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RNA-Seq analysis of murine pro-B BAF3 cells transfected with oncogenic form of receptor tyrosine kinases

ABSTRACT: RNA-Seq analysis of murine pro-B BAF3 cells transfected with oncogenic form of receptor tyrosine kinases

PROVIDER: PRJNA436468 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6794370_1.fastq.gz	Fastqsanger.gz
	SRR6794370_2.fastq.gz	Fastqsanger.gz
	SRR6794380_1.fastq.gz	Fastqsanger.gz
	SRR6794380_2.fastq.gz	Fastqsanger.gz
	SRR6794371_1.fastq.gz	Fastqsanger.gz

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RNA-Seq analysis of murine pro-B BAF3 cells transfected with oncogenic form of receptor tyrosine kinases

Project description:To identify gene expression changes associated with receptor tyrosine kinase (RTK) activation, we performed RNA-Seq analysis of murine pro-B BAF3 cells over-expressing the oncogenic form of EGFR (EGFR-L858R-T790M), FGFR (TEL-FGFR1 fusion), MET (TPR-MET fusion) or RET (CCDC6-RET fusion) genes. We reported the RTK-driven transcriptional reprogramming of metabolic genes.

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Project description:The aim of this study is to compare the expression patterns of tyrosine kinases and their ligand activators between matched myometrium and leiomyoma tissues. For this, total RNA samples extracted from 42 pairs of matched fibroid and adjacent myometrial tissues were hybridized to a set of 840 customized oligonucleotide microarrays to compare the expression profiles of 244 selected human genes including all 90 tyrosine kinases and 103 ligands. Among the 244 genes surveyed, 38 were found to be differentially expressed between pairs of myometrium and fibroid tissues. Clustering analysis of the expression ratios of these 38 genes from 42 pairs of samples has led to the subdivision of fibroid samples into three groups, based on the expression ratios of two peptide ligands, CYR61 and EFNA4. Real-time quantitative RT-PCR measurements of additional 32 pairs of samples further confirmed the existence of these three groups of fibroid samples. In conclusion, peptide ligand activators of protein tyrosine kinases are differentially expressed between myometrium and fibroid tissues. This finding supports the notion that tyrosine kinases may be exploited as medical targets to treat symptomatic fibroids without surgical intervention.Â Â This study has been accomplished with 42 patients fibroid specimen and their matched myometrium, each pair of specimen has been repeated at least 3 times.

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JAK2 Naive and Persitent Murine BaF3 cells infected with MPLW515L

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Analysis of mouse T cell transcription profile after co-culture with BaF3 cells with or without the oncogenic point mutation JAK2 V617F

Project description:The activation of PD-1 (Programmed Death receptor-1) on T cells can cause T cell exhaustion and immune tolerance. Some tumors up-regulate the expression of the ligand of PD-1, namely PD-L1 (Programmed Death Receptor-Ligand 1), thus preventing anti-tumor immune response and promoting immune-escape. Previous studies have shown that JAK2 (Janus Kinase 2) signaling can promote PD-L1 expression in Hodgkin Lymphoma. In Myeloproliferative Neoplasms (MPN), JAK2 is frequently characterized by the the presence of the point-mutation V617F, which leads to its constitutive activation and to uncontrolled cell proliferation and survival. Accordingly, tumor cell lines expressing JAK2 V617F express higher levels of PD-L1 as compared to tumor cell lines negative for such mutations. In this experiment, we transfected BaF3 cells with a vector (plasmid for Murine Stem Cell Virus) containing the gene for JAK2 with the point-mutation V617F. As control, we used BaF3 cells transfected with the same vector, but without the gene for JAK2 V617F (empty vector). Both the cell lines (with/without JAK2 V617F) were co-cultured with primary murine T cells. When co-cultured with BaF3 cells expressing JAK2 V617F, T cells upregulated genes connected to senescence pathways, showed increased apoptosis, less cytokine production, and displayed other forms of dysfunction which can be associated with the activation of PD-1.

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