Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human blood leukocytes and T-cells

ABSTRACT: Monitoring genome-wide, cell-specific responses to human disease, although challenging, holds great promise for medicineâs future. Patients with injury severe enough to develop multiple organ dysfunction syndrome (MODS) are known to have multiple immune derangements, including T-cell apoptosis and anergy combined with depressed monocyte antigen presentation. Genome-wide expression analysis of highly-enriched circulating leukocyte subpopulations, combined with cell-specific pathway analyses, offers a previously unavailable opportunity to discover novel leukocyte regulatory networks in critically injured patients. Severe injury induced significant changes in the T-cell, monocyte, and total leukocyte transcriptome, with only 12% of these genomic changes common to all three cell populations. T-cell-specific pathway analyses identified increased gene expression of several novel inhibitory receptors (PD-1, CD152, NRP-1, Lag3), and concomitant decreases in stimulatory receptors (CD28, CD4, IL-2Rï¡). Functional analysis of T-cells and monocytes confirmed reduced T-cell proliferation and increased cell surface expression of negative signaling receptors paired with decreased monocyte costimulation ligands. Thus, genome-wide expression from highly-enriched cell populations combined with knowledge-based pathway analyses leads to the identification of novel regulatory networks differentially expressed in injured patients. Importantly, application of cell separation, genome-wide expression, and cell specific pathway analyses can be used to discover novel pathway alterations in human disease. Experiment Overall Design: Type of experiment: Gene expression profiling of circulating total blood Experiment Overall Design: leukocytes, T-Cells, and Monocytes in severe trauma patients and healthy subjects. Experiment Overall Design: Experimental factors: Healthy subjects, 7 severely traumatized patients Experiment Overall Design: and 7 healthy subjects for transcriptome analysis. Venous blood samples Experiment Overall Design: were collected. Total blood leukocytes were isolated, and T-cell and Experiment Overall Design: monocyte populations were obtained from two subsequent aliquots of the Experiment Overall Design: leukocytes. Total leukocytes, enriched T-cells, and enriched monocytes were analyzed using Affymetrix GeneChip arrays. Experiment Overall Design: Number of hybridizations: 42 Human U133A GeneChip arrays (Affymetrix)

ORGANISM(S): Homo sapiens

SUBMITTER: IDDC Inflammation the Host Response to Injury

PROVIDER: E-GEOD-5580 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Cell-specific expression and pathway analyses reveal alterations in trauma-related human T cell and monocyte pathways.

Laudanski Krzysztof K Miller-Graziano Carol C Xiao Wenzhong W Mindrinos Michael N MN Richards Daniel R DR De Asit A Moldawer Lyle L LL Maier Ronald V RV Bankey Paul P Baker Henry V HV Brownstein Bernard H BH Cobb J Perren JP Calvano Steve E SE Davis Ronald W RW Tompkins Ronald G RG

Proceedings of the National Academy of Sciences of the United States of America 20061010 42

Monitoring genome-wide, cell-specific responses to human disease, although challenging, holds great promise for the future of medicine. Patients with injuries severe enough to develop multiple organ dysfunction syndrome have multiple immune derangements, including T cell apoptosis and anergy combined with depressed monocyte antigen presentation. Genome-wide expression analysis of highly enriched circulating leukocyte subpopulations, combined with cell-specific pathway analyses, offers an opportu ...[more]

PMID: 17032758

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Project description:Objective. Meningococcal sepsis remains an important cause of childhood morbidity and mortality. Largely due to logistic complexities of research in young children with acute life-threatening disease, very little is known regarding differential expression kinetics and molecular regulation of immune response genes in leukocyte subsets. Materials and methods. In this prospective case-control study, six children with meningococcal sepsis were included. Blood was drawn at four time points (t=0, t=8, t=24 and t=72 h after admission to the paediatric intensive care unit). Blood was also collected from matched controls. Detailed immunophenotyping of leukocytes was performed; RNA isolated from whole blood, lymphocytes, monocytes, and granulocytes was used to perform Affymetrix micro-array gene expression analysis. Results and conclusion. There were no differences in total leukocyte count between patients and controls. In contrast to previous in vitro studies we observed an unexpected decrease in NK cell numbers, as well as downregulation of NK cell specific and cytotoxic T-cell related gene expression in patients with meningococcal septic shock. By contrast, expression of genes, involved in innate immunity and several other pathways, differed between the different leukocyte subpopulations in a dynamic fashion. Compared to previously reported gene expression profiles, it was possible to define a meningococcal sepsis specific expression profile. Experiment Overall Design: In this prospective case-control study, six children with meningococcal sepsis were included. Blood was drawn at four time points (t=0, t=8, t=24 and t=72 h after admission to the paediatric intensive care unit). Blood was also collected from matched controls. Detailed immunophenotyping of leukocytes was performed; RNA isolated from whole blood, lymphocytes, monocytes, and granulocytes was used to perform Affymetrix micro-array gene expression analysis. Experiment Overall Design: No replicates were performed. Experiment Overall Design: Table 4. Results of between-subject analyses. Experiment Overall Design: Source Time (h) ca co/ca at t=T Experiment Overall Design: Blood t0: ca:2 3, co: a b c; t8: 2; t24 :ca:1 2 3; t72: ca:1 2. Experiment Overall Design: Lym t0: ca:2 3, co:a b c d;t8: ca:1 3 4;t24: ca:1 2 3 4 6; t72: ca: 1 2. Experiment Overall Design: Mono t0:ca: 1 3 4 6, co: a b d; t8: ca:1 2 3; t24:ca: 1 2 3; t72: ca:1. Experiment Overall Design: Numbers represent the patient identification numbers. Experiment Overall Design: Characters represent the individual controls.

Project description:Background---For decades, plasma lipid levels have been known risk factors of atherosclerosis. Recently, inflammation has gained acceptance as a crucial event in the pathogenesis and development of atherosclerosis. A number of studies have provided some insights into the relationships between the two aspects of atherosclerosis: plasma lipids --- the risk factors, and circulating leukocytes --- the effectors of inflammation. In this study, we investigate the relationships between plasma lipids and leukocytes. Methods and Results---No significant correlation was found between leukocyte counts and plasma lipid levels in 74 individuals. Profiling and analyzing the leukocyte gene expression of 32 individuals revealed distinctive patterns in response to plasma lipid levels: 1) genes involved in lipid metabolism and in the electron transport chain were positively correlated with triglycerides and low-density lipoprotein cholesterol levels, and negatively correlated with high-density lipoprotein cholesterol levels; 2) genes involved in platelet activation were negatively correlated with high-density lipoprotein cholesterol levels; 3) transcription factors regulating lipidgenesis-related genes were correlated with plasma lipid levels; 4) a number of genes correlated to plasma lipid levels were found located in the regions of known QTLs associated with hyperlipemia. Conclusions--- We discovered interesting patterns of leukocyte gene expression in response to plasma lipid levels. Most importantly, genes involved in lipid metabolism, the electron transportation chain, and platelet activation were found correlated with plasma lipid levels. We suggest that leukocytes respond to changing plasma lipid levels by regulating a network of genes, including genes involved in lipid and fatty acid metabolism, through the activation of key transcription factors, such as sterol regulatory element binding transcription factors and peroxisome proliferative activated receptors. Experiment Overall Design: 1. Profile gene expression in human peripheral blood cells. Experiment Overall Design: 2. Test blood biochemistry and blood cell differential counts Experiment Overall Design: 3. Examine the correlation between blood gene expression and blood lipid levels. Experiment Overall Design: 4. Explore possible pathways with significant genes. Experiment Overall Design: 5. Validate a number of significant genes with RT-PCR

Dataset Information

Transcription profiling of human blood leukocytes and T-cells

Publications

Cell-specific expression and pathway analyses reveal alterations in trauma-related human T cell and monocyte pathways.

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