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High-throughput transcriptome sequencing of an AML-M2 patient in two stages: primary tumor and remission.

ABSTRACT: In order to detect the transcriptomic differences during chemotherapy treatment of de novo AML, we adopted massively parallel pyrosequencing of mRNAs (RNA-seq) using blood tissues of an patient with AML (FAB subtype M2) in tumor stage and remission stage. We obtained a total of 34.6 and 30.8 million paired reads from the two samples. The RNA-seq data derived from the sample illustrated the differentially expression genes between the two stages.

ORGANISM(S): Homo sapiens

PROVIDER: GSE36866 | GEO | 2013/03/28

SECONDARY ACCESSION(S): PRJNA157037

REPOSITORIES: GEO

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High-throughput transcriptome sequencing of an AML-M2 patient in two stages: primary tumor and remission.

Project description:In order to detect the transcriptomic differences during chemotherapy treatment of de novo AML, we adopted massively parallel pyrosequencing of mRNAs (RNA-seq) using blood tissues of an patient with AML (FAB subtype M2) in tumor stage and remission stage. We obtained a total of 34.6 and 30.8 million paired reads from the two samples. The RNA-seq data derived from the sample illustrated the differentially expression genes between the two stages. Blood samples of an AML-M2 patient in two stages examined: primary tumor and chemotherapy induced remission.

2013-03-28 | E-GEOD-36866 | biostudies-arrayexpress

Global gene expression profile of primary human leukemic blasts

Project description:The goal of this study is to define the global gene expression profile of primary leukemic blasts from patients with different forms of myeloid leukemia and different FAB subtypes. Here we report the global gene expression profile of 2 patients with AML FAB M5, 2 patients with AML FAB M7, 3 patients with Down syndrome AML FAB M7 and 3 patients with Down syndrome transient leukemia.

2009-12-29 | GSE19681 | GEO

Gene expression profiling of acute myeloid leukemia samples from Polish adult AML-M1 and M2 patients

Project description:Acute myeloid leukemia (AML) is the most common and severe acute leukemia diagnosed in adults. Although it is one of the most studied cancers, this is the first study of Polish population of AML patients. The data were collected with the use of home-made boutique array. The additional advantage is pre-selection of patients - our sample set includes only two AML FAB subtypes with the highest content of immature myeloid cells: M1 (11 samples) and M2 (22 samples). From the majority of patients two sources of material were used for mononuclear cell separation and RNA extraction: bone marrow and peripheral blood. 15 samples from healthy volunteers were used as a control.

2017-12-31 | E-MTAB-5434 | biostudies-arrayexpress

Epigenetically Induced Ectopic Expression of UNCX in Acute Myeloid Leukemia Associated with Impaired Proliferation and Differentiation of Myeloid Cells

Project description:We performed gene-expression profiling (GEP) of UNCX-positive versus UNCX-negative AML patients using exon-array and gene-pathway analyses. UNCX is a homeobox gene ectopically expressed in acute myeloid leukemia (AML) patients and cell lines, whose activation is induced by epigenetic modifications. Our results showed a novel leukemogenic role of UNCX in slowing myeloid cell proliferation with a differentiation arrest in AML blasts. Accordingly, UNCX expression characterizes AML cells at early stage of differentiation, mainly M2 and M3 FAB types carrying wild-type NPM1. Overall, our findings provide new relevant insights into the role of epigenetically activated homeobox genes in leukemogenesis, defining a new subgroup of AML patients.

2016-11-01 | E-MTAB-4098 | biostudies-arrayexpress

Transcriptome of primary acute myeloid leukemia (AML) cells treated with AICAr

Project description:Ribonucleoside AICAr, a precursor in purine synthesis and a known activator of AMPK, was shown to induce monocytic differentiation in AML cell lines by inducing pyrimidine depletion followed by activation of ATR/Chk1 pathway and cell cycle arrest. Here we report transcriptional changes induced by AICAr in the primary AML sample (FAB-M2, FLT3 negative, NPM1 negative) in which AICAr induced differentiation and accumulation of macrophage cells in vitro. RNA-seq transcriptome analysis of primary AML cells isolated from the bone marrow of a patient with de novo FAB-M2 AML. Mononuclear cells were isolated from the bone marrow sample by density gradient separation and grown in RPMI supplemented with 10% FBS, 2 mM L-glutamine, 50 U/ml penicillin, 50 μg/ml streptomycin and 50 ng/ml IL-3, IL-6, SCF and FLT3L. Cells were treated with AICAr (0.4 mM) for 24 h. Experiment was performed in biological triplicates and total RNA was isolated for transcriptome analysis using Illumina high throughput sequencing.

2020-11-01 | E-MTAB-9209 | biostudies-arrayexpress

Pediatric AML classification according to C/EBPδ expression

Project description:We examined if pediatric AMLs rank-ordered according to C/EBPδ expression showed the activation of similar pathways. AML samples were dichotomized into groups including the upper quartile (Q1) and the lower three quartiles (Q2-4) according to their C/EBPδ expression values. Moreover, AML samples were associated to French-American-British (FAB) classification.

2016-06-21 | GSE75461 | GEO

Homo sapiens

Project description:Gene expression profiling of 35 AML FAB-M0 samples

| PRJNA119839 | ENA

CENAT-AML-experiment1

Project description:Acute myeloid leukemia (AML) is the most common and severe acute leukemia in adults. It is a heterogeneous disease where the subset of molecularly different types, presenting various morphological features and differentiation stage, can be distinguished. Genomic research of leukemias is conducted since 1999 and large cohort studies shown that particular genetic alterations correspond with specific gene expression signatures. However, not always they provide clinically relevant information. The most unknown group is cytogenetically normal acute myeloid leukemia (CN-AML, 40-49% of all AML cases). The aim of our experiment was to determine selected gene expression profiles in CN-AML, using small, boutique microarray. The array contained 933 oligonucleotide probes, mainly complementary to acute myeloid leukemia markers, genes involved in leukemic transformation and myeloid cell proliferation, differentiation and maturation. Our test dataset included 40 hybridizations: 24 corresponding with blood and bone marrow samples collected from 12 patients with AML M1 or M2 FAB subtype and 16 corresponding with healthy control samples. Total RNA was extracted from the mononuclear cell fractions, reversibly transcribed to cDNA and labeled with Alexa 647 dye. The common reference was RNA isolated from HL-60 cell culture, labeled with Alexa 555 dye.

2013-07-01 | E-MEXP-3647 | biostudies-arrayexpress

Transcriptome Sequencing of Pediatric AML FAB-M7

Project description:<p>High resolution analysis of DNA copy number abnormalities and loss-of-heterozygosity on acute myeloblastic leukemia samples utilizing SNP arrays has demonstrated that in contrast to pediatric ALL, de novo AML is characterized by a very low burden of genomic alterations (Radtke, et al., PNAS, 2009). Samples for this study represented a cross-section of the different subtypes of pediatric AML. The only AML subtype that was an outlier from the above observations was acute megakaryocytic leukemia (AML FAB-M7), with the majority of these cases being characterized by complex chromosomal rearrangements and a high number of copy number alterations. To more fully define the genomic landscape of this subtype, we performed transcriptome sequence analysis on 14 pediatric FAB-M7 cases and mutation recurrence screening in a panel of 62 adult and pediatric AML FAB-M7 samples using the Illumina platform. Our results identified chromosomal rearrangements resulting in the expression of novel fusion transcripts in 11/14 cases. Remarkably, in 7/14 cases we detected an inversion on chromosome 16 that results in the juxtaposition of the CBFA2T3 gene next to the GLIS2 gene resulting in a CBFA2T3-GLIS2 chimeric gene that encoded an in frame fusion protein. This fusion led to the acquisition or preservation of self-renewal in colony forming assays, providing functional evidence for a role in leukemogenesis. In addition to novel chimeric transcripts, we found mutations in genes previously identified to play a role in megakaryoblastic leukemia that carry a proliferative advantage to the cell, such as JAK2 and MPL. These data demonstrate that AML FAB-M7 is characterized by cooperating Class I and Class II mutations leading to leukemogenesis.</p>

| phs000413 | dbGaP

Transcription profiling of human T cells from patients presenting with AML compared with healthy T cells

Project description:Work previously published by our group has demonstrated that T cells from patients with chronic lymphocytic leukaemia (CLL) show differentially regulated genes compared with healthy T cells. This study was initiated to examine if these gene expression changes were unique to CLL T cells or common to an alternative leukaemia, acute myeloid leukaemia (AML). Experiment Overall Design: The study was composed of four groups of samples: AML CD4 (n=10), AML CD8 (n=10), Healthy CD4 (n=10), Healthy CD8 (n=11). AML samples were chosen to represent the range of FAB types, prognostic groups and patient outcomes. Healthy T cells were obtained from volunteers. The purity of isolated T cell fractions was greater than 70% in all cases.

2009-06-01 | E-GEOD-14924 | biostudies-arrayexpress

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