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MDS Sequencing Project Cancer Cell

ABSTRACT: Myelodysplastic syndromes (MDS) are uncommon entities, heterogeneous clinically and cytogenetically. The aim of the present study is to determine genetic alteration in this subset of patients. Expected results: Identification of new aberrations and genetic markers in order to detect novel genes involved in MDS 5q-response to Lenalidomide's treatment.

OTHER RELATED OMICS DATASETS IN: PRJNA254802

PROVIDER: EGAS00001001011 | EGA |

REPOSITORIES: EGA

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Role of casein kinase 1A1 in the biology and targeted therapy of del(5q) MDS.

Schneider Rebekka K RK Ademà Vera V Heckl Dirk D Järås Marcus M Mallo Mar M Lord Allegra M AM Chu Lisa P LP McConkey Marie E ME Kramann Rafael R Mullally Ann A Bejar Rafael R Solé Francesc F Ebert Benjamin L BL

Cancer cell 20140918 4

The casein kinase 1A1 gene (CSNK1A1) is a putative tumor suppressor gene located in the common deleted region for del(5q) myelodysplastic syndrome (MDS). We generated a murine model with conditional inactivation of Csnk1a1 and found that Csnk1a1 haploinsufficiency induces hematopoietic stem cell expansion and a competitive repopulation advantage, whereas homozygous deletion induces hematopoietic stem cell failure. Based on this finding, we found that heterozygous inactivation of Csnk1a1 sensitiz ...[more]

PMID: 25242043

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Affymetrix SNP array data for 5q- myelodysplastic syndromes

2014-10-07 | GSE59244 | GEO

Affymetrix SNP array data for 5q- myelodysplastic syndromes

Project description:Myelodysplastic syndromes (MDS) are uncommon entities, heterogeneous clinically and cytogenetically. Recently, a new drug, Lenalidomide, has demonstrated to be very effective in patients with MDS and 5q- reaching 70% of hematological responses whereas patients with MDS without 5q- has only 20-30% of hematological responses. The aim of the present study is to determine genetic alteration in this subset of patients, and describe candidate genes related with response or resistance to Lenalidomide. The aim of the present study is to determine genetic alteration in this subset of patients, and describe candidate genes related with response or resistance to Lenalidomide. Copy number analysis of Affymetrix GenomeWide SNP 6.0 arrays was performed for 2 patients with MDS an isolated 5q- by conventional cytogenetics. There are also 2 samples from separated CD3+ lymphocytes, which were used as references for copy number and LOH inference.

2014-10-07 | E-GEOD-59244 | biostudies-arrayexpress

Precise Delination of 5q-Breakpoints and Detection of Hidden Aberrations in patients with MDS using Array CGH

Project description:Isolated deletions of the long arm of chromosome 5 (del(5q)) are observed in 10% of myelodysplastic syndromes (MDS) and are associated with a more favorable prognosis, although the clinical course varies considerably. If one or more additional chromosomal aberration/s are present this correlates with a significant shorter overall survival. To assess the frequency of hidden abnormalities in cases with an isolated cytogenetic del(5q), we have performed a genome wide high resolution 44K 60mer oligonucleotide array CGH study using DNA from bone marrow cells of 12 MDS and one AML patient. Additional chromosomal aberrations were identified in three of 13 cases (23%): in one case, a single additional hidden 5.6 Mb deletion of 13q14 and in two cases, multiple larger aberrations involving many chromosomes. Fluorescence in situ hybridization (FISH) demonstrated that aberrations present in only 10% of the bone marrow cells were detectable by aCGH. Furthermore with oligonucleotide aCGH the deletion end points in 5q were mapped precisely, revealing a cluster of proximal break points in band q14.3 (n=8) and a distal cluster between bands q33.2 to q34 (n=11). This study shows the high resolution of oligonucleotide CGH arrays for precisely mapping genomic alterations and for refinement of deletion end points. In addition the high sensitivity of this method enables the study of whole bone marrow cells from MDS patients, a disease with a low blast count. Future studies of more patients with isolated del(5q) for hidden abnormalities will be necessary to evaluate the impact of these on the variable prognosis in these patients and to further define new genetic subgroups. Keywords: Myelodysplastic syndromes, MDS, array CGH, del(5q), hidden aberrations

2007-09-11 | GSE8804 | GEO

Epistasis between TIFAB and miR-146a, neighboring genes in del(5q) MDS

Project description:Interstitial deletion of a single copy of chromosome 5q is the most frequent cytogenetic alteration in Myelodysplastic Syndromes (MDS), which results in reduced dosage of numerous genes. Furthermore, the extent of the 5q deletion determines disease severity, suggesting cooperation between deleted genes in the proximal and distal regions of del(5q). Although the contribution of individual genes to the pathogenesis of del(5q) MDS has been investigated, less is known about the epistatic interactions and/or cooperation between neighboring deleted genes. Deletion of TRAF-interacting protein with forkhead-associated domain B (TIFAB) and miR-146a, two haploinsufficient genes in del(5q) MDS, has been previously reported to activate the Toll-like receptor (TLR) signaling cascade in hematopoietic stem/progenitor cells (HSPC) by increasing TRAF6 protein stability and mRNA translation, respectively. To investigate the epistasis of TIFAB and miR-146a, we generated a mouse model in which Tifab and miR-146a were simultaneously deleted (Tifab-/-;miR-146a-/-, dKO). Herein, we report that combined hematopoietic-specific deletion of Tifab and miR-146a results in more rapid and severe cytopenia, and progression to a fatal bone marrow (BM) failure-like disease as compared to Tifab- or miR-146adeficiency alone. HSPC from Tifab-/-, miR-146a-/-, and dKO mice exhibit enrichment of gene 69 regulatory networks associated with innate immune signaling. Moreover, a subset of the differentially expressed genes is controlled synergistically following deletion of Tifab and miR-146a. Notably, nearly half of these defined synergy response genes identified in the mouse models were aberrantly expressed in del(5q) MDS HSPC when TIFAB (5q31) and miR-146a (5q33.3) were both deleted. Thus, synergistic control of gene expression following deletion of epistatic haploinsufficient genes in del(5q) MDS may be an underlying mechanism of the diseased state.

2016-09-29 | GSE87453 | GEO

A genome-wide analysis of MDS and MDS/MPN patients

Project description:To characterize the molecular changes in myelodysplastic syndromes (MDS) and to explore novel genetic abnormalities occurring in these disorders through a genome-wide study in a series of MDS and MDS/MPN patients. A total of 285 abnormalities were identified in 71 patients. Three high-risk MDS cases displayed chromothripsis. In addition, cryptic deletions were identified in genomic regions where MDS-related genes, such as DNMT3A (2p23.3), TET2 (4q24), RUNX1 (21q22) and BCOR (Xp11.4), are located.

2016-11-21 | GSE67682 | GEO

The National Myelodysplastic Syndromes (MDS) Study

Project description:The National Myelodysplastic Syndromes (MDS) Study

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The National Myelodysplastic Syndromes (MDS) Study

Project description:The National Myelodysplastic Syndromes (MDS) Study

| PRJNA783119 | ENA

Gene expression data from bone marrow CD34+ cells of patients with myelodysplastic syndromes (MDS) and healthy controls

Project description:We aimed to determine the impact of the common mutations on the transcriptome in myelodysplastic syndromes (MDS). We linked genomic data with gene expression microarray data and we deconvoluted the expression of genes into contributions stemming from each genetic and cytogenetic alteration, providing insights into how driver mutations interfere with the transcriptomic state. We modelled the influence of mutations and expression changes on diagnostic clinical variables as well as survival.

2015-01-06 | GSE58831 | GEO

Expression data of ribosomal proteins from sorted hematopoietic stems cells from patients with low risk MDS.

Project description:A role for reduced ribosomal protein gene dosage in both DBA and 5q- MDS suggests that other forms of MDS might also involve altered expression of ribosomal protein genes. We used microarrays to interrogate the expression of ribosomal proteins from purified hematopoietic stems cells from patients with low risk myelodysplastic syndrome and age-matched healthy controls. Hematopoietic stem cells were sorted from 8 patients with low risk myelodysplastic syndrome and 11 age-matched healthy controls, and total RNA was hybridized to Affymetrix microarrays.

2011-08-13 | E-GEOD-30201 | biostudies-arrayexpress

Expression data from bone marrow CD34+ cells of MDS patients and healthy controls

Project description:In order to gain insight into the molecular pathogenesis of the myelodysplastic syndromes (MDS), we performed global gene expression profiling and pathway analysis on the hematopoietic stem cells (HSC) of 183 MDS patients as compared with the HSC of 17 healthy controls. The most significantly deregulated pathways in MDS include interferon signaling, thrombopoietin signaling and the Wnt pathway. Among the most significantly deregulated gene pathways in early MDS are immunodeficiency, apoptosis and chemokine signaling, whereas advanced MDS is characterized by deregulation of DNA damage response and checkpoint pathways. We have identified distinct gene expression profiles and deregulated gene pathways in patients with del(5q), trisomy 8 or –7/del(7q). Patients with trisomy 8 are characterized by deregulation of pathways involved in the immune response, patients with –7/del(7q) by pathways involved in cell survival, whilst patients with del(5q) show deregulation of integrin signaling and cell cycle regulation pathways. This is the first study to determine deregulated gene pathways and ontology groups in the HSC of a large group of MDS patients. The deregulated pathways identified are likely to be critical to the MDS HSC phenotype and give new insights into the molecular pathogenesis of this disorder thereby providing new targets for therapeutic intervention.

2010-03-13 | GSE19429 | GEO

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