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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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NCI-H1299 lung cancer cell line transfected with miR-34a and ghR-34a

ABSTRACT: Analysis NCI-H1299 lung cancer cells transfected with synthetic oligo mimics for microRNAs (miRNAs) miR-34a and ghR-34a. We developed a 30-nucleotide single-strand RNA (ssRNA), termed “guide hairpin RNA (ghR),” that has a physiological function similar to that of miRNA and siRNA. The ghR caused no innate cytokine response either in vitro or in vivo. In addition, its structure does not contain a passenger strand seed sequence, reducing the potential for off-target effects relative to existing short RNA reagents. Systemic injection of ghR-form miR-34a (ghR-34a) suppressed tumor growth in a mouse model of RAS-induced lung cancer. Furthermore, ghR-34a functioned in a Dicer- and Ago2-independent manner. This novel RNAi technology may provide a novel, safe, and effective nucleic acid drug platform that will increase the clinical usefulness of nucleic acid therapy. MiR-34a–targeted mRNAs regulated by mRNA degradation rather than translational inhibition were identified using microarray data from miR-34 and ghR-34a transfectants.

ORGANISM(S): Homo sapiens

SUBMITTER: Shin-ichiro Ohno

PROVIDER: E-GEOD-71423 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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NCI-H1299 lung cancer cell line transfected with miR-34a and ghR-34a

Project description:Analysis NCI-H1299 lung cancer cells transfected with synthetic oligo mimics for microRNAs (miRNAs) miR-34a and ghR-34a. We developed a 30-nucleotide single-strand RNA (ssRNA), termed “guide hairpin RNA (ghR),” that has a physiological function similar to that of miRNA and siRNA. The ghR caused no innate cytokine response either in vitro or in vivo. In addition, its structure does not contain a passenger strand seed sequence, reducing the potential for off-target effects relative to existing short RNA reagents. Systemic injection of ghR-form miR-34a (ghR-34a) suppressed tumor growth in a mouse model of RAS-induced lung cancer. Furthermore, ghR-34a functioned in a Dicer- and Ago2-independent manner. This novel RNAi technology may provide a novel, safe, and effective nucleic acid drug platform that will increase the clinical usefulness of nucleic acid therapy.

2015-07-29 | GSE71423 | GEO

miR-34a targets PDGFRA in proneural malignant glioma

Project description:To identify potential targets of miR-34a, we performed transcriptional profiling on proneural TS543 GBM cells, focusing on mRNAs whose levels decreased in response to miR-34a transfection as compared to control oligonucleotide. Proneural TS543 GBM cells were transfected with 100 nM hsa-miR-34a or control oligonucleotide using Hiperfect transfection reagent (Qiagen). After 3 days, RNA was isolated and expression analyses were performed using Illumina HT-12 bead array. The microarray dataset was normalized using a variance stable normalization (VSN) procedure in the ‘lumi’ package from the Bioconductor framework.

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Transcription profiling of human K562 cells overexpressing miR-34a

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Transcriptional profiling of lung cancer cells over-expression miR-34a.

Project description:The Zeb1 transcriptional repressor plays a key role in metastasis through the down-regulation of genes that are strong inducers of epithelial differentiation and inhibitors of stem-ness. Here we report that Zeb1 controls the expression of numerous oncogenic and tumor suppressive microRNAs (miRs). Zeb1 stimulated pro-migratory cytoskeletal processes by down-regulating miR-34a and activated Rho GTPases through Arhgap1, a Cdc42 GTPase activating protein and novel miR-34a target gene. Poor-prognosis human lung adenocarcinomas were highly enriched in a cytoskeletal gene signature activated by miR-34a down-regulation. These findings suggest that Zeb1 regulates a miR network and drives pro-migratory cytoskeletal processes through miR-34a. Total RNA was extracted from primary tumors from mice injected with 344SQ-vector and -miR-34a cells, and then hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 array. Determination of differentially expressed genes was carried out.

2012-08-08 | E-GEOD-38341 | biostudies-arrayexpress

Gene expression signatures in GIST-T1 cells transfected with a miR-34a mimic molecule

Project description:To clarify the effect of miRNAs, we carried out a gene expression microarray analysis using GIST-T1 cells transfected with a miR-34a mimic or a negative control. We found that 2,621 probe sets (1,933 unique genes) were downregulated (>1.5-fold) by ectopic miR-34a expression, including PDGFRA gene which was previously reported as a miR-34a target gene. GIST-T1 cells were transfected with a mirVana miR-34a mimic (Ambion) or mirVana miRNA mimic Negative Control #1 (Ambion). Forty-eight hours after transfection, total RNA extraction was carried out, and gene expression signatures were analyzed.

2015-05-25 | E-GEOD-68740 | biostudies-arrayexpress

Identification of SART3 as a pre-miR-34a–binding protein

Project description:MicroRNAs (miRNAs or miRs) are small, noncoding RNAs that are implicated in the regulation of nearly all biological processes. Global miRNA biogenesis is altered in many cancers and RNA-binding proteins (RBPs) have been shown to play a role in this process, presenting a promising avenue for targeting miRNA dysregulation in disease. miR-34a exhibits tumor-suppressive functions by targeting cell cycle regulators CDK4/6 and anti-apoptotic factor Bcl-2, among other regulatory pathways such as Wnt, TGF-, and Notch signaling. Many cancers show downregulation or loss of miR-34a, and synthetic miR-34a supplementation has been shown to inhibit tumor growth in vivo; however, the post-transcriptional mechanisms by which miR-34a is lost in cancer are not entirely understood. Here, we have used a proteomics-mediated approach to identify Squamous cell carcinoma antigen recognized by T-cells 3 (SART3) as a putative pre-miR-34a-binding protein. SART3 is a spliceosome recycling factor and nuclear RBP with no previously reported role in miRNA regulation. We demonstrate that SART3 binds pre-miR-34a with specificity over pre-let-7d and begin to elucidate a new functional role for this protein in non-small lung cancer cells. Overexpression of SART3 led to increased miR-34a levels, downregulation of the miR-34a target genes CDK4 and CDK6, and cell cycle arrest in the G1 phase. In vitro binding studies showed that the RNA-recognition motifs within the SART3 sequence are responsible for selective pre-miR-34a binding. Collectively, our results present evidence for an influential role of SART3 in miR-34a biogenesis and cell cycle progression.

2019-10-14 | PXD015278 | Pride

Transcription profiling of human cells transfected with a miR-34a LNA inhibitor to investigate its role in oncogene-induced senescence

Project description:To understand the role of miR-34a in oncogene-induced senescence, we tested global mRNA expression using microarrays of TIG3 TERT/ deltaB-RAF:ER cells transfected with a miR-34a LNA inhibitor or a scrambled control LNA in the presence or absence of deltaB-RAF activation.<br>TIG3 TERT/ deltaB-RAF:ER cells are primary human diploid fibroblasts immortalized by hTERT. deltaB-RAF is constitutively active due to truncation of the regulatory N-terminal domain and fused to the hormone-binding domain of the oestrogen receptor, which was modified to respond to 4-hydroxytamoxifen (4-OHT) but not beta-estradiol.<br>TIG3 TERT/ deltaB-RAF:ER cells were treated with 500nM 4-OHT or equal amounts of ethanol the day after seeding at 1E6 per 10cm plate, in three biological replicates. After 2 days of 4-OHT treatment, cells were transfected with LNA-miR-34a or a control LNA-scramble using Lipofectamine 2000 (Invitrogen). Total RNA was harvested 24 h post-transfection (3 days of 4-OHT treatment in total) using TRIzol reagent. Affymetrix microarray analysis (HG-U133 Plus 2.0 human) was performed.

2009-08-01 | E-MEXP-2241 | biostudies-arrayexpress

Transcription profiling of human colon cancer cell line HCT116 expressing miR-43a vs. controls to investigate miR-43a induced gene expression

Project description:In order to examine the consequences of human miR-34a induction on the transcriptome, HCT116 cells (a colon cancer cell line) were infected with a retrovirus that produces miR-34a. Gene expression profiles were then monitored using Affymetrix microarrays. Affymetrix microarrays were used to examine the transcriptomes of HCT116 cells infected with an empty retroviral vector (pMSCV-PIG) or a retroviral vector that expresses human miR-34a. Experiment Overall Design: RNA from retrovirally-infected cells was isolated and hybridized to Affymetrix microarrays.

2008-06-15 | E-GEOD-7754 | biostudies-arrayexpress

Identification of human miR-34a-responsive transcripts

Project description:In order to examine the consequences of human miR-34a induction on the transcriptome, HCT116 cells (a colon cancer cell line) were infected with a retrovirus that produces miR-34a. Gene expression profiles were then monitored using Affymetrix microarrays. Affymetrix microarrays were used to examine the transcriptomes of HCT116 cells infected with an empty retroviral vector (pMSCV-PIG) or a retroviral vector that expresses human miR-34a. Keywords: comparison of cells with or without enforced miR-34a expression

2007-06-07 | GSE7754 | GEO

Poll II ChIP-Seq in miR-34a transfectant

Project description:To investigate the behavior of RNA Pol II during RNA activation by miR-34a,the ChIP-Seq analysis of RNA Poll II in NCI-H1299 cell line was performed. This experiment analyzes how RNA pol II is activated by the introduction of miR-34a in some genes whose transcription is induced by miR-34a. From the analysis of this data, the purpose is to clarify the molecular mechanism of RNA activation by miR-34a.

2021-02-01 | GSE161321 | GEO

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