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Expression Analysis of dic(1 7)(q10 p10) in Myelodysplastic Syndromes (MDS) compared to control cohort and therapy-related Myeloid Neoplasms (t-MN)

ABSTRACT: Expression Analysis of dic(1 7)(q10 p10) in Myelodysplastic Syndromes (MDS) compared to control cohort and therapy-related Myeloid Neoplasms (t-MN)

PROVIDER: PRJNA485753 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7688940.fastq.gz	Fastqsanger.gz
	SRR7688941.fastq.gz	Fastqsanger.gz
	SRR7688932.fastq.gz	Fastqsanger.gz
	SRR7688942.fastq.gz	Fastqsanger.gz
	SRR7688933.fastq.gz	Fastqsanger.gz

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Expression Analysis of dic(1;7)(q10;p10) in Myelodysplastic Syndromes (MDS) compared to control cohort and therapy-related Myeloid Neoplasms (t-MN)

Project description:The unbalanced translocation t(1;7)(q10;p10), generating 1q trisomy and 7q monosomy, is due to centromere-centromere juxtaposition. This dicentric chromosome is a recurrent change in myelodysplastic syndromes (MDS), with half the cases arising after chemo/radio-therapy. To date, given the absence of genes within the centromeric regions, no specific molecular events have been identified in this cytogenetic subgroup. We first identified a comprehensive genetic and epigenetic landscape of MDS with dic(1;7)(q10;p10) and compared it to normal controls and other therapy-related Myeloid Neoplasms (t-MNs). RNA-seq showed a unique downregulated signature in dic(1;7) cases, affecting more than 80% of differentially expressed genes. As revealed by pathway and gene ontology analyses, downregulation of ATP-binding cassette (ABC) transporters and of genes related to lipid metabolism, and upregulation of p53 signaling were the most relevant biological features of dicentric-positive MDS. Despite 1q trisomy, more than 50% of 1q deregulated genes were downregulated. This partial gene dosage effect was clarified by epigenetic analysis, which highlighted the presence of a specific hypermethylated pattern on 1q. Furthermore, in a supervised analysis, hypermethylation in all dicentrics clustered at intronic enhancers and was enriched for Krüppel-like transcription factors binding sites. Low expression levels of enhancer putative target genes accounted for more than 30% of the downregulated signature. Our findings demonstrate that alteration of centromeric DNA in dic(1;7) cases imposes a specific transcriptional program, driven by a unique epigenomic signature.

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Affymetrix SNP array data for dic(1;7)(q10;p10) in Myelodysplastic Syndromes (MDS)

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Multiplex Enhanced Reduced Representation Bisulfite Sequencing (mERRBS) Analysis of dic(1;7)(q10;p10) in Myelodysplastic Syndromes (MDS) compared to control cohort and therapy-related Myeloid Neoplasms (t-MN)

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Expression data from MDS patients with der(1;7)(q10;p10)

Project description:Gene expression profiling was significantly different between der(1;7)(q10;p10) and -7/7q- patients by cluster analysis. There were total 1628 dysregulated genes in both der(1;7)(q10;p10) and -7/del(7q) cohorts.

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Affymetrix SNP array data for dic(1 7)(q10 p10) in Myelodysplastic Syndromes (MDS)

Project description:Affymetrix SNP array data for dic(1 7)(q10 p10) in Myelodysplastic Syndromes (MDS)

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Multiplex Enhanced Reduced Representation Bisulfite Sequencing (mERRBS) Analysis of dic(1 7)(q10 p10) in Myelodysplastic Syndromes (MDS) compared to control cohort and therapy-related Myeloid Neoplasms (t-MN)

Project description:Multiplex Enhanced Reduced Representation Bisulfite Sequencing (mERRBS) Analysis of dic(1 7)(q10 p10) in Myelodysplastic Syndromes (MDS) compared to control cohort and therapy-related Myeloid Neoplasms (t-MN)

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Affymetrix SNP array data for myelodysplastic syndromes (MDS) and related neoplasms

Project description:In this study, to obtain a complete registry of genetic lesions in MDS and to identify novel therapeutic targets, we performed SNP array analysis and whole exome analysis for novel mutations using high-throughput sequencing technologies. In whole exome analysis, paired CD3-positive T cells were used as a normal control. By comparing sequences in tumors and paired T cells, 268 non-synonymous somatic mutations were confirmed with an overall true positive rate of 53.9 %, including 206 missense, 25 nonsense, and 10 splice site mutations, and 27 frameshift-causing insertions/deletions (indels). The mutations of the known gene targets, however, accounted for only 12.3 % of all detected mutations (N = 33), and the remaining 235 mutations involved previously unreported genes. Combined with the genomic copy number profile obtained by SNP array karyotyping, this array of somatic mutations provided a landscape of myelodysplasia genomes. Copy number analysis of Affymetrix 250K SNP arrays was performed for 29 MDS or related neoplasms and paired 29 germline samples.

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Project description:Myelodysplastic syndromes (MDS) comprise a heterogeneous group of myeloid neoplasms characterized by peripheral cytopenia, dysplasia, and a variable clinical course with about 30% risk to transform to secondary acute myeloid leukemia (AML). In the past 15 years, diagnostic evaluations, prognostication, and treatment of MDS have improved substantially. However, with the discovery of molecular markers and advent of novel targeted therapies, new challenges have emerged in the complex field of MDS. For example, MDS-related molecular lesions may be detectable in healthy individuals and increase in prevalence with age. Other patients exhibit persistent cytopenia of unknown etiology without dysplasia. Although these conditions are potential pre-phases of MDS they may also transform into other bone marrow neoplasms. Recently identified molecular, cytogenetic, and flow-based parameters may add in the delineation and prognostication of these conditions. However, no generally accepted integrated classification and no related criteria are as yet available. In an attempt to address this challenge, an international consensus group discussed these issues in a working conference in July 2016. The outcomes of this conference are summarized in the present article which includes criteria and a proposal for the classification of pre-MDS conditions as well as updated minimal diagnostic criteria of MDS. Moreover, we propose diagnostic standards to delineate between ´normal´, pre-MDS, and MDS. These standards and criteria should facilitate diagnostic and prognostic evaluations in clinical studies as well as in clinical practice.

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