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Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions
2010
PLoS Computational Biology
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Public repositories of microarray data, such as the Gene Expression Omnibus (GEO), contain RNA expression profiles for more than 16,000 biological conditions, covering more than 30% of United States mortality ...
We hypothesized that genes coding for serum-and urine-detectable proteins, and showing differential expression of RNA in disease-damaged tissues would make ideal diagnostic protein biomarkers for those ...
Acknowledgments We thank Alex Skrenchuk and Boris Oskotsky from Stanford University for computer support, and Maarten Naesens, Shai Shen-Orr, and Annie P. ...
doi:10.1371/journal.pcbi.1000940
pmid:20885780
pmcid:PMC2944782
fatcat:7rhemnv2xnaefijtsznopfbrai
Applying genomics to organ transplantation medicine in both discovery and validation of biomarkers
2007
International Immunopharmacology
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They concluded that proteomic analysis of urine might offer a noninvasive way to differentiate this condition from acute rejection. ...
Two of these proteins alphaB-crystallin and tropomyosin were found to be cardiac-specific heat shock proteins and their levels were then measured post-transplant in serum from transplant recipients. ...
doi:10.1016/j.intimp.2007.07.017
pmid:18039531
pmcid:PMC2215739
fatcat:jbvdqbuzwfgzxgrpw3vnmuumbe
The Use of Genomics and Pathway Analysis in Our Understanding and Prediction of Clinical Renal Transplant Injury
2016
Transplantation
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These data have shed new light on our understanding of the pathogenesis of specific disease conditions following renal transplantation but their utility as a biomarker of disease has been hampered by study ...
, chronic allograft injury and tolerance is discussed, as is the current published data regarding other "omics" strategies-proteomics, metabolomics and the micro-RNA transcriptome. ...
, aimed to evaluate and validate a panel of candidate urinary mRNA and protein biomarkers chosen from other published work for diagnosing and predicting acute rejection. ...
doi:10.1097/tp.0000000000000943
pmid:26447506
pmcid:PMC4826324
fatcat:ooqo4g3punginlaaaluqv3p6wq
The proteogenomic path towards biomarker discovery
2008
Pediatric Transplantation
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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 highthroughput ...
The desire for biomarkers for diagnosis and prognosis of diseases has never been greater. ...
provides an unbiased high-throughput approach to identify differentially expressed proteins in the healthy and disease states. ...
doi:10.1111/j.1399-3046.2008.01018.x
pmid:18764911
pmcid:PMC2574627
fatcat:qh2vo35ns5dibio5h4t2dyyhve
MicroRNAs as Biomarkers in Solid Organ Transplantation
2012
American Journal of Transplantation
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biomarker research and the evaluation of specific applications in the transplant field. miRNA expression might develop as excellent biomarkers of allograft injury and function. ...
MiRNA expression has been associated with different diseases and physiological conditions. ...
Acknowledgments The research results included in this report were supported by a National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) grant, R01DK080074. ...
doi:10.1111/j.1600-6143.2012.04313.x
pmid:23136949
pmcid:PMC3927320
fatcat:gvydagprvjeq7hrcseb2dkcmwu
Identifying biomarkers as diagnostic tools in kidney transplantation
2011
Expert Review of Molecular Diagnostics
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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 ...
This article will discuss the existing gap between biomarker discovery and clinical application in the kidney transplant setting. ...
An approach that combines data from individual research groups conducted on similar disease conditions and then applies this approach for robust cross-validation in a large dataset may be one way to address ...
doi:10.1586/erm.10.119
pmid:21405969
pmcid:PMC3116652
fatcat:rivexgj3ojhxdakcaj7wyeuda4
Impact of animal strain on gene expression in a rat model of acute cardiac rejection
2009
BMC Genomics
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Using a rat heart transplant model and 2 different rat strains (Dark Agouti, and Brown Norway), microarrays were performed on native hearts, transplanted hearts, and peripheral blood mononuclear cells ...
Only 13 genes were affected by both strain and rejection, which was < 1% (13/1368) of all probesets differentially expressed in ACR. ...
Zoila Rangel for carrying out the identification of human homologs to rat genes identified in our study using publicly available tools; and Kelly Byrne for her assistance in manuscript preparation and ...
doi:10.1186/1471-2164-10-280
pmid:19552812
pmcid:PMC2711118
fatcat:hdkdctj3yvgyrmrqshz3i3vo4a
Transplantation proteomics
2005
Pediatric Transplantation
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We also review recent publications pertaining to transplantation proteomics, and discuss the implications and utility of urine proteomics for non-invasive investigation of transplant outcomes. ...
In this review, we provide an overview of proteomics approaches and techniques, and proteomics informatics for clinical transplantation investigators. ...
Acknowledgements This work supported by NIH grant K23 RR 16080 (ADS) and NIH Training Grant T32 DK 007726 (AZT). ...
doi:10.1111/j.1399-3046.2005.00408.x
pmid:16269039
pmcid:PMC1343536
fatcat:taslxabwyfbetiulisn4fmo7ae
Gene expression profiling in acute allograft rejection: challenging the immunologic constant of rejection hypothesis
2011
Journal of Translational Medicine
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Here, we challenge the ICR hypothesis by using a meta-analytical approach and systematically reviewing microarray studies evaluating gene expression on tissue biopsies during acute allograft rejection. ...
In humans, the role and relationship between molecular pathways that lead to tissue destruction during acute allograft rejection are not fully understood. ...
[27] applied this model to cross-organ acute allograft rejection datasets. In this analysis, three existing gene expression datasets were analyzed to identify candidate serum protein biomarkers. ...
doi:10.1186/1479-5876-9-174
pmid:21992116
pmcid:PMC3213224
fatcat:3xysu4aiebblpm3i2m7xala44i
Small Extracellular Vesicles in Transplant Rejection
2021
Cells
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We also summarize and discuss potential applications of plasma and urinary sEV as biomarkers in the context of transplantation. ...
Here, we review the influence of sEV on the development of rejection or tolerance in the setting of solid organ and tissue allotransplantation. ...
Data Availability Statement: Not applicable.
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/cells10112989
pmid:34831212
pmcid:PMC8616261
fatcat:exw5xnoetne4naxn2afpdrkagy
Early Identification of Chronic Lung Allograft Dysfunction: The Need of Biomarkers
2019
Frontiers in Immunology
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Many researchers and clinicians have searched for CLAD biomarkers to improve diagnosis, to refine the phenotypes associated with differential prognosis and to identify early biological processes that lead ...
A growing number of patients with end-stage lung disease have benefited from lung transplantation (LT). ...
In addition to protein-expressing genes, non-coding RNAs can also be profiled and used as biomarkers. ...
doi:10.3389/fimmu.2019.01681
pmid:31379869
pmcid:PMC6650588
fatcat:nweb4owx2bhnxfxit34s4vppqq
A Three-Gene Peripheral Blood Potential Diagnosis Signature for Acute Rejection in Renal Transplantation
2021
Frontiers in Molecular Biosciences
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After differential expression analysis and machine learning algorithms, selected biomarkers were applied to the least absolute shrinkage and selection operator (LASSO) logistic regression to construct ...
identified and validated a novel three-gene diagnostic model with high accuracy for AR in renal transplant patients, and the model also performed well in distinguishing TCMR. ...
Since many conditions other than AR may lead to renal allograft dysfunction, the diagnosis of AR cannot be made by monitoring insensitive functional indicators alone like serum creatine or urine protein ...
doi:10.3389/fmolb.2021.661661
pmid:34017855
pmcid:PMC8129004
fatcat:flmauigqxzatfiu2ts3pc5nbva
Systems biology approaches to investigating the roles of extracellular vesicles in human diseases
2019
Experimental and Molecular Medicine
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They have been implicated in a wide variety of biological processes in health and disease. They are also considered to hold promise for future diagnostics and therapy. ...
The heterogeneity and molecular complexity of EVs necessitates high-throughput analytical platforms for detailed analysis. ...
public transcriptomic and genomic data, as well as different types of biomedical data. ...
doi:10.1038/s12276-019-0226-2
pmid:30872567
pmcid:PMC6418293
fatcat:zkn4hxcyu5dp3diarzltwnzody
The need to embrace molecular profiling of tumor cells in prostate and bladder cancer
2003
Clinical Cancer Research
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As well as being of diagnostic and prognostic use, these molecular profiles will identify putative molecular abnormalities within tumor cells that may be appropriate for therapeutic modulation. ...
A Medline search of publications relating to MP of prostate and bladder cancer was carried out. ...
(36) have examined changes in bladder tumors after genistein therapy using microarrays, and microarrays are already being used to research the molecular basis of allograft rejection in transplant urology ...
pmid:12684390
fatcat:mq4ogtoiibfgrltwazxsux5ioq
Antibody Arrays in Biomarker Discovery
[chapter]
2015
Advances in Clinical Chemistry
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ACKNOWLEDGMENTS We would like to express our thanks for the support of RayBiotech Innovative Research ...
To diagnose and monitor acute kidney rejection, Hu et al. used a large human cytokine antibody array to profile 120 urine proteins from renal transplants experiencing acute rejection (AR). ...
Compared to healthy controls, a Significance Analysis of Microarray (SAM) algorithm identified 42 proteins that were differentially expressed, including commonly associated proteins like amyloid precursor ...
doi:10.1016/bs.acc.2015.01.002
pmid:25934364
fatcat:ps2cphoagrhircnbitw4chyhqu
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