of progressive kidney transplant injury. The defining histology is tubular atrophy with interstitial fibrosis (IFTA). Using a meta-analysis of microarrays from 84 kidney transplant biopsies, we revealed growth factor and integrin adhesion molecule pathways differentially expressed and correlated with histological progression. A bioinformatics approach mining independent datasets leverages new and existing data to identify correlative changes in integrin and growth factor signaling pathways. RESULTS Analysis of CAN/IFTA Banff grades showed that hepatocyte growth factor (HGF), and epidermal growth factor (EGF) pathways are significantly differentially expressed in all classes of CAN/IFTA. MAPK-dependent pathways were also significant. However, the TGFβ pathways, albeit present, failed to differentiate CAN/IFTA progression. The integrin subunits β8, αv, αμ and β5 are differentially expressed, but β1, β6 and α6 specifically correlate with progression of chronic injury. Results were validated using our published proteomic profiling of CAN/IFTA. CONCLUSIONS CAN/IFTA with chronic kidney injury is characterized by expression of distinct growth factors and specific integrin adhesion molecules as well as their canonical signaling pathways. Drug target mapping suggests several novel candidates for the next generation of therapeutics to prevent or treat progressive transplant dysfunction with interstitial fibrosis.
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Affiliation(s)
- Amrita Dosanjh
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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Bajpai AK, Davuluri S, Chandrashekar DS, Ilakya S, Dinakaran M, Acharya KK. MGEx-Udb: a mammalian uterus database for expression-based cataloguing of genes across conditions, including endometriosis and cervical cancer. PLoS One 2012; 7:e36776. [PMID: 22606288 PMCID: PMC3350469 DOI: 10.1371/journal.pone.0036776] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 04/05/2012] [Indexed: 12/04/2022] Open
Abstract
Background Gene expression profiling of uterus tissue has been performed in various contexts, but a significant amount of the data remains underutilized as it is not covered by the existing general resources. Methodology/Principal Findings We curated 2254 datasets from 325 uterus related mass scale gene expression studies on human, mouse, rat, cow and pig species. We then computationally derived a ‘reliability score’ for each gene's expression status (transcribed/dormant), for each possible combination of conditions and locations, based on the extent of agreement or disagreement across datasets. The data and derived information has been compiled into the Mammalian Gene Expression Uterus database (MGEx-Udb, http://resource.ibab.ac.in/MGEx-Udb/). The database can be queried with gene names/IDs, sub-tissue locations, as well as various conditions such as the cervical cancer, endometrial cycles and disorders, and experimental treatments. Accordingly, the output would be a) transcribed and dormant genes listed for the queried condition/location, or b) expression profile of the gene of interest in various uterine conditions. The results also include the reliability score for the expression status of each gene. MGEx-Udb also provides information related to Gene Ontology annotations, protein-protein interactions, transcripts, promoters, and expression status by other sequencing techniques, and facilitates various other types of analysis of the individual genes or co-expressed gene clusters. Conclusions/Significance In brief, MGEx-Udb enables easy cataloguing of co-expressed genes and also facilitates bio-marker discovery for various uterine conditions.
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Affiliation(s)
- Akhilesh K. Bajpai
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru (Bangalore), Karnataka State, India
| | - Sravanthi Davuluri
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru (Bangalore), Karnataka State, India
| | - Darshan S. Chandrashekar
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru (Bangalore), Karnataka State, India
| | - Selvarajan Ilakya
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru (Bangalore), Karnataka State, India
| | - Mahalakshmi Dinakaran
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru (Bangalore), Karnataka State, India
| | - Kshitish K. Acharya
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru (Bangalore), Karnataka State, India
- Shodhaka Life Sciences Pvt. Ltd., Bengaluru (Bangalore), Karnataka State, India
- * E-mail:
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Tsoi LC, Qin T, Slate EH, Zheng WJ. Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior. BMC Bioinformatics 2011; 12:438. [PMID: 22078224 PMCID: PMC3251006 DOI: 10.1186/1471-2105-12-438] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 11/11/2011] [Indexed: 01/03/2023] Open
Abstract
Background To utilize the large volume of gene expression information generated from different microarray experiments, several meta-analysis techniques have been developed. Despite these efforts, there remain significant challenges to effectively increasing the statistical power and decreasing the Type I error rate while pooling the heterogeneous datasets from public resources. The objective of this study is to develop a novel meta-analysis approach, Consistent Differential Expression Pattern (CDEP), to identify genes with common differential expression patterns across different datasets. Results We combined False Discovery Rate (FDR) estimation and the non-parametric RankProd approach to estimate the Type I error rate in each microarray dataset of the meta-analysis. These Type I error rates from all datasets were then used to identify genes with common differential expression patterns. Our simulation study showed that CDEP achieved higher statistical power and maintained low Type I error rate when compared with two recently proposed meta-analysis approaches. We applied CDEP to analyze microarray data from different laboratories that compared transcription profiles between metastatic and primary cancer of different types. Many genes identified as differentially expressed consistently across different cancer types are in pathways related to metastatic behavior, such as ECM-receptor interaction, focal adhesion, and blood vessel development. We also identified novel genes such as AMIGO2, Gem, and CXCL11 that have not been shown to associate with, but may play roles in, metastasis. Conclusions CDEP is a flexible approach that borrows information from each dataset in a meta-analysis in order to identify genes being differentially expressed consistently. We have shown that CDEP can gain higher statistical power than other existing approaches under a variety of settings considered in the simulation study, suggesting its robustness and insensitivity to data variation commonly associated with microarray experiments. Availability: CDEP is implemented in R and freely available at: http://genomebioinfo.musc.edu/CDEP/ Contact: zhengw@musc.edu
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Affiliation(s)
- Lam C Tsoi
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 135 Cannon St, Charleston, SC 29425, USA
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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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Wang YY, Ye ZY, Zhao ZS, Tao HQ, Li SG. Systems biology approach to identification of biomarkers for metastatic progression in gastric cancer. J Cancer Res Clin Oncol 2011; 136:135-41. [PMID: 19649653 DOI: 10.1007/s00432-009-0644-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2009] [Accepted: 07/17/2009] [Indexed: 10/20/2022]
Abstract
PURPOSE Gastric cancer is usually diagnosed at later stages (stages III and IV) in China, and the overall 5-year survival rate is low at 40%. Metastases are responsible for the majority of cancer fatalities. The molecular mechanisms governing metastasis are poorly understood. METHODS We have analyzed gene expression data based on gene interaction networks and molecular pathways rather than separate genes utilizing hierarchical cluster analysis, Gene ontology analysis and pathway analysis. RESULTS We have analyzed gene expression data from advanced gastric cancer tissues, corresponding adjacent noncancerous gastric tissues and its peritonium metastasis. Our studies indicated that metastatic tumor was related to changes in apoptosis pathway and proteasome degradation pathway, TRAF2 and IRF3 are up-regulated in apoptosis pathway, NEDD4 and UBE1 are up-regulated in proteasome degradation pathway. CONCLUSION The advent of high-throughput investigation of gene using Microarray technology, a systems approach relying on groups of interacting genes is essential for understanding the processes of cancer. We have identified apoptosis pathway and proteasome degradation pathway associated with metastasis.
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Affiliation(s)
- Yuan-Yu Wang
- Department of Surgery, Zhejiang Provincial People's Hospital, 310014 Hangzhou, Zhejiang, People's Republic of China
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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 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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