Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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IGR_JUNCONCO_STUDY_LM

ABSTRACT: Antineoplastic effects of siRNA against TMPRSS2-ERG junction oncogene in prostate cancer: from molecular and cellular studies to preclinical investigations. Background of the study.:TMPRSS2-ERG junction oncogene is present in more than 50% of patients with prostate cancer, and its expression is frequently associated with poor prognosis. We knockdown by siRNA the two TMPRSS2-ERG fusion variants (III and IV) most frequently identified in patients’ biopsies and found an inhibition of TMPRSS2-ERG of above 70% in human prostate cancer VCaP cell line expressing TMPRSS2-ERG junction oncogene. To point out genes regulated after TMPRSS2-ERG oncogene silencing, microarray analysis was performed.. Materiel and Methods. Human prostate cancer VCaP cell line expressing TMPRSS2-ERG oncogene (ATCC® CRL-2876™ Manassas, USA) was grown in Dulbecco's Modified Eagle Medium (DMEM) (Invitrogen, Cergy-Pontoise, France) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin (Invitrogen). Cells were incubated at 37°C in a humidified atmosphere containing 5% CO2. Transfection was carried out using Lipofectamine RNAiMAX transfecting agent (Invitrogen) according to manufacturer's instructions. Briefly, 8×105 VCaP cells were seeded in six-well plates in DMEM supplemented with 10% FCS, penicillin (100U/ml) and streptomycin (10µg/ml) and transfected with 50 nM siRNA TMPRSS2-ERG III, siRNA TMPRSS2-ERG IV and siRNA Control and 6 μL Lipofectamine® RNAiMAX. Cells were incubated with siRNA for 48h. At the end of the treatments, total RNAs of untreated cells (NT) and transfected cells were extracted using RNeasy mini-kit (Quiagen, Courtaboeuf, France). Three independent experiments were performed. Results. Microarray analysis confirmed ERG inhibition by both siRNA TMPRSS2-ERG III and IV and revealed a common down-regulated gene, ADRA2A, involved in cell proliferation and migration. Experiments are performed with Agilent Whole Genome 8x60K (028004) microarray. In triplicate with a non treated control cells, a control with ascramble siRNA, a siRNA TMPRSS2-ERG III, a siRNA TMPRSS2 IV.

ORGANISM(S): Homo sapiens

SUBMITTER: Philippe Dessen

PROVIDER: E-MTAB-2838 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Genomic rearrangements leading to intragenic gene fusion are mainly found in some types of haematopoietic malignancies and sarcomas. Recently they have been described also in carcinomas such as the papillary thyroid histotype (60%-70%) and the Hürthle thyroid tumours (58%). The presence of junction oncogene constitutes an area of exciting research for emerging therapy as targeting the RET-PTC1 fusion oncogene by using small interfering RNA (siRNA) strategies since it is present only in the tumour cells and not in the surrounding normal cells. Therefore, we developed a siRNA against RET-PTC1 junction and assess its efficiency on the human papillary thyroid carcinoma cell line TPC-1 which spontaneously harbours the RET-PTC1 oncogene. The targeted genes are assessed by microarray analysis by comparing the regulated genes by the siRNA_RET-PTC1 vs a siRNA_RET developed on the RET part of the mRNA minus the siRNA_control that contain four mutation within the RET-PTC1 sequence. To test the targeted genes in the TPC-1 cell line that spontaneously harbours RET-PTC1 junction of two siRNAs developed: Within the RET-PTC1 junction, and in the mRNA RET part. A non-specific siRNA harbouring 4 mutations within the RET-PTC1 sequence was used as negative control (siRNA_control). By real-time PCR (Q-RT-PCR) we demonstrated that both siRNAs (siRNA_RET-PTC1 and siRNA_RET) significantly reduce RET mRNA levels of about 85 % in TPC-1 cells. The negative control did not show an effect of RET mRNA levels. Three independent transfections were performed on TPC-1 cells using 5 µl of Lipofectamine 2000 transfection reagent (Invitrogen, Cergy-Pontoise, France) and 50nM of i) siRNA_RET-PTC1 or ii) siRNA_RET or iii) siRNA_control that harbour 4 mutations within its sequence. Total RNAs of untreated cells and transfected cells were purified using the RNA cleanup and concentration kit (QIAGEN, Hilden, Germany) and gathered in 4 pools : 1) TPC-1 harbouring RET-PTC1 ; 2) TPC-1 silenced for RET-PTC1 with siRNA RET-PTC1 ; 3) TPC-1 silenced for siRNA RET ; 4) TPC-1 treated with the siRNA control.

Project description:Melanoma cells from three surgical specimens of nodular melanoma were grown as anchorage-independent melanospheres in stem cell bFGF(+)EGF(+) medium and as adherent monolayer cultures in the presence of serum. RNA from melanospheres (DMBC2s, DMBC8s, DMBC10s) and their adherent monolayer counterparts (DMBC2a, DMBC8a, DMBC10a) were hybridized to the dual-color Agilent human genome array G4450A. A transcriptome profile was generated to explore the molecules governing phenotypes of melanospheres and monolayers. We demonstrated that melanospheres contained more pigmented cells which was consistent with higher expression of MITF and MITF-dependent genes responsible for differentiation, including TYR, TYRP1, MLANA and DCT. Expression of MITF-dependent BIRC7, BCL2 and BCL2A1 was reduced in monolayers, thus limiting the anti-apoptotic protection. The enhanced activity of MITF shown as the elevated expression of 74 MITF-dependent genes in melanospheres, identified MITF as a central regulator of this phenotype. Importantly, our study revealed that MITF and MITF-dependent genes were expressed in melanospheres at similar levels as in original tumors, much higher than in monolayers. The reduced MITF level in monolayers might be partially explained by suppression of the Wnt/beta-catenin pathway. Differential expression of Wnt/beta-catenin pathway components and target genes in melanospheres and monolayers points to strong influence of the microenvironment on the functional outcome of Wnt/beta-catenin pathway in melanoma, including differentiation, survival, proliferation and invasiveness. Silencing of the Wnt inhibitor DKK1 in monolayers increased the percentage of clonogenic cells. In summary, melanospheres more accurately mirrored the morphology, heterogeneity and gene expression profiles of original tumors than monolayers. Our study demonstrates the feasibility of utilizing melanospheres to unravel the molecular pathways sustaining melanoma heterogeneity and potentially to select compounds with anticancer activities.

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IGR_JUNCONCO_STUDY_LM

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