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Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature [RNA-seq]

ABSTRACT: Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature [RNA-seq]

PROVIDER: PRJNA657555 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12461610_1.fastq.gz	Fastqsanger.gz
	SRR12461610_2.fastq.gz	Fastqsanger.gz
	SRR12461611_1.fastq.gz	Fastqsanger.gz
	SRR12461611_2.fastq.gz	Fastqsanger.gz
	SRR12461612_1.fastq.gz	Fastqsanger.gz

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Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature

Project description:Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature

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Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature [array]

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Gene expression data from CD34+ BMMCs/PBMCs from JAK2V617F positive and CALR mutated MPN patients

Project description:Philadelphia chromosome-negative myeloproliferative neoplasms (MPN) consist of primary myelofibrosis (PMF), polycythemia vera (PV), essential thrombocythemia (ET) In this dataset, we compare the gene expression data of patients JAK2V617F vs. CALR-mutated MPN patients.

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JAK2V617F but not CALR mutations confer increased molecular responses to interferon-alpha via JAK1/STAT1 activation

Project description:Pegylated interferon-alpha (peg-IFNa) treatment induces molecular remissions (MR) in patients with myeloproliferative neoplasms (MPN), including partial MR (PMR) in 30-40% of patients. Here, we compared the efficacy of IFNa treatment in JAK2V617F vs. CALR-mutated cells and investigated the mechanisms of differential response. Retrospective analysis of MPN patients treated with peg-IFNa demonstrated that patients harboring the JAK2V617F mutation were more likely to achieve PMR than those with mutated CALR (p=0.004), while there was no significant difference in hematological response. In vitro experiments confirmed an upregulation of interferon-stimulated genes in JAK2V617F-positive 32D cells compared to their CALR-mutated counterparts, and higher IFNa doses were needed to achieve the same IFNa response in CALR- as in JAK2V617F mutant 32D cells.

2018-10-29 | GSE120363 | GEO

Patients with triple-negative, JAK2V617F- and CALR-mutated essential thrombocythemia share a unique gene expression signature.

Project description:Approximately 10% to 15% of patients with essential thrombocythemia (ET) lack the common driver mutations, so-called "triple-negative" (TN) disease. We undertook a systematic approach to investigate for somatic mutations and delineate gene expression signatures in 46 TN patients and compared the results to those with known driver mutations and healthy volunteers. Deep, error-corrected, next-generation sequencing of peripheral blood mononuclear cells using the HaloPlexHS platform and whole-exome sequencing was performed. Using this platform, 10 (22%) of 46 patients had detectable mutations (MPL, n = 6; JAK2V617F, n = 4) with 3 of 10 cases harboring germline MPL mutations. RNA-sequencing and DNA methylation analysis were also performed by using peripheral blood mononuclear cells. Pathway analysis comparing healthy volunteers and ET patients (regardless of mutational status) identified significant enrichment for genes in the tumor necrosis factor, NFκB, and MAPK pathways and upregulation of platelet proliferative drivers such as ITGA2B and ITGB3. Correlation with DNA methylation showed a consistent pattern of hypomethylation at upregulated gene promoters. Interrogation of these promoter regions highlighted enrichment of transcriptional regulators, which were significantly upregulated in patients with ET regardless of mutation status, including CEBPβ and NFκB. For "true" TN ET, patterns of gene expression and DNA methylation were similar to those in ET patients with known driver mutations. These observations suggest that the resultant ET phenotype may, at least in part and regardless of mutation type, be driven by transcriptional misregulation and may propagate downstream via the MAPK, tumor necrosis factor, and NFκB pathways with resultant JAK-STAT activation. These findings identify potential novel mechanisms of disease initiation that require further evaluation.

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Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-03-02 | GSE156547 | GEO

Gene and miRNA expression profiles in Polycythemia Vera and Essential Thrombocythemia according to CALR and JAK2 mutations [miEP]

Project description:Polycythemia vera (PV) and essential thrombocythemia (ET) are Philadelphia-negative myeloproliferative neoplasms (MPNs) characterized by erythrocytosis and thrombocytosis, respectively. Approximately 95% of PV and 50–70% of ET patients harbour the V617F mutation in the exon 14 of JAK2 gene, while about 20-30% of ET patients carry CALRins5 or CALRdel52 mutations. These ET CARL-mutated subjects show higher platelet count and lower thrombotic risk compared to JAK2-mutated patients. Here we showed that CALR-mutated and JAK2V617F-positive CD34+ cells have different gene and miRNA expression profiles. Indeed, we highlighted several pathways differentially activated between JAK2V617F- and CALR-mutated progenitors, i.e. mTOR, MAPK/PI3K and MYC pathways. Furthermore, we unveiled that the expression of several genes involved in DNA repair, chromatin remodelling, splicing and chromatid cohesion are decreased in CALR-mutated cells. According to the low risk of thrombosis in CALR-mutated patients, we also found the down-regulation of several genes involved in thrombin signalling and platelet activation. As a whole, these data support the model in which CALR-mutated ET could be considered as a distinct disease entity from JAK2V617F-positive MPNs and may provide the molecular basis supporting the different clinical features of these patients.

2018-03-01 | GSE103238 | GEO

Gene and miRNA expression profiles in Polycythemia Vera and Essential Thrombocythemia according to CALR and JAK2 mutations [GEP]

2018-03-01 | GSE103237 | GEO

Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature [array]

Project description:Using gene expression analysis in combination with genome-wide methylation profiling, we discovered a unique signature pattern that is consistent across the essential thrombocythaemia population regardless of mutation status.

2021-03-02 | GSE156546 | GEO

Gene expression data from CD34+ BMMCs/PBMCs from JAK2V617F positive and CALR mutated MPN patients

Project description:Gene expression data from CD34+ BMMCs/PBMCs from JAK2V617F positive and CALR mutated MPN patients

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