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Transcriptomic consequence of Fyn knock-out in glioblastoma

ABSTRACT: To investigate the role of Fyn in glioblastoma, transcriptomic comparison between WT and Fyn-KO glioblastoma was done by bulk RNA sequencing.

ORGANISM(S): Mus musculus

PROVIDER: GSE188771 | GEO | 2021/11/30

REPOSITORIES: GEO

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Transcriptomic consequence of Fyn knock-out in glioblastoma

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Transcriptomic consequence of Fyn knock-out in glioblastoma, and regional heterogeneity of glioblastoma upon single-cell RNA sequencing

Project description:Transcriptomic consequence of Fyn knock-out in glioblastoma, and regional heterogeneity of glioblastoma upon single-cell RNA sequencing

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Transcriptomic consequence of Fyn knock-out in glioblastoma, and regional heterogeneity of glioblastoma upon single-cell RNA sequencing

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

2022-01-12 | GSE188773 | GEO

Fyn-dependent prefrontal cortex gene networks in acute ethanol sensitivity

Project description:Fyn kinase has been implicated in multiple behavioral responses to ethanol and in the regulation of myelin gene expression. Here we tested whether Fyn kinase modulated basal or ethanol-responsive expression of genes regulated by acute ethanol in brain regions of the mesolimbocortical dopamine pathway. Using expression profiling, we sought to define Fyn-dependent gene networks underlying ethanol behavioral traits; with emphasis on ethanol-induced loss of righting reflex (LORR) due to the reproducible association of Fyn kinase genotype with this behavioral phenotype (Miyakawa et al., 1997, Boehm et al., 2003, Yaka et al., 2003, Boehm et al., 2004b). Our expression profiling and bioinformatics results suggest multiple Fyn-related mechanisms, especially those affecting a network of myelin-related gene expression within the medial PFC, as contributing to the sedative-hypnotic properties of ethanol. Variation in the expression of these Fyn-dependent gene networks may be critical molecular endophenotypes affecting the behavioral level of response to acute ethanol, and subsequently, the long-term risk for alcohol use disorders. Adult male control (B6129SF2/J) and Fyn-kinase null (B6;129S7-Fyntm1Sor/J) mice were treated with saline or ethanol (3.0 g/kg x 4 hours) and brain regions harvested by microdissection for total RNA expression profiling by Affymetrix microarrays. Samples were randomly assigned to batch groups prior to total RNA extraction, cRNA synthesis and hybridization. Each microarray represents a pooling of 3 animals and 3 arrays were analyzed per treatment group for a total of 12 arrays per brain region. Statistical and bioinformatics analysis was used to identify Fyn-dependent effects on basal and ethanol-responsive gene expression, with a particular focus on myelin-related gene expression. This series of samples includes medial prefrontal cortex (PFC).

2014-08-31 | E-GEOD-49028 | biostudies-arrayexpress

Fyn-dependent prefrontal cortex gene networks in acute ethanol sensitivity

2014-08-31 | GSE49028 | GEO

FYN-TRAF3IP2 activating fusion oncogene in peripheral T-cell lymphoma

Project description:FYN-TRAF3IP2 expression in hematopoietic progenitors induces T cell transformation in mice and cooperates with loss of the Tet2 tumor suppressor in PTCL development. To investigate the oncogenic activity of FYN-TRAF3IP2, we analyzed the lymphomagenic effects of expressing this gene fusion alone and in cooperation with loss of the Tet2 tumor suppressor gene in vivo. In these experiments, we first infected hematopoietic progenitors from CD4-specific tamoxifen-inducible Cre Tet2 conditional knockout mice (CD4 Cre-ERT2, Tet2fl/fl) with bicistronic retroviruses expressing wild type TRAF3IP2 and GFP, FYN-TRAF3IP2 and GFP, or GFP alone and injected these intravenously into isogenic recipients. Transplanted mice were then treated with vehicle only, to test the oncogenic effects of TRAF3IP2, FYN-TRAF3IP2 or GFP expression; or with tamoxifen, to evaluate the effects of TRAF3IP2, FYN-TRAF3IP2 or GFP expression in concert with genetic loss of Tet2 in CD4 T cells. In this setting, all animals transplanted with GFP-expressing progenitors remained lymphoma free at the end of follow up and one animal transplanted with wild type TRAF3IP2 GFP expressing cells developed a CD8+ T cell lymphoma. In contrast, 4/10 (40%) vehicle treated mice transplanted with FYN-TRAF3IP2-expressing cells and 5/10 (50%) tamoxifen treated mice transplanted with FYN-TRAF3IP2-expressing cells developed clonal CD4-restricted mature T cell lymphomas. To further analyze the lymphomagenic effect of the fusion gene, we performed transcriptomic profiling of FYN-TRAF3IP2-induced mouse CD4+ GFP+ PTCL tumor lymphocytes compared with normal mouse CD4+ T cells by RNAseq.

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Whole cell proteomics of NDUFAF8 knock-out cell line and NDUFAF5 knock-out cell line

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Analysis of the liver transcriptome from wild-type and Gpr151 knock-out mice

Project description:Purpose: The goal of this study is to identify genes and molecular pathways whose expression is altered in the livers of Gpr151 knock-out (KO) mice compared to Gpr151 wild-type (WT). Methods: Total RNA was isolated from livers of fasted (5h) 16-week-old male mice. Deep sequencing of RNA from three wild-type and three knock-out mice was done using the mRNA-Seq pipeline at Novogene. The sequence reads that passed quality filters were aligned to the mouse GRCm38.p6 genome using STAR 2.6.1d. Differential expression testing was conducted using DESeq2. Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the mouse genome (build mm10) and identified 54,532 transcripts in the livers of Gpr151 WT and KO mice. RNA-seq data identified 79 transcripts which were significantly upregulated in KO (p-adj < 0.05, log2FoldChange>1) and 338 transcripts which were significantly downregulated (p-adj<0.05, log2FoldChange<-1) in KO. Conclusions: Our study represents the first detailed analysis of the liver transcriptome of Gpr151 KO mice.

2022-10-14 | GSE196535 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of SETD6 Knock-out and stable expression of TWIST1 in Glioblastoma cells

Project description:The goal of this study was to identifiy shared target genes for SETD6 and TWIST1 in Glioblastoma.

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To find out different expression lncRNAs between glioblastoma cancer and adjacent normal glioblastoma tissue

Project description:To further understand the molecular mechanisms in the development of glioblastoma cancer, we employed this microarray to identify lncRNAs associated with glioblastoma cancer.

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