Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genomic profiles for human peripheral blood T cells, B cells, natural killer cells, monocytes, and polymorphonuclear cells: comparisons to ischemic stroke, migraine, and Tourette syndrome

ABSTRACT: Blood genomic profiling has been applied to disorders of the blood and various organ systems including brain to elucidate disease mechanisms and identify surrogate disease markers. Since most studies have not examined specific cell types, we performed a preliminary genomic survey of major blood cell types from normal individuals using microarrays. CD4+ T cells, CD8+ T cells, CD19+ B cells, CD56+ natural killer cells, and CD14+ monocytes were negatively selected using the RosetteSep antibody cocktail, while polymorphonuclear leukocytes were separated with density gradient media. Genes differentially expressed by each cell type were identified. To demonstrate the potential use of such cell subtype-specific genomic expression data, a number of the major genes previously reported to be regulated in ischemic stroke, migraine, and Tourette syndrome are shown to be associated with distinct cell populations in blood. These specific gene expression, cell-type-related profiles will need to be confirmed in larger data sets and could be used to study these and many other neurological diseases. This study includes data from major blood cell types from normal individuals. These cell types include CD4+ T cells, CD8+ T cells, CD19+ B cells, CD56+ natural killer cells, CD14+ monocytes and PMN (polymorphonuclear cells). The data were hybridized on 3 separate batches of gene chips.

ORGANISM(S): Homo sapiens

SUBMITTER: Marc Dalod

PROVIDER: E-GEOD-72642 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genomic profiles for human peripheral blood T cells, B cells, natural killer cells, monocytes, and polymorphonuclear cells: comparisons to ischemic stroke, migraine, and Tourette syndrome.

Du Xinli X Tang Yang Y Xu Huichun H Lit Lisa L Walker Wynn W Ashwood Paul P Gregg Jeffrey P JP Sharp Frank R FR

Genomics 20060320 6

Blood genomic profiling has been applied to disorders of the blood and various organ systems including brain to elucidate disease mechanisms and identify surrogate disease markers. Since most studies have not examined specific cell types, we performed a preliminary genomic survey of major blood cell types from normal individuals using microarrays. CD4+ T cells, CD8+ T cells, CD19+ B cells, CD56+ natural killer cells, and CD14+ monocytes were negatively selected using the RosetteSep antibody cock ...[more]

PMID: 16546348

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Project description:White blood cells (WBCs) express tens of thousands of genes. Their expression levels are modified by genetic and external factors. In further study we found that gene expression profiles of these cellls can serve as surrogate markers for monitoring exercise and training load.The purpose of the present study was to investigate the effects of acute exercise on gene expression profiles (GEPs) of PBMCs and T-lymphocytes in order to re-detect the patterns in subpopulations. The use of WBC subpopulations is necessary because of the well known subpopulation shifts that occur during physical activities. Three male probands performed an exhaustive treadmill test (ET) at 80% of their VO2max. PBMCs were isolated using BD Vacutainer CPT tubes containig Ficoll. T-lymphocytes were isolated from the PBMCs via rosetting technology. Gene expression profiles were measured using the Affymetrix GeneChipÂ® technology. After scaling, normalisation, and filtering groupwise and pairwise comparisons of gene expression intensities were performed. We found that sorting increases the detection sensitivity and enables the researcher to observe regulation that is hidden in heterogenous populations. We therefore suggest not to work on mixed nbut instead on sorted cells when performing gene expression analyses. Experiment Overall Design: Three healthy male probands executed an exhaustive treadmill test (80% VO2max) until individual exhaustion. Blood samples (16ml) were drawn before and one hour past the tests. PBMCs were isolated using the Ficoll density centrifugation methode. T-lymphocytes were isolated by adding rosetting anibodies zo the cells before centrifugation. Cells were lysed using Trizol and worked up with Qiagen RNeasy Micro columns. RNA was processed and hybridised on U133A 2.0 Affymetrix GeneChips. Samples were grouped and gene expression changes were detected via multiple algorithms included in GeneSpring 7.2 (Agilent). Experiment Overall Design: The four groups contained three samples related to the cell type "PBMC" or "T-cell" and "before exercise" or "1hour past exercise". TTest, GOs and KEGG classification, principal component analysis and hierarchical clstering were used to scan for gene expression profiles induced through the different exercise conditions.

Project description:Readily accessible samples such as peripheral blood or cell lines are increasingly being used in large cohorts to characterise gene expression differences between a patient group and healthy controls. However, cell and RNA isolation procedures and the variety of cell types that make up whole blood can affect gene expression measurements. We therefore systematically investigated global gene expression profiles in peripheral blood from six individuals collected during two visits by comparing five of the following cell and RNA isolation methods: whole blood (PAXgene), peripheral blood mononuclear cells (PBMCs), lymphoblastoid cell lines (LCLs), CD19 and CD20 specific B-cell subsets. Gene expression measurements were clearly discriminated by isolation method although the reproducibility was high for all methods (range ρ = 0.90-1.00). The PAXgene samples showed a decrease in the number of expressed genes (P<1*10-16) with higher variability (P<1*10-16) compared to the other methods. Differentially expressed probes between PAXgene and PBMCs were correlated with the number of monocytes, lymphocytes, neutrophils or erythrocytes. The correlations (ρ =0.83; ρ =0.79) between the expression levels of detected probes were much lower compared to the two B-cell isolation methods (ρ =0.98). Gene ontology analysis of detected genes showed that genes involved in inflammatory responses are enriched in B-cells CD19 and CD20 whereas genes involved in alcohol metabolic process and the cell cycle were enriched in LCLs. Gene expression profiles in blood-based samples are strongly dependent on the predominant constituent cell type(s) and RNA isolation method. It is crucial to understand the differences and variability of gene expression measurements between cell and RNA isolation procedures, and their relevance to disease processes before application in large clinical studies. In the present study, we investigated variability and consistency in gene expression profiles between five of the most common post venipuncture methods of cell and RNA isolation: whole blood (PAXgene (PAX)), PBMCs, Epstein-Barr virus (EBV) transformed LCLs, CD19-specific B-cells subsets (B-cell CD19), CD20-specific B-cells subsets (B-cell CD20). Using samples from six individuals collected during two visits, we evaluated the differences and concordances of global gene expression profiles, the biological and technical variability seen in these approaches, cell-type specific gene expression signatures and their relevance to large-scale biobanking initiatives.

Dataset Information

Genomic profiles for human peripheral blood T cells, B cells, natural killer cells, monocytes, and polymorphonuclear cells: comparisons to ischemic stroke, migraine, and Tourette syndrome

Publications

Genomic profiles for human peripheral blood T cells, B cells, natural killer cells, monocytes, and polymorphonuclear cells: comparisons to ischemic stroke, migraine, and Tourette syndrome.

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