Gene expression profiling of Lentivirus-mediated Gene Silencing of RARβ Inhibits A549 Non-Small Cell Lung Cancer stem cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA556422 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Retinoic acid Receptor Beta (RARβ) protein encoded by RARβ gene is a nuclear receptor protein that binds to retinoic acid (RA) to mediate RA function in cellular signalling in embryogenic morphogenesis, cell growth and differentiation. However, the function of RARβ in cancer stem cells (CSCs) maintenance of non-small cell lung cancer (NSCLC) is yet to be determined We used microarrays to analyse the trancriptomic changes in lung cancer and cancer stem cells following RARβ silencing.
2020-07-24 | GSE134788 | GEO
Project description:Gene silencing in parasitic nematodes was achieved by infecting Nippostrongylus with lentivirus designed to produce small RNAs to silence specific genes. Small RNA sequencing was used to investigate production of small silencing RNAs in infected nematodes
2020-11-28 | GSE162219 | GEO
Project description:The present study identified that fibroblast growth factor receptor 3 (FGFR3) was significantly upregulated in bone metastasis of lung adenocarcinoma. RNA interference (RNAi) is a powerful approach for treating a wide range of human diseases, including cancer, through downregulating the expression of selected genes. In the present study, the invasiveness of A549 cells cultured in vitro was altered by small interfering (si)RNA targeting FGFR3, and the regulatory effect of silencing FGFR3 on the expression levels of E-cadherin and matrix metalloproteinase (MMP)9 was investigated. Human lung adenocarcinoma A549 cells were transfected with synthetic specific siRNAs targeting a fragment of the FGFR3 gene (namely, siRNA-855, siRNA-1447 and siRNA-2076) or with negative control (NC) siRNA. Cells were divided into five groups (A, siRNA-855 group; B, siRNA-1447 group; C, siRNA-2076 group; D, NC-siRNA group; and E, blank control group). The effect of the above siRNAs targeting FGFR3 on the invasion capacity of A549 cells was detected by Transwell assay. siRNAs against FGFR3 were transfected into A549 cells with by Lipofectamine® 2000, and the expression levels of FGFR3, E-cadherin and MMP9 were measured by reverse transcription-quantitative polymerase chain reaction and western blot assay. The experimental findings indicated that the expression levels of FGFR3 and MMP9 were significantly reduced in the siRNA-FGFR3-transfected groups (A-C groups), compared with those in the D and E groups (P<0.01). In addition, the expression levels of E-cadherin were markedly elevated in the A-C groups, compared with those in the D and E groups (P<0.01). There was no significant difference in E-cadherin expression between the A-C groups, or between the D and E groups (P>0.05). These results indicated that siRNA-FGFR3 was able to decrease the invasiveness of A549 cells, inhibit the expression of MMP9 and increase the expression of E-cadherin by downregulating the expression of FGFR3. Taken together, the results of the present study indicated that the upregulation of E-cadherin expression and the downregulation of MMP9 expression are able to inhibit the migration of A549 cells, and siRNA silencing FGFR3 acts as a tumor suppressor in these cells.
| S-EPMC5228408 | biostudies-literature
Project description:The glycolytic enzyme, pyruvate kinase Pyk1 maintains telomere heterochromatin by phosphorylating histone H3T11 (H3pT11), which promotes SIR (silent information regulator) complex binding at telomeres and prevents autophagy-mediated Sir2 degradation. However, the exact action mechanism of H3pT11 is poorly understood. Here, we report that H3pT11 directly inhibits Dot1-catalyzed H3K79 tri-methylation (H3K79me3) and uncover how this histone crosstalk regulates autophagy and telomere silencing. Mechanistically, Pyk1-catalyzed H3pT11 directly reduces the binding of Dot1 to chromatin and inhibits Dot1-catalyzed H3K79me3, which leads to transcriptional repression of autophagy genes and reduced autophagy. Despite the antagonism between H3pT11 and H3K79me3, they work together to promote the binding of SIR complex at telomeres to maintain telomere silencing. Furthermore, we identify Reb1 as a telomere-associated factor that recruits Pyk1-containing SESAME (Serine-responsive SAM36 taining Metabolic Enzyme) complex to telomere regions to phosphorylate H3T11 and prevent the invasion of H3K79me3 from euchromatin into heterochromatin to maintain telomere silencing. Together, these results uncover a novel histone crosstalk and provide insights into dynamic regulation of silent heterochromatin and autophagy in response to cell metabolism.
2023-02-07 | PXD038138 | Pride
Project description:Thyroid carcinoma (TC) is the most common malignancy of the endocrine organs, and its incidence rate has steadily increased over the last decade. For medullary thyroid cancer (MTC), a type of TC, a high mortality rate has been reported. In previous studies, M-phase phosphoprotein 8 (MPHOSPH8) displayed an elevated expression in various human carcinoma cells. Thus, MPHOSPH8 may be a sensitive biomarker that could be used for the diagnosis and follow-up of MTC. In the present study, plasmids of RNA interference targeting the MPHOSPH8 gene were constructed. Once these lentiviruses targeting MPHOSPH8 were transfected into the MTC cell line TT, cell viability and proliferation were measured by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Flow cytometry was used to assess the cell cycle distribution and apoptosis. The expression levels of MPHOSPH8 were detected by reverse transcription quantitative-polymerase chain reaction and western blot analyses. Depletion of MPHOSPH8 significantly inhibited cell proliferation. Furthermore, knockdown of MPHOSPH8 in TT cells led to G0/G1 phase cell cycle arrest and apoptosis. The results of the present study suggest that MPHOSPH8 promotes cell proliferation and may be a potential target for anticancer therapy of MTC.
| S-EPMC4888193 | biostudies-literature
Project description:In addition to silencing intended target genes, transfected siRNAs regulate numerous unintended transcripts through a mechanism in which the equivalent of a microRNA-like seed region in the siRNA recognizes complementary sequences in transcript 3' UTRs. The ability to limit such off-target effects would substantially facilitate accurate interpretation of RNA interference (RNAi) experiments and thus greatly enhance their value. We tested whether lentivirus-mediated delivery of shRNA is prone to the seed region-based off-target activity prevalent in siRNA experiments. We compared target gene silencing and overall impact on global gene expression caused by multiple 21-mer duplex sequences delivered as both transfected siRNA and lentivirus vector-expressed shRNA. At equivalent levels of target gene silencing, signatures induced by shRNAs were significantly smaller than those induced by cognate siRNAs and arose less frequently from seed region activity. Interestingly, the low level of seed-region based off-target activity exhibited by shRNAs resulted in down-regulation of transcripts that were largely distinct from those regulated by siRNAs. On the basis of these observations, we recommend lentivirus-mediated RNA interference for pathway profiling experiments that measure whole genome transcriptional readouts as well as for large-scale screens when resources for extensive follow up are limited.
2010-06-09 | GSE22209 | GEO
Project description:BackgroundBone morphogenetic protein 2 (BMP-2) is a member of the TGF-β superfamily that is closely correlated with many malignancies, particularly lung cancer. However, the effects of silenced BMP-2 on lung cancer cell proliferation and migration are not clear.MethodsUsing quantitative real-time RT-PCR, BMP-2 mRNA expression was detected in 61 non-small cell lung cancer (NSCLC) samples. Survival curves were generated using follow-up data. Relationships between clinical or pathological characteristics and prognosis were analyzed. Cell viability assays and transwell migration assays were used to evaluate the effects of BMP-2 silencing on cell proliferation and migration of A549 and H460 cells.ResultsBMP-2 mRNA expression was higher in NSCLC tissues compared to matched adjacent normal tissues (P<0.01). High BMP-2 expression levels were significantly associated with the occurrence of lymph node metastases and tumor stage (P<0.05). There were significant differences in survival curves between groups with metastatic lymph nodes and non-metastatic lymph nodes, as well as between groups with low BMP-2 expression and groups with high BMP-2 expression. In addition, we observed decreased proliferation and migration rates of the NSCLC-derived cell lines A549 and H460 that were transfected with siBMP-2 (P<0.05).ConclusionBMP-2 mRNA is overexpressed in NSCLC samples and is a risk factor for survival in patients with NSCLC. BMP-2 silencing can significantly inhibit A549 and H460 cell proliferation and migration.Virtual slidesThe virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/4263254471298866.
| S-EPMC4070338 | biostudies-literature
Project description:Analysis of changes in gene expression after transfection with miR-509-3p mimic in A549 cells Total RNA was obtained from A549 cells transfected with miR-509-3p and negative control mimics, and gene expression was compared using microarrays.
2014-05-31 | E-GEOD-47522 | biostudies-arrayexpress
Project description:We depleted TIMM13 using short interfering RNA (siRNA) in A549 lung cancer cells, and found that silencing of TIMM13 could significantly inhibit A549 cell proliferation. Thus, we conducted RNA-seq in the A549 cells transduced with either nontargeting siRNA or two distinct TIMM13-specific siRNAs. We observed widespread gene expression change in A549 cells upon TIMM13 knockdown.
2023-06-17 | GSE234780 | GEO