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Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions

Rong Chen, Tara K. Sigdel, Li Li, Neeraja Kambham, Joel T. Dudley, Szu-chuan Hsieh, R. Bryan Klassen, Amery Chen, Tuyen Caohuu, Alexander A. Morgan, Hannah A. Valantine, Kiran K. Khush (+3 others)
2010 PLoS Computational Biology  
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

Sunil Kurian, Yevgeniy Grigoryev, Steve Head, Daniel Campbell, Tony Mondala, Daniel R. Salomon
2007 International Immunopharmacology  
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

Madhav C. Menon, Karen L. Keung, Barbara Murphy, Philip J. O'Connell
2016 Transplantation  
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

Tara K. Sigdel, Minnie M. Sarwal
2008 Pediatric Transplantation  
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

V. R. Mas, C. I. Dumur, M. J. Scian, R. C. Gehrau, D. G. Maluf
2012 American Journal of Transplantation  
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

Valeria R Mas, Thomas F Mueller, Kellie J Archer, Daniel G Maluf
2011 Expert Review of Molecular Diagnostics  
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

Katherine J Deans, Peter C Minneci, Hao Chen, Steven J Kern, Carolea Logun, Sara Alsaaty, Kelly J Norsworthy, Stephanie M Theel, Joel D Sennesh, Jennifer J Barb, Peter J Munson, Robert L Danner (+1 others)
2009 BMC Genomics  
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

Avram Z. Traum, Asher D. Schachter
2005 Pediatric Transplantation  
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

Tara L Spivey, Lorenzo Uccellini, Maria Ascierto, Gabriele Zoppoli, Valeria De Giorgi, Lucia Delogu, Alyson M Engle, Jaime M Thomas, Ena Wang, Francesco M Marincola, Davide Bedognetti
2011 Journal of Translational Medicine  
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

Justyna E. Gołębiewska, Anna Wardowska, Monika Pietrowska, Anna Wojakowska, Alicja Dębska-Ślizień
2021 Cells  
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

Adrien Tissot, Richard Danger, Johanna Claustre, Antoine Magnan, Sophie Brouard
2019 Frontiers in Immunology  
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

Yicun Wang, Di Zhang, Xiaopeng Hu
2021 Frontiers in Molecular Biosciences  
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

András Gézsi, Árpád Kovács, Tamás Visnovitz, Edit I. Buzás
2019 Experimental and Molecular Medicine  
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

Brian J Duggan, John J McKnight, Kate E Williamson, Maurice Loughrey, Declan O'Rourke, Peter W Hamilton, Samuel R Johnston, Claude C Schulman, Alexandre R Zlotta
2003 Clinical Cancer Research  
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]

Jarad J. Wilson, Rob Burgess, Ying-Qing Mao, Shuhong Luo, Hao Tang, Valerie Sloane Jones, Bao Weisheng, Ren-Yu Huang, Xuesong Chen, Ruo-Pan Huang
2015 Advances in Clinical Chemistry  
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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