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Gene expression profiling of Acute Myeloid Leukemia (AML) samples

ABSTRACT: The aim was to analyze the expression of genes in cytogenetically distinct cases of AML. We used total RNA obtained from 6 AML samples, consisting of 3 cytogenetically distinct subtypes, to establish the expression levels of 27,868 individual human genes. Expression data from the ABI Human Genome Survey Microarray were filtered, quantile-normalized and subjected to significance analysis of microarrays. Established gene expression profiles were further compared with corresponding DNA methylation in analyzed AML patients.

ORGANISM(S): Homo sapiens

SUBMITTER: Jacek Marzec

PROVIDER: E-GEOD-34722 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome wide analysis of acute myeloid leukemia reveal leukemia specific methylome and subtype specific hypomethylation of repeats.

Saied Marwa H MH Marzec Jacek J Khalid Sabah S Smith Paul P Down Thomas A TA Rakyan Vardhman K VK Molloy Gael G Raghavan Manoj M Debernardi Silvana S Young Bryan D BD

PloS one 20120329 3

Methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq) has the potential to identify changes in DNA methylation important in cancer development. In order to understand the role of epigenetic modulation in the development of acute myeloid leukemia (AML) we have applied MeDIP-seq to the DNA of 12 AML patients and 4 normal bone marrows. This analysis revealed leukemia-associated differentially methylated regions that included gene promoters, gene bodies, CpG islands a ...[more]

PMID: 22479372

Similar Datasets

Gene expression profiling in Acute Myeloid Leukaemia (AML)

Project description:We used total RNA obtained from 97 AML samples, consisting of 6 cytogenetically distinct subtypes, to establish expression level of 27,868 individual human genes. Expression data from ABI Human Genome Survey Microarray were filtered, quantile-normalized and subjected to significance analysis of microarrays. We wanted to identify clusters of genes differentially expressed among AML subtypes.

2019-03-15 | E-MTAB-906 | biostudies-arrayexpress

Genome-Wide Analysis of Acute Myeloid Leukemia Reveals Leukemia-Specific Methylome and Subtype-Specific Hypomethylation of Repeats

Project description:This SuperSeries is composed of the following subset Series: GSE28314: Genome-wide study of DNA methylation in AML by MeDIP-seq GSE34722: Gene expression profiling of Acute Myeloid Leukemia (AML) samples Refer to individual Series

2012-04-02 | E-GEOD-37022 | biostudies-arrayexpress

Molecular profiling of temporal fossa arachnoid cysts

Project description:The gene expression signature of seven surgically removed intracranial temporal fossa arachnoid cysts was generated with two normal arachnoid membrane samples as control. Briefly, we used the Qiagen RNeasy minikit (QIAGEN GmbH Germany, Qiagen) to extract total RNA. After RNA quality and quantity assessment, we then constructed cDNA with RT-PCR reagents (Applied Biosystems, U.S). Gene expression microarray analysis was performed on the ABI 1700 Expression Array System (Applied Biosystems, U.S) using the Applied Biosystems Chemo luminescent RT-IVT Labeling Kit and Human Genome microarray (Applied Biosystems, U.S). Signal intensities generated with the ABI 1700 Expression Array System (Applied Biosystems, U.S) were imported into the J-Express Pro 2.7 software (MolMine AS, Bergen, Norway), where inter-array quantile normalization was performed to minimize the effect of external variables into the data. All control spots and flagged spots were removed, leaving 33096 gene probes available for analysis. First, we performed an unsupervised hierarchical cluster analysis in which the group belonging of the samples was defined. Second, we used Significance Analysis of Microarrays (SAM) with 400 and 1000 permutations to compare AC and AM samples and generate gene lists of differentially expressed genes between these groups. With SAM the false discovery rate (FDR) of the gene lists was calculated. FDR returned the number of false positive genes present on the gene list. A measure of FDR is the Q value, which conveniently shows an estimation of the FDR in percent. In the current study only genes with a Q value <1.0 % were accepted as being differentially expressed. A quantile normalized data set consisting of 33096 individual gene probes for each sample was subjected to Significance Analysis of Microarrays.

2010-05-16 | E-GEOD-19727 | biostudies-arrayexpress

Expression and Prognostic impact of LncRNAs in AML

Project description:Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides located within the intergenic stretches or overlapping antisense transcripts of protein coding genes. LncRNAs are involved in numerous biological roles including imprinting, epigenetic regulation, apoptosis and cell-cycle. To determine whether lncRNAs are associated with clinical features and recurrent mutations in older patients (aged M-bM-^IM-%60 years) with cytogenetically normal (CN) acute myeloid leukemia (AML), we evaluated lncRNA expression in 148 untreated older CN-AML cases using a custom microarray platform. We analyzed 148 older cytogenetically normal(CN)-AML patients samples using a custom microarray platform and describe the expression of lncRNAs among the AML samples.

2014-11-26 | E-GEOD-63614 | biostudies-arrayexpress

Lacerated muscle gene expression

Project description:We investigated the inflammatory gene profile of surgically-repaired lacerated muscles during the recovery phase and examined if it was influenced by the integrity/injury of the IM, intramuscular nerve using 3 lacerated rat muscle models: DN, where the IM-nerve was concomitantly cut; RN, where the IM-nerve was crushed but leaving an intact nerve sheath; and PN, a control where the IM-nerve was preserved intact. After 2, 4 and 8 weeks, the animals were sacrificed and their gastrocnemius muscles were removed and total RNA was extracted with Qiagen RNeasy Fibrous Tissue Mini Kit according to manufacturers instructions. Biotin-labelled cRNA probes were synthesized from total RNA by using a TrueLabeling-AMP Linear RNA amplification kit (SABiosciences Corp, Frederick, MD). The labeled cRNA probes were hybridized to oligonucleotide fragments spotted on the gene array membranes. Membranes were washed to remove any unincorporated probe and incubated with alkaline phosphatase-conjugated streptavidin (AP-streptavidin). Relative expression levels of specific genes were detected from signals generated by chemiluminescence from the alkaline phosphatase substrate, CDP-Star. The luminizing blots were used to expose X-ray films and quantified by spot densitometry with the aid of GEArray expression analysis suite (SABiosciences Corp, Frederick, MD). The abundance of each transcript was normalized to the normal un-operated muscle of the opposite limb, and to the housekeeping gene markers on each array (Aldoa, GAPdH and BAS2C). The results were presented as log2-fold expression with PN used as a control, to compare the two different types of nerve injuries (RN and DN).

2012-01-11 | E-MTAB-755 | biostudies-arrayexpress

Gene expression profiling of chemokines and chemokine receptors on B-cells in chronically HIV-1 infected patients

Project description:From the analysis of all genes included in the array a number of individual genes were identified as dys-regulated in HIV-1 infected patients compared to healthy controls. In particular, increased CXCL13 expression in all individual patient samples. Abstract from publication: HIV-1 infection is associated with B-cell abnormalities such as hypergammaglobulinemia, poor immunisation responses and loss of serological memory. To determine whether altered expression of chemokine receptors and their ligands may play a role in B-cell dysfunctions during HIV-1 infection, the expression of CXCR4, CXCR5 and CCR7 receptors and their respective ligands on CD19+ B-cells were examined in HIV-1 infected patients and controls. We report a decreased CXCR5 expression on B-cells from patients (p<0.05), a phenomenon associated with a low CD4 T-cell count (<350 cells/Âµl). Interestingly, an increased expression of CXCL13, the ligand for CXCR5, was found in peripheral B-cells from HIV-1 infected patients. Moreover upon B-cell activation in vitro, CXCL13 was secreted in culture. In addition, CXCL13 positive B-cells were also found in the lymph nodes of HIV-1 infected patients, but not in control tissue. B-cell migration towards CXCL13, CXCL12 and CCL21, ligands for CXCR5, CXCR4 and CCR7, was also evaluated. In patients with a low CD4 Tcell count, migration towards all ligands was increased. Our findings indicate that altered expression of the chemokine receptor-ligand pair, CXCR5/CXCL13 may participate in the establishment of B-cell dysfunctions during HIV-1 infection. Total RNA was extracted from purified peripheral B-cells from 4 controls and 4 patients.

2010-06-25 | E-GEOD-12597 | biostudies-arrayexpress

RNA-seq expression profiling of NPM1mutated normal-AML with methylome status for HIST1 gene, i.e. H3K27me3 high (N=16) and H3K27me3 low (N=11). Transcriptome was done with Affymetrix HG-133+2.0 and Affymetrix Human Gene 2.0 ST microarrays

Project description:The epigenetic machinery is frequently altered in acute myeloid leukemia (AML). Focusing on cytogenetically normal (CN) AML, we previously described an abnormal H3K27me3 enrichment covering 70 kb on the HIST1 cluster (6.p22). Here, we further investigate the molecular, functional, and prognosis significance of this epigenetic alteration in NPM1-mutated (NPM1mut) CN-AML. H3K27me3 HIST1high group of patients

2020-08-25 | E-MTAB-6997 | biostudies-arrayexpress

MicroRNA profiling by array of older patients with cytogenetically normal AML with or without FLT3 internal tandem duplications

Project description:microRNA expression microarray data used for expression signature associated with FLT3-ITD in samples from older patients with cytogenetically normal AML

2010-07-22 | E-TABM-1032 | biostudies-arrayexpress

Prognostic DNA Methylation Patterns in Cytogenetically Normal Acute Myeloid Leukemia are predefined by Stem Cell Chromatin Marks [methylation]

Project description:Cytogenetically normal acute myeloid leukemia (CN-AML) comprise between forty and fifty percent of all adult acute myeloid leukemia (AML) cases. In this clinically diverse group molecular aberrations such as FLT3ITD, NPM1 and CEBPA mutations recently have added to the prognostic accuracy. Aberrant DNA methylation is a hallmark of cancer including AML. We investigated in total 89 CN-AML samples in a test and a validation cohort for genome-wide promoter DNA methylation with Illumina Methylation Bead arrays and compared them to normal myeloid precursors and global gene expression. IDH and NPM1 mutations were associated with different methylation patterns (p=0.0004 and 0.04, respectively). Genome-wide methylation levels were elevated in IDH mutated samples (p=0.006). We observed a negative impact of DNA methylation on transcription. Genes targeted by Polycomb group (PcG) proteins and genes associated with bivalent histone marks in stem cells showed increased aberrant methylation in AML (p<0.0001). Furthermore, high methylation levels of PcG target genes were independently associated with better progression free (OR 0.47, p=0.01) and overall survival (OR 0.36, p=0.001). In summary, genome wide methylation patterns show preferential methylation of PcG targets with prognostic impact in CN-AML. Genome wide methylation pattern study of cytogenetically normal AML

2011-09-20 | E-GEOD-32251 | biostudies-arrayexpress

Transcription profiling of human proximal tubular epithelial cells inclubated with 5% plasma from septic patients or healthy volunteers

Project description:proximal tubular epithelial cell apoptosis were incubated with 5% plasma of septic patients or healthy volunteers diluited in RPMI 1640

2008-03-15 | E-MEXP-1510 | biostudies-arrayexpress

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