Journal: Cancer Management and Research

Article Title: The Maturation of Tumor Suppressor miR-497 in Hepatocellular Carcinoma is Inhibited by Oncogenic circRNA SCARB1

doi: 10.2147/CMAR.S304125

Figure Lengend Snippet: The expression of circRNA SCARB1, mature miR-497 and miR-497 precursor was altered in HCC. HCC and paired non-tumor tissues were collected from the 64 HCC patients included in this study, and the expression of circRNA SCARB1 ( A ), mature miR-497 ( B ) and miR-497 precursor ( C ) in these tissue samples was determined by RT-qPCR. Average values of three technical replicates were used to express gene expression data in paired HCC and non-tumor tissues, ** p < 0.01.

Article Snippet: To overexpress circRNA SCARB1, pcDNA3.1(+) CircRNA Mini Vector (Addgene) was used as the backbone to construct the expression vector of circRNA SCARB1.

Techniques: Expressing, Quantitative RT-PCR, Gene Expression

Journal: Cancer Management and Research

Article Title: The Maturation of Tumor Suppressor miR-497 in Hepatocellular Carcinoma is Inhibited by Oncogenic circRNA SCARB1

doi: 10.2147/CMAR.S304125

Figure Lengend Snippet: The Correlations Between Clinicopathological Variables and the Expression of circRNA SCARB1 in HCC

Article Snippet: To overexpress circRNA SCARB1, pcDNA3.1(+) CircRNA Mini Vector (Addgene) was used as the backbone to construct the expression vector of circRNA SCARB1.

Techniques: Expressing, Infection

Journal: Cancer Management and Research

Article Title: The Maturation of Tumor Suppressor miR-497 in Hepatocellular Carcinoma is Inhibited by Oncogenic circRNA SCARB1

doi: 10.2147/CMAR.S304125

Figure Lengend Snippet: CircRNA SCARB1 and mature miR-497 were inversely correlated across HCC samples. Pearson’s correlation coefficient analysis was used to analyze the correlations between circRNA SCARB1 and mature miR-497 ( A ) or miR-497 precursor ( B ) across HCC tissue samples.

Article Snippet: To overexpress circRNA SCARB1, pcDNA3.1(+) CircRNA Mini Vector (Addgene) was used as the backbone to construct the expression vector of circRNA SCARB1.

Techniques:

Journal: Cancer Management and Research

Article Title: The Maturation of Tumor Suppressor miR-497 in Hepatocellular Carcinoma is Inhibited by Oncogenic circRNA SCARB1

doi: 10.2147/CMAR.S304125

Figure Lengend Snippet: Overexpression of circRNA SCARB1 downregulated mature miR-497 in HCC cells. To explore the effects of overexpression of circRNA SCARB1 on the maturation of miR-497, SNU-423 and SNU-387 cells were transfected with either circRNA SCARB1 expression vector or miR-497 mimic, followed by the confirmation of transfections at 48 h post-transfection by RT-qPCR ( A ). The effects of overexpression of circRNA SCARB1 of the expression of mature miR-497 ( B ) and miR-497 precursor ( C ), as well as the effects of the transfection of miR-497 mimic on circRNA SCARB1 expression ( D ) were also analyzed by RT-qPCR. Mean ± SD values were used to express data of 3 biological replicates of in vitro cell experiments. * p < 0.05.

Article Snippet: To overexpress circRNA SCARB1, pcDNA3.1(+) CircRNA Mini Vector (Addgene) was used as the backbone to construct the expression vector of circRNA SCARB1.

Techniques: Over Expression, Transfection, Expressing, Plasmid Preparation, Quantitative RT-PCR, In Vitro

Journal: Cancer Management and Research

Article Title: The Maturation of Tumor Suppressor miR-497 in Hepatocellular Carcinoma is Inhibited by Oncogenic circRNA SCARB1

doi: 10.2147/CMAR.S304125

Figure Lengend Snippet: Overexpression of circRNA SCARB1 increased HCC cell proliferation through miR-497. CCK-8 assay was performed to analyze the effects of overexpression of circRNA SCARB1 and miR-497 on the proliferation of SNU-423 ( A ) and SNU-387 cells ( B ). Mean ± SD values were used to express data of three biological replicates of in vitro cell experiments. * p < 0.05.

Article Snippet: To overexpress circRNA SCARB1, pcDNA3.1(+) CircRNA Mini Vector (Addgene) was used as the backbone to construct the expression vector of circRNA SCARB1.

Techniques: Over Expression, CCK-8 Assay, In Vitro

Journal: Cancer Management and Research

Article Title: The Maturation of Tumor Suppressor miR-497 in Hepatocellular Carcinoma is Inhibited by Oncogenic circRNA SCARB1

doi: 10.2147/CMAR.S304125

Figure Lengend Snippet: Overexpression of circRNA SCARB1 increased HCC cell migration through miR-497. Transwell assay was conducted to analyze the effects of overexpression of circRNA SCARB1 and miR-497 on the migration of SNU-423 ( A and C ) and SNU-387 cells ( B and D ). Mean ± SD values were used to express data of three biological replicates of in vitro cell experiments. * p < 0.05.

Article Snippet: To overexpress circRNA SCARB1, pcDNA3.1(+) CircRNA Mini Vector (Addgene) was used as the backbone to construct the expression vector of circRNA SCARB1.

Techniques: Over Expression, Migration, Transwell Assay, In Vitro

Journal: Cell & Bioscience

Article Title: Circular RNA expression profile in blood according to ischemic stroke etiology

doi: 10.1186/s13578-020-00394-3

Figure Lengend Snippet: Distribution by chromosomes ( a ) and chromosome’s region ( b ). Differentially expressed circRNA distribution in chromosomes and chromosome´s region (exonic, intronic, antisense, sense overlapping and intergenic) for each comparison

Article Snippet: To this end, we used Arraystar Human circRNA Array (8 × 15 K, Arraystar), which surveys up to 13,617 probes to identify human circRNAs, in 30 acute stroke patients with different etiologies by TOAST classification [ ].

Techniques:

Journal: Cell & Bioscience

Article Title: Circular RNA expression profile in blood according to ischemic stroke etiology

doi: 10.1186/s13578-020-00394-3

Figure Lengend Snippet: Deregulated circRNA chosen for qPCR validation

Article Snippet: To this end, we used Arraystar Human circRNA Array (8 × 15 K, Arraystar), which surveys up to 13,617 probes to identify human circRNAs, in 30 acute stroke patients with different etiologies by TOAST classification [ ].

Techniques:

Journal: Cell & Bioscience

Article Title: Circular RNA expression profile in blood according to ischemic stroke etiology

doi: 10.1186/s13578-020-00394-3

Figure Lengend Snippet: RT-qPCR validation of hsa_circRNA_102488. a Schematic representation of the UBA52 gene, origin of hsa_circRNA_102488. The graph shows the map of hsa_circRNA_102488 which is originated from exons 2 and 3 of its host mRNA (NCBI RefSeq track shown in the UCSC Genome Browser). b hsa_circRNA_102488 backsplicing. The Sanger-Sequencing electropherogram specifies the sequence of the backspliced junction that results in the circRNA formation. c – e hsa_circRNA_102488 and UBA52 mRNA expression levels between atherotrombotic vs cardioembolic samples. Percentage of hsa_circRNA_102488 expression relative to GAPDH mRNA ( c ) or UBA52 mRNA ( d ) is decreased in atherotrombotic with respect to cardioembolic stroke patients. However, we found similar expression levels of UBA52 mRNA in atherotrombotic and cardioembolic samples groups ( e ). Error bars: 95% CI. **p-value < 0.01; ***p-value < 0.001

Article Snippet: To this end, we used Arraystar Human circRNA Array (8 × 15 K, Arraystar), which surveys up to 13,617 probes to identify human circRNAs, in 30 acute stroke patients with different etiologies by TOAST classification [ ].

Techniques: Quantitative RT-PCR, Sequencing, Expressing

Journal: Cell & Bioscience

Article Title: Circular RNA expression profile in blood according to ischemic stroke etiology

doi: 10.1186/s13578-020-00394-3

Figure Lengend Snippet: GO analysis by mirPath v.3. The image shows the heatmaps corresponding to the analysis performed with the overrepresented miRNAs in the three comparisons (atherotrombotic-cardioembolic-undetermined) by TargetScan ( a ) and the analysis involving the target miRNAs for hsa_circRNA_102488 in accordance with molecular function ( b , by Tarbase) or biological process ( c , by microT-CDS)

Article Snippet: To this end, we used Arraystar Human circRNA Array (8 × 15 K, Arraystar), which surveys up to 13,617 probes to identify human circRNAs, in 30 acute stroke patients with different etiologies by TOAST classification [ ].

Techniques:

Journal: Cell & Bioscience

Article Title: Circular RNA expression profile in blood according to ischemic stroke etiology

doi: 10.1186/s13578-020-00394-3

Figure Lengend Snippet: hsa_circRNA_102488 impact pathways. The cartoon shows miRNAs (in blue) sharing a target site with hsa_circRNA_102488 (in black) and the pathways in which they converge (in dark orange), within those associated with the overrepresented miRNAs in the three comparisons (in light orange). RBPs sites matching to hsa_circRNA_102488 clustered around AGO2 (in dark green) and RBPs sites that matched to its flanking regions clustered around FUS (in light green). ARVC: Arrhythmogenic Right Ventricular Cardiomyopathy; HCM: Hypertrophic Cardiomyopathy

Article Snippet: To this end, we used Arraystar Human circRNA Array (8 × 15 K, Arraystar), which surveys up to 13,617 probes to identify human circRNAs, in 30 acute stroke patients with different etiologies by TOAST classification [ ].

Techniques:

Journal: BioMed Research International

Article Title: Circular RNA Profiling and Bioinformatic Modeling Identify Its Regulatory Role in Hepatic Steatosis

doi: 10.1155/2017/5936171

Figure Lengend Snippet: circRNA profiles differentiate the normal group from model group. (a) Principal component analysis (PCA) shows the difference between normal and model groups. (b) Scatter plots assess the variation of circRNA expression between two groups. The values plotted on x and y axes are the normalized signal values of each group (log2 scaled). Dots above the top green line and below the bottom green line represent differentially expressed circRNAs. (c, d) Unsupervised hierarchical clustering (c) and volcano plot (d) demonstrate the differential expression of circRNAs during hepatic steatosis. Both downregulated (green) and upregulated (red) circRNAs were visualized in the cluster. In similar, the red points in volcano plot represent the differentially expressed circRNAs with statistical significance. (e, f) Validation of the upregulated (e) and downregulated circRNAs (f) using QPCR. (g) The results of QPCR exhibit well consistence with those of microarray. Pairwise scatter plots reflect the fold changes (log2 transformed) of both microarray (horizontal axis) and the QPCR (vertical axis). The R stands for linear correlation coefficient. The presented results are expressed as means ± SD. ∗∗ P < 0.01.

Article Snippet: To remove linear RNAs and enrich circRNA, total RNA from each sample was treated with Rnase R. circRNA was then transcribed into fluorescent cRNA by random primer according to the Arraystar Super RNA Labeling protocol (Arraystar, Inc., USA) and hybridized onto the Arraystar Human circRNA Arrays V2.0 (Arraystar, Inc., USA) at 65°C for 17 hours.

Techniques: Expressing, Quantitative Proteomics, Biomarker Discovery, Microarray, Transformation Assay

Journal: BioMed Research International

Article Title: Circular RNA Profiling and Bioinformatic Modeling Identify Its Regulatory Role in Hepatic Steatosis

doi: 10.1155/2017/5936171

Figure Lengend Snippet: Predicted targets of top-20 differentially expressed circRNAs.

Article Snippet: To remove linear RNAs and enrich circRNA, total RNA from each sample was treated with Rnase R. circRNA was then transcribed into fluorescent cRNA by random primer according to the Arraystar Super RNA Labeling protocol (Arraystar, Inc., USA) and hybridized onto the Arraystar Human circRNA Arrays V2.0 (Arraystar, Inc., USA) at 65°C for 17 hours.

Techniques:

Journal: BioMed Research International

Article Title: Circular RNA Profiling and Bioinformatic Modeling Identify Its Regulatory Role in Hepatic Steatosis

doi: 10.1155/2017/5936171

Figure Lengend Snippet: Enumeration data of differentially expressed circRNAs and target miRNAs/mRNAs.

Article Snippet: To remove linear RNAs and enrich circRNA, total RNA from each sample was treated with Rnase R. circRNA was then transcribed into fluorescent cRNA by random primer according to the Arraystar Super RNA Labeling protocol (Arraystar, Inc., USA) and hybridized onto the Arraystar Human circRNA Arrays V2.0 (Arraystar, Inc., USA) at 65°C for 17 hours.

Techniques:

Journal: BioMed Research International

Article Title: Circular RNA Profiling and Bioinformatic Modeling Identify Its Regulatory Role in Hepatic Steatosis

doi: 10.1155/2017/5936171

Figure Lengend Snippet: circRNA-miRNA-mRNA regulatory network uncovers the circRNA_021412-miR-1972-LPIN1 signaling underlying circRNAs' effects. (a) The circRNA-miRNA-mRNA network related to transcriptional regulation. Red cycles, violet squares, and blue cycles represent circRNAs, miRNAs, and mRNAs, respectively. The size of each symbol reflects its degree, which is scored by the number of downstream targets. (b) circRNA_021412-miR-1972-LPIN1 signaling within the circRNA-miRNA-mRNA network is recognized to underlie the actions of circRNAs. (c) The circRNA_021412-miR-1972-LPIN1 signaling controls the pathway of lipid degradation via PPAR α -induced ACSLs expression.

Article Snippet: To remove linear RNAs and enrich circRNA, total RNA from each sample was treated with Rnase R. circRNA was then transcribed into fluorescent cRNA by random primer according to the Arraystar Super RNA Labeling protocol (Arraystar, Inc., USA) and hybridized onto the Arraystar Human circRNA Arrays V2.0 (Arraystar, Inc., USA) at 65°C for 17 hours.

Techniques: Expressing

Journal: BioMed Research International

Article Title: Circular RNA Profiling and Bioinformatic Modeling Identify Its Regulatory Role in Hepatic Steatosis

doi: 10.1155/2017/5936171

Figure Lengend Snippet: Diagram of circRNA_021412-based regulation of hepatic steatosis. Arrow, blunt-headed line, and red cross represent effects of activation, inhibition, and blocking, respectively.

Article Snippet: To remove linear RNAs and enrich circRNA, total RNA from each sample was treated with Rnase R. circRNA was then transcribed into fluorescent cRNA by random primer according to the Arraystar Super RNA Labeling protocol (Arraystar, Inc., USA) and hybridized onto the Arraystar Human circRNA Arrays V2.0 (Arraystar, Inc., USA) at 65°C for 17 hours.

Techniques: Activation Assay, Inhibition, Blocking Assay

Journal: Journal of Cellular and Molecular Medicine

Article Title: Screening differential circular RNA expression profiles reveals the regulatory role of circMARS in anti‐tuberculosis drug‐induced liver injury

doi: 10.1111/jcmm.17157

Figure Lengend Snippet: Study flow chart. First, the difference of circRNA expression profiles between anti‐tuberculosis drug‐induced liver injury (ADLI) and non‐ADLI patients were explored. Then, a differentially expressed circRNA was selected for verification in a cohort of 300 patients. Finally, the function of this circRNA was verified in a self‐controlled cohort of 35 patients based on the results of the experimental study

Article Snippet: The circRNAs in the discovery cohort were profiled using the CapitalBio Technology CircRNA Human Gene Expression Microarray v2.0 (CapitalBio Technology, Beijing, China).

Techniques: Expressing

Journal: Journal of Cellular and Molecular Medicine

Article Title: Screening differential circular RNA expression profiles reveals the regulatory role of circMARS in anti‐tuberculosis drug‐induced liver injury

doi: 10.1111/jcmm.17157

Figure Lengend Snippet: Identification of circRNA expression profiles in ADLI. (A) The scatter plots of circRNAs expression variations in the ADLI patients and in vitro assays. The red and green points in the plot indicate the upregulated and downregulated circRNAs. (B) Venn diagrams of the co‐expression circRNAs in the serum and cells. Two drugs: cells with Isoniazid (INH) + Rifampicin (RFP); three drugs: cells with INH + RFP + Pyrazinamide (PZA)

Article Snippet: The circRNAs in the discovery cohort were profiled using the CapitalBio Technology CircRNA Human Gene Expression Microarray v2.0 (CapitalBio Technology, Beijing, China).

Techniques: Expressing, In Vitro

Journal: Cell Cycle

Article Title: Analysis of co-expression networks for circular RNAs and mRNAs reveals that circular RNAs hsa_circ_0047905, hsa_circ_0138960 and has-circRNA7690-15 are candidate oncogenes in gastric cancer

doi: 10.1080/15384101.2017.1380135

Figure Lengend Snippet: Heat map of the circRNA and mRNA profiles in GC tissues versus paired normal gastric mucosa tissues. Red indicates high relative expression, and green indicates low relative expression. The expression of mRNA (A) and circRNA (B) were hierarchically clustered on the y-axis, and the tissue samples are hierarchically clustered on the x-axis (Fold change ≧ 2, p < 0.05). Expression levels are presented in red and green, indicating upregulated and downregulated RNAs, respectively. Numbers marked with T and N are from five paired gastric cancer tissues and paired adjacent normal tissues, respectively.

Article Snippet: The labeled cRNAs were hybridized onto the CapitalBio Technology Human CircRNA Microarray v2.0 (V2.0,4 × 180K) and mRNA Human Gene Expression Microarray (V4.0,4 × 180K), including the global profiling of 170,340 circRNAs and 34,235 coding transcripts (from 21,901 genes).

Techniques: Expressing

Journal: Cell Cycle

Article Title: Analysis of co-expression networks for circular RNAs and mRNAs reveals that circular RNAs hsa_circ_0047905, hsa_circ_0138960 and has-circRNA7690-15 are candidate oncogenes in gastric cancer

doi: 10.1080/15384101.2017.1380135

Figure Lengend Snippet: Co-expression network in GC tissues and adjacent normal tissues. The co-expression network consists of 204 circRNAs and 169 mRNAs. (A) GC tissues; (B) Normal tissues. A round node represents a protein-coding gene, and a triangular node represents a circRNA. Solid lines between two nodes indicate positively-correlated interactions between genes, and dashed lines indicate negatively-correlated interactions. Structural cohesion levels are presented in different colors; red indicates a high cohesion level.

Article Snippet: The labeled cRNAs were hybridized onto the CapitalBio Technology Human CircRNA Microarray v2.0 (V2.0,4 × 180K) and mRNA Human Gene Expression Microarray (V4.0,4 × 180K), including the global profiling of 170,340 circRNAs and 34,235 coding transcripts (from 21,901 genes).

Techniques: Expressing

Journal: Cell Cycle

Article Title: Analysis of co-expression networks for circular RNAs and mRNAs reveals that circular RNAs hsa_circ_0047905, hsa_circ_0138960 and has-circRNA7690-15 are candidate oncogenes in gastric cancer

doi: 10.1080/15384101.2017.1380135

Figure Lengend Snippet: Top 3 Critical circRNAs.

Article Snippet: The labeled cRNAs were hybridized onto the CapitalBio Technology Human CircRNA Microarray v2.0 (V2.0,4 × 180K) and mRNA Human Gene Expression Microarray (V4.0,4 × 180K), including the global profiling of 170,340 circRNAs and 34,235 coding transcripts (from 21,901 genes).

Techniques:

Journal: Cell Cycle

Article Title: Analysis of co-expression networks for circular RNAs and mRNAs reveals that circular RNAs hsa_circ_0047905, hsa_circ_0138960 and has-circRNA7690-15 are candidate oncogenes in gastric cancer

doi: 10.1080/15384101.2017.1380135

Figure Lengend Snippet: siRNAs targeted at circRNA backspliced junction sequences.

Article Snippet: The labeled cRNAs were hybridized onto the CapitalBio Technology Human CircRNA Microarray v2.0 (V2.0,4 × 180K) and mRNA Human Gene Expression Microarray (V4.0,4 × 180K), including the global profiling of 170,340 circRNAs and 34,235 coding transcripts (from 21,901 genes).

Techniques:

Journal: Journal of Cellular and Molecular Medicine

Article Title: Circular RNA circANAPC2 mediates the impairment of endochondral ossification by miR‐874‐3p/SMAD3 signalling pathway in idiopathic short stature

doi: 10.1111/jcmm.16419

Figure Lengend Snippet: Microarray analysis of differentially expressed circRNAs. A, Four pairs of ISS patients and age‐/sex‐matched controls were screened via circRNA microarray analysis. Thirty differentially expressed circRNAs were shown, including top 22 up‐regulated circRNAs and top 8 down‐regulated circRNAs. B, 145 circRNAs were significantly differentially expressed, including 83 up‐regulation and 62 down‐regulation. C, D, The top 30 KEGG pathway and GO enrichment are exhibited. The ubiquitin‐mediated proteolysis and Wnt signalling pathway are closely associated with chondrocyte proliferation, hypertrophy and endochondral ossification. CircRNAs, circular RNAs; KEGG, Kyoto Encyclopedia of Genes and Genomes; GO, Gene ontology; and Wnt, wingless/integrated

Article Snippet: The labelled coding RNAs were then hybridized onto the Human circRNAs Array v2 (8 × 15 K, Arraystar).

Techniques: Microarray