Project description:Oncogenic ras activates several signaling pathways that cooperate in cell transformation. They include the ERK/MAP kinase pathway, the PI3K pathway and the Ral pathway among others. Surprisingly, in primary human fibroblasts, oncogenic ras expression induces senescence not transformation, but upon knockdown of ERK2 senescence is bypassed and transformation is stimulated. We used microarrays to characterize the gene expression programme of cells transformed by oncogenic ras, telomerase and knockdown of the ERK2 kinase. Primary human fibroblasts were co-infected with a retroviral vector that expresses oncogenic ras and either a control shRNA or an shRNA against ERK2. Cells with oncogenic ras and shRNA control entered senescence while cells with oncogenic ras and shRNA ERK2 bypassed senescence and underwent malignant transformation. Triplicates of these populations were used to purify total RNA, which we sent to Genome Quebec service for hybridization with Affymetrix microarrays.
Project description:Transcriptional profiling of MKN45 cells comparing control stably expressing Non-Targeting shRNA cells with stably expressing SET/I2PP2A targeting shRNA cells. Goal was to determine the effects of SET knockdown on MKN45 gene expression.
Project description:We stably infected IMR90 fibroblasts with lentiviral vectors expressing doxycycline-inducible TRF2dBdM or vector control. Cells were treated with 1mg/ml of doxycycline for 7 days to induce senescence in the cells expressing TRF2dBdM before collecting RNA. IMR90 cells, either young (passage 10, population doubling ~20) or old (passage 24, population doubling ~40-48) were also used as a model of replicative senescence. The transcriptomes were analyzed using RNA microarrays.
Project description:To determine the biological mechanisms underlying the oncogenic properties of YAP in ccRCC the human ccRCC cell line MZ1774 was transduced with lentivirus containing a shRNA-cassette targeting YAP-mRNA. Expression profiles of MZ1774 YAP knockdown cells were compared to mock-transduced control cells. Total RNA from MZ1774 cells stably expressing shRNA directed against YAP compared to mock-transduced MZ1174 cells
Project description:HuH7 cells stably transfected with siRNA against TFPI2, MAFB, or MAFF, as well as non-targeting control shRNA were established. We showed that all-trans-retinoic acid (ATRA) induces TFPI2 expression through RARalpha, while MAFB and MAFF regulate this effect positively and negatively, respectively. To investigate global regulation of ATRA-induced transcription, this microarray analysis was performed with the shRNA-expressing cells following ATRA treatment.
Project description:Mouse embryonic fibroblasts deficient for p53 and expressing mutant RasV12 were infected with lentiviral constructs carrying short hairpin RNAs targeting ARF or a scrambled control. Four days post infection, cells were harvested for microarray analysis.
Project description:We report that H2B deubiquitinating enzymes USP22, USP27x and USP51 have both unique and overlapping target loci. Comparing gene expression profiles of MCF7 cells stably expressing shRNA targeting either USP22, USP27X or USP51 and cells expressing non-targeting shRNA.
Project description:We report that the H2B deubiquitinating enzymes USP22, USP27x and USP51 have both unique and overlapping target loci. Comparing H2Bb1 (K120) distribution profiles of MCF7 cells stably expressing shRNA targeting ATXN7L3, USP22, USP27X or USP51 and cells expressing non-targeting shRNA.
