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Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional and post-transcriptional analysis of CD4+ T cell clones deriving from HTLV-1 infected individuals

ABSTRACT: T-cell clones were obtained by limiting dilution culture of PBMC of HTLV-1 carriers. Exon expression profiling was performed using Affymetrix exon array (Affymetrix Human Exon 1.0 ST Array) according to the manufacturer's instructions. The main objectives were to assess whether transcriptional and post-transcriptional modifications associate with HTLV-1 infection in vivo. To this end, T-cell clones, infected or not by HTLV-1, were obtained by limiting dilution culture of PBMC derived from HTLV-1 carriers. Exon expression profiles of cloned T cells was analyzed using Affymetrix exon array (Affymetrix Human Exon 1.0 ST Array) according to the manufacturer's instructions.

ORGANISM(S): Homo sapiens

SUBMITTER: franck mortreux

PROVIDER: E-GEOD-46518 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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HTLV-1 bZIP factor HBZ promotes cell proliferation and genetic instability by activating OncomiRs.

Vernin Céline C Thenoz Morgan M Pinatel Christiane C Gessain Antoine A Gout Olivier O Delfau-Larue Marie-Hélène MH Nazaret Nicolas N Legras-Lachuer Catherine C Wattel Eric E Mortreux Franck F

Cancer research 20140909 21

Viruses disrupt the host cell microRNA (miRNA) network to facilitate their replication. Human T-cell leukemia virus type I (HTLV-1) replication relies on the clonal expansion of its host CD4(+) and CD8(+) T cells, yet this virus causes adult T-cell leukemia/lymphoma (ATLL) that typically has a CD4(+) phenotype. The viral oncoprotein Tax, which is rarely expressed in ATLL cells, has long been recognized for its involvement in tumor initiation by promoting cell proliferation, genetic instability, ...[more]

PMID: 25205102

Similar Datasets

Exon-expression profiling of CD4+ T cells derived from HTLV-1-infected individuals with or without malignancy

Project description:T-cell clones were obtained by limiting dilution culture of PBMC of HTLV-1 carriers. Exon expression profiling was performed using Affymetrix exon array (Affymetrix Human Exon 1.0 ST Array) according to the manufacturer's instructions. Gene version of CEL files 01 to 12 are presented in GSE46518. The main objectives were to assess whether transcriptional and post-transcriptional modifications associate with HTLV-1 infection in vivo. To this end, T-cell clones, infected or not by HTLV-1, were obtained by limiting dilution culture of PBMC derived from HTLV-1 carriers. Tumor cells derived from patients with an acute form ATLL. Exon expression profiles of cloned T-cells and ATLL cells was analyzed using Affymetrix exon array (Affymetrix Human Exon 1.0 ST Array) according to the manufacturer's instructions. Given that T-cell activation is known to modify alternative exon usage, microarray analysis was carried-out with unstimulated and PHA-stimulated CD4+ T cell clones.

2015-11-01 | E-GEOD-52244 | biostudies-arrayexpress

Transcriptional and post-transcriptional analysis of CD4+ T cell clones deriving from HTLV-1 infected individuals

2014-12-03 | GSE46518 | GEO

Exon-expression profiling of CD4+ T cells derived from HTLV-1-infected individuals with or without malignancy

2015-11-01 | GSE52244 | GEO

miRNA expression profiles of cloned CD4+ and CD8+ T cells infected or not by HTLV-1 in vivo

Project description:To address whether changes in miRNA expression accompany cell-associated replication of HTLV-1 in vivo, we carried out the miRNA expression profiling of CD4+ and CD8+ T-cells derived from naturally HTLV-1 infected individuals with no clinical sign of malignancy. T-cell clones were obtained by limiting dilution culture of PBMCs of HTLV-1 carriers. miRNA expression was assessed by Agilent V3 miRNA array according to the manufacturer's instructions.

2014-12-03 | GSE46345 | GEO

miRNA expression profiles of cloned CD4+ and CD8+ T cells infected or not by HTLV-1 in vivo

2014-12-03 | E-GEOD-46345 | biostudies-arrayexpress

MicroRNAs Implicated in Dysregulation of Gene Expression Following Human Lung Transplantation

Project description:Lung transplantation remains the only viable treatment option for the majority of patients with advanced lung diseases. However, 5-year post-transplant survival rates remain low primarily secondary to chronic rejection. Novel insights from global gene expression profiles may provide molecular phenotypes and therapeutic targets to improve outcomes after lung transplantation. We compared whole-genome transcriptional expression profiled using the Affymetrix Human Exon Array in peripheral blood mononuclear cells (PBMCs) in lung transplant patients and normal individuals. 364 dysregulated genes in Caucasian lung transplant patients relative to normal individuals. Enriched Gene Ontology biological processes and pathways included defense response, immune response” and response to wounding”. We then compared the expression profiles of potential regulating miRNAs which suggested that dysregulation of a number of lung transplant-associated genes (e.g., ATR, FUT8, LRRC8B, NFKBIA) may be attributed to the differential expression of their regulating miRNAs. This exploratory analysis of the relationship between these miRNAs and their gene targets in the context of lung transplantation warrants further investigation and may serve as novel therapeutic targets in lung transplant complications. PBMC samples were collected from 18 patients (14 Caucasian Americans and 4 African Americans) who underwent single-lung transplant or bilateral single-lung transplant surgery during 2005-2008. Control samples were collected from healthy individuals (27 Caucasians and 8 African Americans). Whole-genome expression profiles were performed using the Affymetrix Human Exon 1.0ST Array. The expression levels of miRNAs were profiled using the Exiqon miRCURY™0. *This represents the Affymetrix Human Exon component of the study only.

2014-07-20 | E-GEOD-49081 | biostudies-arrayexpress

Exon-Level Expression Data from Primary Human B Cells and Lymphoblastoid Cell Lines (LCLs) on HuEx and U133 2.0 plus Platforms

Project description:Eptstein-Barr Virus, an oncogenic herpesvirus, infects and immortalizes human B cells in culture into indefinitely-prolerifating LCLs. We examined the gene expression of primary B cells during the process of infection and growth transformation at the exon level to analyze virus-induced changes in expression and exon usage. 4 samples each of total RNA were extracted from purified resting B Cells and monoclonal LCLs, for a total of 8. These samples were subjected to either Human Exon Array 1.0 or Affymetrix U133 2.0 plus. Data was then RMA normalized and analyzed using SplicerEx

2011-05-16 | E-GEOD-29301 | biostudies-arrayexpress

Expression and Splicing Analysis of Myotonic Dystrophy and Other Dystrophic Muscle

Project description:The prevailing patho-mechanistic paradigm for myotonic dystrophy (DM) is that the aberrant presence of embryonic isoforms is responsible for many, if not most, aspects of the pleiotropic disease phenotype. In order to identify such aberrantly expressed isoforms in skeletal muscle of DM type 1 (DM1) and type 2 (DM2) patients, we utilized the Affymetrix exon array to characterize the largest collection of DM samples analyzed to date, and included non-DM dystrophic muscle samples (NMD) as disease controls. For the exon array profiling on the Human Exon 1.0 ST array (Affymetrix Santa Clara, CA) we used a panel of 28 skeletal muscle biopsies from DM1 (n=8), DM2 (n=10), Becker muscular dystrophy, BMD, (n=3), Duchenne muscular dystrophy, DMD (n=1), Tibial muscular dystrophy, TMD, (n=2) and normal skeletal muscle (n=4). Normal control RNAs were purchased commercially. .CEL files were generated with a pre-commercial version of the Affymetrix processing software, and the headers might be non-standard. In our lab, users of the Partek software could use them, whereas users of GeneSpring had to modify the header information.

2016-01-05 | E-GEOD-48828 | biostudies-arrayexpress

Genome-wide analysis of differentially expressed genes and splicing isoforms in clear cell Renal Cell Carcinoma

Project description:In this study we performed a genome wide analysis of the entire complement of mRNAs in clear cell renal cell carcinomas (ccRCC) by means of the Affymetrix Exon Array platform. The analyses were performed both at gene and exon level. Under our parameters over 2,000 genes resulted differentially expressed, and about 250 genes resulted alternative spliced showing differential inclusion of specific cassette exons comparing tumor and non tumoral tissues. 20 total samples were used for exon array analysis: 10 ccRCC tumor sample (T) and their matched non-tumor (NT) kidney tissues samples. All exon array data were analyzed using Partek Genomic Suite 6.4 software (Partek). The robust multi-array average (RMA) algorithm was used for the gene- and exon-level intensity analyses. Data were M-oM-,M-^Altered to consider only those probe sets included in the M-bM-^@M-^\Core Meta-ProbesetM-bM-^@M-^]. Lists of genes and exons with significant variation of the expression levels were generated by using a 0.01 FDR criterion as a significant cutoff. Partek list of significant exon-level probesets (FDR corrected p-value < 0.01) and exon level ANOVA test list were used to create - by an ad hoc Python script - a database of significant probesets from Exon Array experiments. To make more stringent the analysis criteria we excluded from the final exon lists all those cases in which Exon Array revealed a significant change at gene-level. This database we created has been used to explore simple exon skipping events using as reference ASPicDB single exon skipping splicing events after mapping Affymetrix probesets on ASPicDB .gtf files. A single exon from the Partek list was defined significantly skipped only if its adjacent exons were not, by using 0.01 and 0.05 p-value criterions as a significant cutoff for the M-bM-^@M-^\skippedM-bM-^@M-^] and adjacent exons, respectively.

2013-09-06 | E-GEOD-47032 | biostudies-arrayexpress

Exon array profiles of primary human Ewing sarcoma tumors

Project description:Affymetrix exon array data were generated from total RNA that was isolated from localized Ewing sarcoma biopsy specimens. Expression of transcript summarized data was compared to data generated from normal stem cells and normal adult tissues. Total RNA was extracted from 32 archived tumor biopsy specimens obtained from patients with localized Ewing sarcoma. Samples were analyzed by Affymetrix exon arrays using standard procedures. Data were compared to human neural crest and mesenchymal stem cells (in triplicate: GSE21511) as well as to 33 normal adult tissues (Affymetrix tissue controls; 11 tissues in triplicate: cel files obtained from: http://www.affymetrix.com/support/technical/sample_data/exon_array_data.affx). Normalization was achieved by RMA using Parkek Genomics Suite

2015-05-12 | E-GEOD-68776 | biostudies-arrayexpress

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