Journal: Leukemia

Article Title: Regulation of PI3K signaling in T cell acute lymphoblastic leukemia: a novel PTEN/Ikaros/miR-26b mechanism reveals a critical targetable role for PIK3CD

doi: 10.1038/leu.2017.80

Figure Lengend Snippet: A: miRNA profile of Array data. KO576, KO577, KO578 and KO579 are Pten -knockout mouse T-ALL samples. WT580 and WT581 are wild-type mouse thymocytes. B: Decreased miR-26b expression level in mouse Pten deficient T-ALL cell lines (LPN248, LPN236 and LPN228) compared with mouse Ink4a/Arf knock-out T-ALL cell line (LPN211) and mouse wild type thymocytes (P<0.001). C. Decreased miR-26b in human T-ALL cell lines, CCRF-CEM, SUPT1, LOUCY, KOPT-K1, JURKAT and MOLT4 compared with postnatal normal human thymus (P<0.001). D: Decreased expression level of miR-26b in human primary T-ALL samples (P<0.001). E. Correlation of miR-26b expression level with PTEN level in human primary T-ALL samples (r=0.3987, P=0.039).

Article Snippet: Hybridization of biotin-labeled cDNA was carried out on a miRNA microarray chip (MD Anderson miRNA expression Bioarray Version 5), which contains 2300 miRNA probes, including 1400 human and 900 mouse miRNA genes, in duplicate.

Techniques: Knock-Out, Expressing

Journal: Cell Death & Disease

Article Title: Downregulation of miR-205 and miR-31 confers resistance to chemotherapy-induced apoptosis in prostate cancer cells

doi: 10.1038/cddis.2010.85

Figure Lengend Snippet: miR-205 targets Bcl-w and miR-31 targets E2F6. ( a ) Upper panel, predicted duplex formation between human BCL2L2 3′UTR and miR-205. Lower panel, predicted duplex formation between human E2F6 3′UTR and miR-31. ( b ) Left, WPE1-NB26 cells were transfected with GFP- BCL2L2 ( 3′UTR) or GFP- BCL2L2 (3′UTR)-mut plasmids together with plasmids expressing miR-205 or a negative control miRNA. Western blotting was performed with anti-GFP and anti-actin antibodies. Right, WPE1-NB26 cells were transfected with GFP- E2F6 ( 3′UTR) or GFP- E2F6 (3′UTR)-mut plasmids together with plasmids expressing miR-31 or a negative control miRNA. Western blotting was performed with anti-GFP and anti-actin antibodies. ( c ) Proteins were isolated from the indicated cell lines, western blots were done using indicated antibodies. ( d ) Left, WPE1-NB26 cells were transfected with pcDNA6.2-GW/EmGFP-miR-negative control or pcDNA6.2-GW/EmGFP-miR205, or pcDNA6.2-GW/EmGFP-miR31 plasmids. Expression of miRNAs was confirmed by real-time PCR. At 48 h after transfection, cell lysates were analyzed by western blots with the indicated antibodies (Middle). Right, WPE1-NA22 cells were transfected with synthetic miRNA inhibitors specific to miR-205 or miR-31, or the negative control inhibitor. At 48 h after transfection, cell lysates were analyzed by western blots with the indicated antibodies. Representative images of three independent experiments were shown

Article Snippet: To determine whether differential miRNA expression has a role in the apoptosis resistance in WPE1-NB26 cells, we compared miRNA expression profiles between WPE1-NA22 and WPE1-NB26 cells, using the mir Vana miRNA Bioarray.

Techniques: Transfection, Expressing, Negative Control, Western Blot, Isolation, Real-time Polymerase Chain Reaction

Journal: Cell Death & Disease

Article Title: Downregulation of miR-205 and miR-31 confers resistance to chemotherapy-induced apoptosis in prostate cancer cells

doi: 10.1038/cddis.2010.85

Figure Lengend Snippet: miR-205 and miR-31 sensitize WPE1-NB26 cells to chemotherapy-induced apoptosis. ( a ) WPE1-NB26 cell line stably expressing miR-205 was established and miR-205 expression was confirmed by real-time PCR. Negative control miRNA or miR-205 expressing cells were treated with various doses of Docetaxel for 24 h, and apoptosis was measured by Cell Death Detection Elisa analysis as described in Materials and Methods section. ( b ) Negative control or miR-205 expressing WPE1-NB26 cells were treated with various doses of Cisplatin for 24 h, and apoptosis was detected as above. ( c ) WPE1-NB26 cell line stably expressing miR-31 was established and miR-31 expression was confirmed by real-time PCR. Negative control miRNA or miR-31 expressing cells were treated with various doses of Docetaxel for 24 h, and apoptosis was measured as above. ( d ) Negative control miRNA or miR-31 expressing WPE1-NB26 cells were treated with various doses of Cisplatin for 24 h, and apoptosis was detected as above. The experiments have been repeated three times, data shown are mean values+S.D. ( * P <0.05, *** P <0.001)

Article Snippet: To determine whether differential miRNA expression has a role in the apoptosis resistance in WPE1-NB26 cells, we compared miRNA expression profiles between WPE1-NA22 and WPE1-NB26 cells, using the mir Vana miRNA Bioarray.

Techniques: Stable Transfection, Expressing, Real-time Polymerase Chain Reaction, Negative Control, Enzyme-linked Immunosorbent Assay

Journal: BMC Medical Genomics

Article Title: Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

doi: 10.1186/1755-8794-2-15

Figure Lengend Snippet: Bicluster of microRNA expression . Hierarchical clustering was carried out using correlation distance as the distance metric and average linkage between clusters to perform the analysis. This is a non-supervised method to illustrate potential relationships between the miRNA expression profiles from different samples. Hierarchical clustering was carried out for all samples and miRNA. The top of the figure indicates relationships between the various samples. The left-hand side shows the relationships between the miRNA identified on the right-hand side. The color of each cell reflects fold-change of the observed hybridization intensity relative to average hybridization intensity across all samples. Saturated green cells represent decrease in hybridization intensity, whereas saturated red cells represent an increase.

Article Snippet: Expression profiling was then performed using the mir Vana miRNA Bioarrays V2 (Asuragen, Inc., Austin, Texas) which contains probes for all mouse, rat, and human miRNAs (266, 238, 482 confirmed miRNAs, respectively) in miRBase .

Techniques: Expressing, Hybridization

Journal: BMC Medical Genomics

Article Title: Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

doi: 10.1186/1755-8794-2-15

Figure Lengend Snippet: Correlation of miRNAs with at least one target site in miRanda-predicted target mRNA . In each panel, the reference distribution of t-statistics from all probes of the mRNA expression arrays is given by a dotted line. These are compared with the distribution of t-statistics for those probes that are predicted targets of given miRNAs, shown as a solid line. 'N' represents the number of transcripts in the reference sample (dotted line), and therefore is the same in each plot. Sample size (n) is the number of genes predicted to have target(s) of given microRNA(s) (solid line), and therefore changes from plot to plot. Note that n depends on the number of predicted target probes contained within the dataset, either combined among all miRNAs, or specific to an individual miRNA. The plotted distributions are Gaussian kernel density estimates (loosely, smoothed histograms), and the indicated bandwidth is in terms of the standard deviation of the smoothing kernel. The x -axis in each figure reflects the t -statistics for the comparison between groups (dotted line represents random distribution). The y -axis represents the density of observations at a given t -statistic value. a. Combined t -statistics for all significantly changed miRNAs with 1 site in the 3'UTR of predicted target miRNAs. b. Combined t -statistics for a set of non-significant miRNAs with 1 predicted target site. c. Representative significantly changed miRNA compared to all of its predicted targets. d. Representative non-significantly changed miRNA compared to all of its predicted targets.

Article Snippet: Expression profiling was then performed using the mir Vana miRNA Bioarrays V2 (Asuragen, Inc., Austin, Texas) which contains probes for all mouse, rat, and human miRNAs (266, 238, 482 confirmed miRNAs, respectively) in miRBase .

Techniques: Expressing, Standard Deviation, Comparison

Journal: BMC Medical Genomics

Article Title: Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

doi: 10.1186/1755-8794-2-15

Figure Lengend Snippet: Correlation of miRNAs with at least one target site in PicTar-predicted target mRNA . a. Combined t-statistics for all significantly changed miRNAs with 1 site in the 3'UTR of predicted target mRNAs. b. Combined t-statistics for a set of non-significant miRNAs with 1 predicted target site. c. Representative significantly changed miRNA compared to all of its predicted targets. d. Representative non-significantly changed miRNA compared to all of its predicted targets.

Article Snippet: Expression profiling was then performed using the mir Vana miRNA Bioarrays V2 (Asuragen, Inc., Austin, Texas) which contains probes for all mouse, rat, and human miRNAs (266, 238, 482 confirmed miRNAs, respectively) in miRBase .

Techniques:

Journal: BMC Medical Genomics

Article Title: Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

doi: 10.1186/1755-8794-2-15

Figure Lengend Snippet: Correlation of miRNAs with at least one target site in TargetScanS (with total context score)-predicted target mRNA . a. Combined t-statistics for significantly changed miRNAs (top 15%) with 1 site in the 3'UTR of predicted target mRNAs. b. Combined t-statistics for a set of non-significant miRNAs with 1 predicted target site. c. Representative significantly changed miRNA compared to top 15% of its predicted targets. d. Representative non-significantly changed miRNA compared to top 15% of its predicted targets.

Article Snippet: Expression profiling was then performed using the mir Vana miRNA Bioarrays V2 (Asuragen, Inc., Austin, Texas) which contains probes for all mouse, rat, and human miRNAs (266, 238, 482 confirmed miRNAs, respectively) in miRBase .

Techniques:

Journal: BMC Medical Genomics

Article Title: Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

doi: 10.1186/1755-8794-2-15

Figure Lengend Snippet: Correlation of miRNAs with at least one target site in miRanda(miRBase)-predicted target mRNA . a. Combined t-statistics for all significantly changed miRNAs with 1 site in the 3'UTR of predicted target mRNAs. b. Combined t-statistics for a set of non-significant miRNAs with 1 predicted target site. c. Representative significantly changed miRNA compared to all of its predicted targets. d. Representative non-significantly changed miRNA compared to all of its predicted targets.

Article Snippet: Expression profiling was then performed using the mir Vana miRNA Bioarrays V2 (Asuragen, Inc., Austin, Texas) which contains probes for all mouse, rat, and human miRNAs (266, 238, 482 confirmed miRNAs, respectively) in miRBase .

Techniques:

Journal: BMC Medical Genomics

Article Title: Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

doi: 10.1186/1755-8794-2-15

Figure Lengend Snippet: Correlation of miRNAs with at least 3 target sites in miRanda-predicted target mRNA . Same as Figure 3 , except that probes identified as targets of a miRNA are required to have at least three target sites in the 3'UTR region according to the miRanda(microrna.org) target prediction software. Arrows indicate deviation from the reference graph.

Article Snippet: Expression profiling was then performed using the mir Vana miRNA Bioarrays V2 (Asuragen, Inc., Austin, Texas) which contains probes for all mouse, rat, and human miRNAs (266, 238, 482 confirmed miRNAs, respectively) in miRBase .

Techniques: Software

Journal: BMC Medical Genomics

Article Title: Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

doi: 10.1186/1755-8794-2-15

Figure Lengend Snippet: Correlation of specific genes with predicted groups of miRNAs (miRanda, microrna.org) . The expression levels in hypoxia and normoxia of each gene specific miRNA group were plotted. Significant deviation of the regression line (solid) from the line of equality (dotted line) indicates co-regulation of the group. Panel a shows histogram of the p -values for miRNA groups of all coding genes represented in the study for miRanda. Frequency on y -axis refers to the number of genes involved. Panels b-d depict CFTR, KIAA2026, and C16orf73 as examples of mRNA regulation by gene-specific miRNA groups. The red dots indicate gene-specific miRNAs for each given gene; this includes 9 miRNAs predicted by miRanda(microrna.org) for CFTR, 28 each for KIAA2026 and C16orf73.

Article Snippet: Expression profiling was then performed using the mir Vana miRNA Bioarrays V2 (Asuragen, Inc., Austin, Texas) which contains probes for all mouse, rat, and human miRNAs (266, 238, 482 confirmed miRNAs, respectively) in miRBase .

Techniques: Expressing

Journal: BMC Medical Genomics

Article Title: Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

doi: 10.1186/1755-8794-2-15

Figure Lengend Snippet: Correlation of specific genes with predicted groups of miRNAs (PicTar) . The expression levels in hypoxia and normoxia of each gene specific miRNA group were plotted. Significant deviation of the regression line (solid) from the line of equality (dotted line) indicates co-regulation of the group. Panel a shows histogram of the p-values for miRNA groups of all coding genes represented in the study for PicTar. Frequency on y-axis refers to the number of genes involved. Panels b-d depict CFTR, NRBF2, and GALNT3 as examples of mRNA regulation by gene-specific miRNA groups. The red dots indicate gene specific miRNAs for each given gene.

Article Snippet: Expression profiling was then performed using the mir Vana miRNA Bioarrays V2 (Asuragen, Inc., Austin, Texas) which contains probes for all mouse, rat, and human miRNAs (266, 238, 482 confirmed miRNAs, respectively) in miRBase .

Techniques: Expressing

Journal: BMC Medical Genomics

Article Title: Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

doi: 10.1186/1755-8794-2-15

Figure Lengend Snippet: Correlation of specific genes with predicted groups of miRNAs (TargetScanS) . Panel a shows histogram of the p-values for miRNA groups of all coding genes represented in the study for TargetScanS. Frequency on y-axis refers to the number of genes involved. Panels b-d depict CFTR, KIAA1468, and ARID4B as examples of mRNA regulation by gene-specific miRNA groups. The red dots indicate gene specific miRNAs for each given gene.

Article Snippet: Expression profiling was then performed using the mir Vana miRNA Bioarrays V2 (Asuragen, Inc., Austin, Texas) which contains probes for all mouse, rat, and human miRNAs (266, 238, 482 confirmed miRNAs, respectively) in miRBase .

Techniques:

Journal: BMC Medical Genomics

Article Title: Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

doi: 10.1186/1755-8794-2-15

Figure Lengend Snippet: Correlation of specific genes with predicted groups of miRNAs (miRanda/miRBase) . Panel a shows histogram of the p-values for miRNA groups of all coding genes represented in the study for miRanda/miRBase. Frequency on y-axis refers to the number of genes involved. Panels b-d depict CFTR, NRBF2, and LARP1 as examples of mRNA regulation by gene-specific miRNA groups. The red dots indicate gene specific miRNAs for each given gene.

Article Snippet: Expression profiling was then performed using the mir Vana miRNA Bioarrays V2 (Asuragen, Inc., Austin, Texas) which contains probes for all mouse, rat, and human miRNAs (266, 238, 482 confirmed miRNAs, respectively) in miRBase .

Techniques: