Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Class prediction models of thrombocytosis using genetic biomarkers

ABSTRACT: Using custom spotted oligonucelotide platelet-focused arrays, platelet samples were compared. 48 health controls, 23 reactive thrombocytosis (RT) and 24 essential thrombocythemia (ET) samples were compared. An 11-biomarker gene subset was identified that discriminated among the three cohorts with 86.3% accuracy. 70 mer oligonucleotides were spotted in quadruplicate and hybridized versus reference RNA in two color method. Spiked control RNAs were also included.

ORGANISM(S): Homo sapiens

SUBMITTER: Wadie Bahou

PROVIDER: E-GEOD-12295 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Class prediction models of thrombocytosis using genetic biomarkers.

Gnatenko Dmitri V DV Zhu Wei W Xu Xiao X Samuel Edward T ET Monaghan Melissa M Zarrabi Mohammad H MH Kim Christi C Dhundale Anil A Bahou Wadie F WF

Blood 20090922 1

Criteria for distinguishing among etiologies of thrombocytosis are limited in their capacity to delineate clonal (essential thrombocythemia [ET]) from nonclonal (reactive thrombocytosis [RT]) etiologies. We studied platelet transcript profiles of 126 subjects (48 controls, 38 RT, 40 ET [24 contained the JAK2V(617)F mutation]) to identify transcript subsets that segregated phenotypes. Cross-platform consistency was validated using quantitative real-time polymerase chain reaction (RT-PCR). Class p ...[more]

PMID: 19773543

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Project description:In sickle cell disease, ischemia-reperfusion injury and intravascular hemolysis produce endothelial dysfunction and vasculopathy characterized by reduced nitric oxide (NO) and arginine bioavailability. Recent functional studies of platelets in patients with sickle cell disease reveal a basally activated state, suggesting that pathological platelet activation may contribute to sickle cell disease vasculopathy. Studies were therefore undertaken to examine transcriptional signaling pathways in platelets that may be dysregulated in sickle cell disease. We demonstrate and validate here the feasibility of comparative platelet transcriptome studies on clinical samples from single donors, by the application of RNA amplification followed by microarray-based analysis of 54,000 probe sets. Data mining an existing microarray database, we identified 220 highly abundant genes in platelets and a subset of 72 relatively platelet-specific genes, defined by more than 10-fold increased expression compared to the median of other cell types in the database with amplified transcripts. The highly abundant platelet transcripts found in the current study included 82% or 70% of platelet abundant genes identified in two previous gene expression studies on non-amplified mRNA from pooled or apheresis samples, respectively. On comparing the platelet gene expression profiles in 18 patients with sickle cell disease in steady state to 12 African American controls, at a 3-fold cut-off and 5% false discovery rate, we identified ~100 differentially expressed genes, including multiple genes involved in arginine metabolism and redox homeostasis. Further characterization of these pathways using real time PCR and biochemical assays revealed increased arginase II expression and activity and decreased platelet polyamine levels. These studies suggest a potential pathogenic role for platelet arginase and altered arginine and polyamine metabolism in sickle cell disease and provide a novel framework for the study of disease-specific platelet biology. Experiment Overall Design: There are 18 sickle cell samples and 12 control samples from healthy African American volunteers.

Dataset Information

Class prediction models of thrombocytosis using genetic biomarkers

Publications

Class prediction models of thrombocytosis using genetic biomarkers.

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