Journal: Oncology Letters

Article Title: Modulation of microRNA expression in human lung cancer cells by the G9a histone methyltransferase inhibitor BIX01294

doi: 10.3892/ol.2014.2034

Figure Lengend Snippet: Human miRNAs that showed a differential expression in H1299 cells following BIX01294 treatment through microarray analysis.

Article Snippet: A genome-wide miRNA expression profiling experiment was performed by LC Sciences (Houston, TX, USA).

Techniques: Quantitative Proteomics, Microarray, Sequencing

Journal: Oncology Letters

Article Title: Modulation of microRNA expression in human lung cancer cells by the G9a histone methyltransferase inhibitor BIX01294

doi: 10.3892/ol.2014.2034

Figure Lengend Snippet: Quantitative polymerase chain reaction analysis of selected miRNAs between H1299 cells receiving mock and BIX01294 treatment. Each bar represents the average expression level of the corresponding miRNA from a triplicate measurement of three independent preparations of total RNA samples. * P<0.05. miRNA, microRNA.

Article Snippet: A genome-wide miRNA expression profiling experiment was performed by LC Sciences (Houston, TX, USA).

Techniques: Real-time Polymerase Chain Reaction, Expressing

Journal: Oncology Letters

Article Title: Modulation of microRNA expression in human lung cancer cells by the G9a histone methyltransferase inhibitor BIX01294

doi: 10.3892/ol.2014.2034

Figure Lengend Snippet: Putative target genes of hsa-miR-106b-3p and hsa-miR-151a-3p.

Article Snippet: A genome-wide miRNA expression profiling experiment was performed by LC Sciences (Houston, TX, USA).

Techniques:

Journal: Brain

Article Title: Engineered microRNA-based regulatory element permits safe high-dose mini MECP2 gene therapy in Rett mice

doi: 10.1093/brain/awab182

Figure Lengend Snippet: Schematic of strategy used to rationally synthesize a miRNA target panel tailored for Rett syndrome. (A) The first five steps of a conceptual negative feedback loop are indicated: (1) viral genome in nucleus; (2) exogenous MECP2-myc mRNA in cytoplasm; (3) translation and nuclear localization of MECP2-myc; (4) exogenous MECP2-myc upregulates miRNA expression; (5) mature miRNAs bind to non-coding targets in the 3ʹ UTR of an exogenous MECP2-myc transcript. After mature miRNAs bind to targets in the exogenous MECP2 mRNA, endogenous RNAi machinery (not shown) may conditionally silence exogenous MECP2 expression. The targets inserted into the viral genome may match targets found in the endogenous Mecp2 mRNA. Conceptually, this model could be adapted for other potentially toxic transcription factors that drive the expression of miRNAs in vivo. Alternatively, insertion of miRNA targets into the viral genome could improve the safety of gene therapies encoding potentially toxic cytoplasmic proteins, provided that those proteins indirectly upregulate miRNAs. (B) To identify translationally relevant miRNAs upregulated by toxic MECP2 gene transfer, (1) adolescent wild-type (WT) and knockout (KO) mice were treated intracisternally with saline, 1 × 1012 vg AAV9/MECP2, or 1 × 1012 vg AAV9/EGFP. (2) Two to three weeks later, CNS tissue nearest to the injection site (cerebellum, medulla and cervical cord; see dashed circle) was harvested from treated mice. The image shown in step 2 illustrates the spread of dye after ICM administration. The relatively concentrated dye localization near the cerebellum indicates how vulnerable tissue near the intracisternal site may be after treatment with high titre, toxic virus. (3) RNA was purified from dissected tissue, frozen and shipped to LC Sciences for miRNA profiling. Data from this screen were subsequently used to rank candidate miRNA targets from a secondary bioinformatics approach.

Article Snippet: The relatively concentrated dye localization near the cerebellum indicates how vulnerable tissue near the intracisternal site may be after treatment with high titre, toxic virus. (3) RNA was purified from dissected tissue, frozen and shipped to LC Sciences for miRNA profiling.

Techniques: Expressing, In Vivo, Knock-Out, Saline, Injection, Virus, Purification

Journal: International Journal of Molecular Sciences

Article Title: MicroRNAs as Potential Biomarkers in the Differential Diagnosis of Lipomatous Tumors and Their Mimics

doi: 10.3390/ijms23147804

Figure Lengend Snippet: Biologically distinct soft tissue tumors can be differentiated by microRNA expression profiles. ( A ) Heatmap showing hierarchical clustering of benign (lipoma) and malignant (WDLPS, DDLPS, MFS, UPS) soft tissue tumor FFPE samples using their microRNA expression profiles measured by qPCR. ( B – D ) Results of principal component analysis (PCA) on miRNA expression profiles of soft tissue tumor FFPE samples shown in graphs plotting ( B ) principal component 2 (PC2) against principal component 1 (PC1), ( C ) principal component 3 (PC3) against PC1, and ( D ) PC3 against PC2.

Article Snippet: To evaluate the potential of miRNA expression profiles as diagnostic biomarkers, we performed miRNA profiling of 350 well-annotated miRNA candidates chosen based on their abundant and stable expression in various tissues and serum (unpublished data from MiRXES).

Techniques: Expressing

Journal: Frontiers in Immunology

Article Title: Elevated Expression of miR-19b Enhances CD8 + T Cell Function by Targeting PTEN in HIV Infected Long Term Non-progressors With Sustained Viral Suppression

doi: 10.3389/fimmu.2018.03140

Figure Lengend Snippet: miRNA profiles distinguish LTNPs with different levels of virus. (A) Principal component analysis (PCA) plot of miRNA expression data from LTNPs, TPs, and HCs in the training cohort. Nine LTNPs were divided into two groups, one of which was very close to the TPs (Group A, n = 6) and another that was intertwined with the HCs (Group B, n = 3). (B) Comparison of age, CD4 counts, and viral load between Group A and Group B of LTNPs. * P < 0.05.

Article Snippet: Quantitative real-time polymerase chain reaction (qRT-PCR)-based high-throughput miRNA profiling was performed at QuantoBio Biotechnology Co. Ltd. (Beijing, China).

Techniques: Virus, Expressing, Comparison

Journal: Frontiers in Immunology

Article Title: Elevated Expression of miR-19b Enhances CD8 + T Cell Function by Targeting PTEN in HIV Infected Long Term Non-progressors With Sustained Viral Suppression

doi: 10.3389/fimmu.2018.03140

Figure Lengend Snippet: Expression of miR-19b is high in LTNP-Ls compared with that observed in LTNP-Hs. (A) Heatmap demonstrating 78 miRNAs differentially expressed between LTNP-Hs ( n = 6) and LTNP-Ls ( n = 3) in the training cohort (Benjamini–Hochberg false discovery rate-adjusted P < 0.05 and fold change >2). Hierarchical clustering of change in the threshold cycle (ΔCT) was performed using the complete linkage method and Pearson correlation coefficient. (B) The protocol for the selection of candidate miRNA from the training cohort. Among the 78 miRNAs differentially expressed between LTNP-Hs ( n = 6) and LTNP-Ls ( n = 3), 70 miRNAs differentially expressed between LTNPs and HCs ( P < 0.05) were excluded. Subsequently, five differentially expressed miRNAs between LTNPs and TPs were excluded. Three candidate miRNAs, namely miR-15a, miR-19b, and miR-33 were selected. (C) Comparison of the three candidate miRNAs between LTNP-Ls ( n = 3) and LTNP-Hs ( n = 6) in the training cohort. (D,F) Relative expression of miR-19b (D) , miR-15a (E) and miR-33 (F) in PBMCs obtained from LTNP-Ls ( n = 8) and LTNP-Hs ( n = 10) in the subsequent validation group. (G,H) CD4 + and CD8 + T cells from LTNPs were sorted through flow cytometry. The expression of miR19b in CD4 + (G) and CD8 + T (H) cells was compared between LTNP-Ls ( n = 9, one from training cohort, eight from validation cohort) and LTNP-Hs ( n = 10, two from training cohort, eight from validation cohort) using qRT-PCR. * P < 0.05.

Article Snippet: Quantitative real-time polymerase chain reaction (qRT-PCR)-based high-throughput miRNA profiling was performed at QuantoBio Biotechnology Co. Ltd. (Beijing, China).

Techniques: Expressing, Selection, Comparison, Biomarker Discovery, Flow Cytometry, Quantitative RT-PCR

Journal: PLoS Computational Biology

Article Title: Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification

doi: 10.1371/journal.pcbi.1000516

Figure Lengend Snippet: Marginal correlations of m- and miRNA expression levels are typically and inappropriately positive in all datasets under analysis. Further, in the Madison and Broad datasets the amount of variation in targeted mRNA expression captured by that of targeting miRNA is extremely low. In the combined dataset, high R 2 values are indicative only of the amount of variation in mRNA expression due to data origin.

Article Snippet: The second data source was derived from that produced from a study of miRNA expression patterns over a wide variety of tumor and normal tissue types conducted by the Broad Institute .

Techniques: Expressing

Journal: PLoS Computational Biology

Article Title: Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification

doi: 10.1371/journal.pcbi.1000516

Figure Lengend Snippet: Improvements in the percentages of variation in targeted mRNA expression are observed through use of the adjusted R 2 statistic. Partial correlations of proxies to targeting Ago 2 RISCs and targeted mRNAs are lower than those of m/miRNA expressions. Paired Wilcoxon tests of the hypothesis H 0 : μ 0 −μ 1 = 0 vs. H A : μ 0 −μ 1 ≠0 were rejected for the Madison ( p = 0.0135), Broad ( p = 0.0186) and combined ( p <0.0001) datasets, where μ 0 and μ 1 refer to mean correlations of marginal m/miRNA expression and mean partial correlations respectively.

Article Snippet: The second data source was derived from that produced from a study of miRNA expression patterns over a wide variety of tumor and normal tissue types conducted by the Broad Institute .

Techniques: Expressing

Journal: PLoS Computational Biology

Article Title: Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification

doi: 10.1371/journal.pcbi.1000516

Figure Lengend Snippet: Hash marks denote the 95% confidence level of identification numbers under the no-targeting null for the miRNA and validation technique under consideration. Overall, 7.83% of computational predicted targets were verified using marginal expression level comparisons, and 4 miRNAs showed substantially larger numbers of verifications than what would be typically expected. After compensating for biological and idiosyncratic effects, 25.68% of these targets were verified, and 9 miRNAs showed large numbers of identifications.

Article Snippet: The second data source was derived from that produced from a study of miRNA expression patterns over a wide variety of tumor and normal tissue types conducted by the Broad Institute .

Techniques: Biomarker Discovery, Expressing