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Transcriptome sequencing of myelodysplasia

ABSTRACT: Transcriptome sequencing was performed on 214 patients with myelodysplasia in this study. RNA was obtained from bone marrow CD34+ cells (n=100) and/or bone marrow mononuclear cells (n=165). Transcriptome sequencing was performed for both cell fractions in 51 patients. We also studied bone marrow CD34+ cells and bone marrow mononuclear cells obtained from three healthy adults each.

PROVIDER: EGAS00001002346 | EGA |

REPOSITORIES: EGA

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Gene expression and risk of leukemic transformation in myelodysplasia.

Shiozawa Yusuke Y Malcovati Luca L Gallì Anna A Pellagatti Andrea A Karimi Mohsen M Sato-Otsubo Aiko A Sato Yusuke Y Suzuki Hiromichi H Suzuki Hiromichi H Yoshizato Tetsuichi T Yoshida Kenichi K Yoshida Kenichi K Shiraishi Yuichi Y Chiba Kenichi K Makishima Hideki H Boultwood Jacqueline J Hellström-Lindberg Eva E Miyano Satoru S Cazzola Mario M Ogawa Seishi S

Blood 20171102 24

Myelodysplastic syndromes (MDSs) are a heterogeneous group of clonal hematopoietic disorders with a highly variable prognosis. To identify a gene expression-based classification of myelodysplasia with biological and clinical relevance, we performed a comprehensive transcriptomic analysis of myeloid neoplasms with dysplasia using transcriptome sequencing. Unsupervised clustering of gene expression data of bone marrow CD34<sup>+</sup> cells from 100 patients identified 2 subgroups. The first subty ...[more]

PMID: 29097382

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ena-DATASET-CGP-UT-04-01-2018-02:12:18:566-617 - samples

Project description:Transcriptome sequencing was performed on 214 patients with myelodysplasia in this study. RNA was obtained from bone marrow CD34+ cells (n=100) and/or bone marrow mononuclear cells (n=165). Transcriptome sequencing was performed for both cell fractions in 51 patients. A total of 211 patients were genotyped by targeted deep sequencing. We also studied bone marrow CD34+ cells and bone marrow mononuclear cells obtained from three healthy adults each.

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Identification of genes that may predict response to azacitidine treatment.

Project description:Azacitidine (AZA) is a hypomethylating drug used to treat disorders associated with myelodysplasia and related neoplasms. Approximately 50% of patients do not respond to AZA and have very poor outcomes. It is of great interest to identify predictive biomarkers for AZA responsiveness. Therefore, we searched for specific genes whose expression level was associated with response status.Using microarrays, we analyzed gene expression patterns in bone marrow CD34+ cells from 32 patients with myelodysplastic syndromes, chronic myelomonocytic leukemia, and acute myeloid leukemia with myelodysplasia-related changes before AZA therapy. Total RNA was isolated from bone marrow CD34+ cells obtained from myelodysplasia and related neoplasms patients who underwent treatment with 5-azacytidine (AZA, Vidaza). Using Illumina Human HT-12 v. 4 microarrays, we assayed gene expression profiles in patient CD34+ cells before AZA treatment in order to collect basic data for search for markers of the prediction of therapy response.

2016-02-10 | E-GEOD-77750 | biostudies-arrayexpress

Gene expression profiling in the leukemic stem cell-enriched CD34+ fraction identifies target genes that predict prognosis in normal karyotype AML

Project description:Mononuclear cells from AML patients (n=46) were sorted into CD34+ and CD34- subfractions and genome-wide expression analysis was performed using Illumina BeadChip Arrays (HT12 v3). Of 2 AML samples only the CD34+ fraction could be analyzed. AML CD34+ and CD34- gene expression was compared to a large group of normal CD34+ bone marrow cells (n=31). Mononuclear cells from AML patients (n=46) were sorted into CD34+ (46) and CD34- (44) subfractions and genome-wide expression analysis was performed using Illumina BeadChip Arrays (HT12 v3). AML CD34+ and CD34- gene expression was compared to a large group of normal CD34+ bone marrow cells (n=31).

2011-07-18 | E-GEOD-30029 | biostudies-arrayexpress

Identification of genes that may predict response to azacitidine treatment.

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Bone marrow mononuclear cells

Project description:Bone marrow mononuclear cells

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Gene expression profiling in the leukemic stem cell-enriched CD34+ fraction identifies target genes that predict prognosis in normal karyotype AML

2011-07-19 | GSE30029 | GEO

Whole Genome Sequencing of Waldenstrom's Macroglobulinemia

Project description:<p>Whole genome sequencing was conducted on 10 tumor/germline paired samples along with 20 additional unpaired tumor samples from patients with Waldesntrom's macroglobulinemia. Tumor lymphoplasmacytic lymphoma cells were obtained from CD19+ selected bone marrow mononuclear cells. Germline tissue was obtained from CD19 depleted peripheral blood mononuclear cells. High molecular weight DNA was then submitted for whole genome sequencing with Complete Genomics and aligned to HG19/NCBI human reference build 37.</p>

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Gene expression analysis from erythroid progenitors of patients with Diamond-Blackfan anemia

Project description:Gene expression analysis from erythroid progenitors (CD34+/CD71(high)/CD45- mononuclear cells from the bone marrow) of patients with Diamond-Blackfan anemia (due to RPS19 mutations) and control individuals.

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CD34+ cells from mast cell leukemia and healthy bone marrow

Project description:In patients with mast cell leukemia, the CD34+ bone marrow fraction contains a subset of disease-initiating and propagating cells. The aim of this study was to compare the gene expression profile of these cells with that of CD34+ cells obtained from the bone marrow of healthy donors, in order to find aberrantly expressed genes and pathways.

2020-04-14 | GSE103223 | GEO

Expression data from normal and MDS erythroids cell cutlures ex vivo

Project description:CD34 positive cells of bone marrow samples from normal and MDS samples were cultured ex vivo into erythroid conditions. We used microarrays to detail the gene expression programm of erythroid cells between normal and pathological (MDS) samples Mononuclear cells from bone marrow samples were selected on the expression of the CD34 membran marker. Then, they were cultured ex vivo during 14 days and total RNA samples were analyzed at day 7, 10 and/or 14 then compared between normal and MDS samples.

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