Gene expression profiles of LNCaP miR-582-5p cells and LNCaP empty vector cells.
ABSTRACT: To investigate targets of miR-582-5p that which might participate in the transition to CRPC, we evaluated the gene expression profiles of LNCaP miR-582-5p cells and LNCaP EV cells using DNA microarray analysis. We evaluated the gene expression profiles of LNCaP miR-582-5p cells and LNCaP EV cells using DNA microarray with GeneChip® Human Gene 1.0 ST array.
Project description:MiR-21 is an important suppressor of T-cell apoptosis that is also widely overexpressed in many types of cancers. The exact mechanisms related to the anti-apoptotic effect of miR-21 is not well understood. In this study, we applied AGO2 RNA Immunoprecipitation followed by gene expression profiling (RIP-Chip) in Jurkat cells to identify apoptosis-associated miR-21 target genes. We showed that expression of miR-21 rapidly increases upon αCD3/αCD28 activation of Jurkat cells. Inhibition of miR-21 resulted in reduced cell growth and induced apoptosis. Upon AGO2-RIP-Chip, we observed an overall increased enrichment of miR-21 target genes in the IP fraction of miR-21-overexpressing Jurkat cells as compared to the IP fraction of empty vector control cells. We noted a systematic decrease in transcript levels of predicted miR-21 target genes compared to EV control. We identified 72 genes that were 2-fold enriched in the AGO2-IP fraction of miR-21-overexpressing cells that contained a predicted miR-21 binding site. Of these, 71 were enriched 2-fold more in the miR-21-overexpressing cells as compared to EV Jurkat cells. The target gene for which the enrichment was most prominently increased upon miR-21 overexpression was the pro-apoptotic protein LATS1. Luciferase reporter assays confirmed direct targeting of the LATS1 3'UTR by miR-21. In line with the luciferase results, Western blot analysis revealed a decrease in LATS1 upon miR-21 inhibition. LATS1 qRT-PCR analysis in primary T-cells showed that LATS1 levels decrease upon T-cell stimulation while the miR-21 levels increase. Collectively, these data identify the miR-21 target LATS1 as a likely candidate whose inhibition contributes to the anti-apoptotic function of miR-21 in T-cells and perhaps also many types of cancers. Gene expression array on Jurkat cells overexpressing miR-21 and empty vector (EV).
Project description:Translocation of ETS transcription factors including ERG and ETV1 occur in half of all prostate cancers. LNCaP cells harbor an ETV1 translocation. We performed ChIP-Seq analysis to determine the role of ETV1 on AR binding. The localization of enhancers were determined by H3K4me1 ChIP-Seq. To determine ETV1 and H3K4me1 localization, logarithmically growing cells
Project description:Background: The aim of this study was to identify differentially expressed miRNAs in high-grade serous ovarian carcinoma (HGSC), clear cell ovarian carcinoma (CCC) and ovarian surface epithelium (OSE). Selected miRNAs were evaluated for association with clinical parameters including survival, and miRNA/mRNA interactions were mapped. Results: Differentially expressed miRNAs between HGSC, CCC and OSE were identified, of which 18 were validated (p<0.01) using RT-qPCR in an extended cohort. Compared with OSE, miR-205-5p was the most overexpressed miRNA in HGSC. miR-200 family members and miR-182-5p were the most overexpressed in HGSC and CCC compared with OSE, whereas miR-383 was the most underexpressed. miR-509-3-5p, miR-509-5p, miR-509-3p and miR-510 were among the strongest differentiators between HGSC and CCC, all being significantly overexpressed in CCC compared with HGSC. High miR-200c-3p expression was associated with poor progression-free (p=0.031) and overall (p=0.026) survival in HGSC. Interacting miRNAs and mRNA targets, including those of a TP53-related pathway presented previously, were identified in HGSC. Conclusions: Several miRNAs are overexpressed in HGSC and CCC compared with OSE, including the miR-200 family, among which miR-200c-3p is associated with survival in HGSC. A set of miRNAs differentiates CCC from HGSC, of which miR-509-3-5p and miR-509-5p are the strongest classifiers. Several interactions between miRNAs and mRNAs in HGSC were mapped. Methods: Differences in miRNA expression between HGSC, CCC and OSE scrapings were analyzed by global miRNA expression profiling (Affymetrix GeneChip miRNA 2.0 Arrays, n=30), validated by RT-qPCR (n=63), and evaluated for associations with clinical parameters. For HGSC, differentially expressed miRNAs were linked to differentially expressed mRNAs identified previously (GSE36668).
Project description:LNCaP and its androgen insensitive derivative were profiled in order to identify genes differentially expressed during the conversion to androgen insensitivity. This experiment was performed due to the presence of an ins(7;14) localizing the entire ETV1 locus to chr 14 in LNCaP and C4-2B prostate cancer cells. Keywords: cell type comparison LNCaP and C4-2B were both hybridized to Agilent Whole Human Genome Oligonucleotide Microarrays, with a commercially obtained pool of benign prostate RNA serving as the reference for both cell lines. Dye flips for both cell lines were also performed
Project description:Secreted microRNAs (miRNAs) enclosed within extracellular vesicles (EVs) play a pivotal role in intercellular communication by regulating recipient cell gene expression and affecting target cell function. Here, we report the isolation of three distinct EV subtypes from the human colon carcinoma cell line LIM1863--shed microvesicles (sMVs) and two exosome populations (immunoaffinity isolated A33-exosomes and EpCAM-exosomes). Deep sequencing of miRNA libraries prepared from parental LIM1863 cells/derived EV subtype RNA yielded 254 miRNA identifications, of which 63 are selectively enriched in the EVs--miR-19a/b-3p, miR-378a/c/d, and miR-577 and members of the let-7 and miR-8 families being the most prominent. Let-7a-3p*, let-7f-1-3p*, miR-451a, miR-574-5p*, miR-4454 and miR-7641 are common to all EV subtypes, and 6 miRNAs (miR-320a/b/c/d, miR-221-3p, and miR-200c-3p) discern LIM1863 exosomes from sMVs; miR-98-5p was selectively represented only in sMVs. Notably, A33-Exos contained the largest number (32) of exclusively-enriched miRNAs; 14 of these miRNAs have not been reported in the context of CRC tissue/biofluid analyses and warrant further examination as potential diagnostic markers of CRC. Surprisingly, miRNA passenger strands (star miRNAs) for miR-3613-3p*, -362-3p*, -625-3p*, -6842-3p* were the dominant strand in A33-Exos, the converse to that observed in parental cells. This finding suggests miRNA biogenesis may be interlinked with endosomal/exosomal processing. This work was supported by National Health and Medical Research Council of Australia (NHMRC) program grant #487922. Overall design: qRT-PCR miRNA expression profiling. Same amount of total RNA was used for LIM1863 cells and released extracellular vesicles (sMVs, A33-Exos and EpCAM-Exos).
Project description:miRNAs are related with the initiation and development of prostate cancer. We discover the miR-195 and miR-30 can be as a biomarker of prognosis of prostate cancer in clinical patients. miRNA functions through affecting the mRNA degradation by binding the mRNA 3’UTR. So we test the change of transcriptional profile of miR-195 and miR-30d cell line respectively to further study the function of miR-195 and miR-30d. To study the function of miR-195 and miR-30d in prostate cancer, we setup the over-expression cell line of the miR-195 and miR-30d respectively in prostate cancer cell(LNCap and DU145), then study the change of transcriptional profile in cell line by microarray experiment (Affymetrix PrimeView human gene expression). We order the over-expression plasmid of vector, miR-195 and miR-30d from System Biosciences company (Cat No: Scramble Vector PMIRH000PA-1 as Control, miR-195 PMIRH195PA-1, miR-30d PMIRH30dPA-1), and packaged the virus and construct the stable cell line (LNCaP_Control, LNCaP_mir195, LNCaP_mir30d,DU145_Control, DU145_mir195, DU145_mir30d,). We test the transcriptional profile in cell line by microarray experiment (Affymetrix PrimeView human gene expression).
Project description:Micro RNAs (miRNAs) miR-130a, miR-203 and miR-205 are jointly downregulated in prostate cancer and act as repressors of AR-signaling. MiRNAs are small non-coding RNAs that regulate the expression of specific mRNA targets mainly by translational repression, mRNA deadenylation or cleavage. Reconstitution of these lost miRNAs in the LNCaP PCa cell line cause morphology changes, growth arrest, and apoptosis, increasing when the miRNAs were co-expressed. Bioinformatic target prediction, mRNA expression and protein expression analysis upon overexpression of these miRNAs congruently identified targets known to be overexpressed in PCa and to be involved in AR trans-activation. This series profiles loss in mRNA expression in LNCaP cells transfected with one of the three miRNAs miR-130a, miR-203 and miR-205 compared to LNCaP cells transfected with a scramble miRNA. We analyzed three arrays each for miR-130a, miR-203, miR-205, and a scramble miRNA.
Project description:Micro RNAs (miRNAs) miR-130a, miR-203 and miR-205 are jointly downregulated in prostate cancer and act as repressors of AR-signaling. MiRNAs are small non-coding RNAs that regulate the expression of specific mRNA targets mainly by translational repression, mRNA deadenylation or cleavage. Reconstitution of these lost miRNAs in the LNCaP PCa cell line cause morphology changes, growth arrest, and apoptosis, increasing when the miRNAs were co-expressed. Bioinformatic target prediction, mRNA expression and protein expression analysis upon overexpression of these miRNAs congruently identified targets known to be overexpressed in PCa and to be involved in AR trans-activation. This series profiles loss in mRNA expression in LNCaP cells transfected with one of the three miRNAs miR-130a, miR-203 and miR-205 compared to LNCaP cells transfected with a scramble miRNA. Overall design: We analyzed three arrays each for miR-130a, miR-203, miR-205, and a scramble miRNA.
Project description:To determine the altered microRNA expression signature in human prostate cancer compared to benign prostate tissue. To determine the altered mRNA expression signatures upon overexrpession miR-31 in prostate cancer cells. Two condition experiments:1) Total RNA from 21 pairs of prostate cancers and matched benign prostate tissues were collected and processed for microRNA detection. 2) In LNCaP prostate cancer cells, miR-31 was overexpressed and compared to control miR-NC.