Journal: Frontiers in Genetics

Article Title: Expression Profile and Potential Function of Circular RNAs in Peripheral Blood Mononuclear Cells in Male Patients With Primary Gout

doi: 10.3389/fgene.2021.728091

Figure Lengend Snippet: Primer sequences used in the validation of circRNAs.

Article Snippet: We used the Arraystar Human circRNA Array v2 chip (8 × 15 K) (Arraystar, Rockville, MD, United States), which contains 13,617 human circRNA probes.

Techniques: Biomarker Discovery, Sequencing

Journal: Frontiers in Genetics

Article Title: Expression Profile and Potential Function of Circular RNAs in Peripheral Blood Mononuclear Cells in Male Patients With Primary Gout

doi: 10.3389/fgene.2021.728091

Figure Lengend Snippet: The top 15 upregulated and 15 downregulated circRNAs in gout patients compared with healthy control subjects.

Article Snippet: We used the Arraystar Human circRNA Array v2 chip (8 × 15 K) (Arraystar, Rockville, MD, United States), which contains 13,617 human circRNA probes.

Techniques: Control

Journal: Frontiers in Genetics

Article Title: Expression Profile and Potential Function of Circular RNAs in Peripheral Blood Mononuclear Cells in Male Patients With Primary Gout

doi: 10.3389/fgene.2021.728091

Figure Lengend Snippet: Expression profiles of circRNAs in gout patients compared with healthy controls. (A) Scatter plot demonstrating the heterogeneity of the expression of circRNAs in the gout and HC groups. The values of the X and Y axes represent the averaged normalized signal values of the groups (log2-scaled). The green line represents 1.5-fold changes. The expression of circRNAs above the top green line and below the bottom green line indicates changes by > 2-fold between the two groups. (B) Volcano plots visualizing differentially expressed circRNAs between the two groups. The vertical lines correspond to 1.5-fold up- and downregulated circRNA expression. The horizontal line represents a p -value of 0.05. The red point in the plot represents significantly differentially expressed circRNAs. (C) Clustered heatmap showing the relationships among the expression levels of samples. Expression values are represented by the color scale. The intensity increases from green (relatively low expression) to red (relatively high expression). Each column represents one sample, and each row represents a single circRNA. (D) Genomic region distribution of upregulated circRNAs. (E) Genomic region distribution of downregulated circRNAs. (F) Distribution of significantly dysregulated circRNAs in chromosomes. (G) Relative expression levels of the six circRNAs in five gout patients and three healthy control (HC) subjects. The Y-axis represents the ratio of the relative expression level of circRNAs in the gout group to that of the HC group. Gout: primary gout; HC: healthy controls.

Article Snippet: We used the Arraystar Human circRNA Array v2 chip (8 × 15 K) (Arraystar, Rockville, MD, United States), which contains 13,617 human circRNA probes.

Techniques: Expressing, Control

Journal: Frontiers in Genetics

Article Title: Expression Profile and Potential Function of Circular RNAs in Peripheral Blood Mononuclear Cells in Male Patients With Primary Gout

doi: 10.3389/fgene.2021.728091

Figure Lengend Snippet: Prediction and annotation of hsa_circRNA_103657 and hsa_circRNA_000241 ceRNA mechanism. (A) Construction of the circRNA-miRNA-mRNA network: the network of ceRNA includes 2 circRNAs, 10 miRNAs, and 525 mRNAs. (B) Schematic diagram of the gene category of the PI3K-Akt signaling pathway, which is the top enriched term in the KEGG pathway analysis. Image from the Kyoto Encyclopedia of Genes and Genomes (KEGG) resource ( http://www.genome.jp/kegg/ ).

Article Snippet: We used the Arraystar Human circRNA Array v2 chip (8 × 15 K) (Arraystar, Rockville, MD, United States), which contains 13,617 human circRNA probes.

Techniques:

Journal: Frontiers in Genetics

Article Title: Expression Profile and Potential Function of Circular RNAs in Peripheral Blood Mononuclear Cells in Male Patients With Primary Gout

doi: 10.3389/fgene.2021.728091

Figure Lengend Snippet: Clinical significance of hsa_circRNA_103657 and hsa_circRNA_000241 in primary gout (A,B,C,D) Correlations between the expression levels of circRNAs (hsa_circRNA_103657 and hsa_circRNA_000241) and laboratory data of gout, analyzed using Spearman’s coefficient. (E, F) Receiver operating characteristic (ROC) curve for the analysis of the diagnostic value of hsa_circRNA_103657 and hsa_circRNA_000241 for primary gout. AUC: area under the curve.

Article Snippet: We used the Arraystar Human circRNA Array v2 chip (8 × 15 K) (Arraystar, Rockville, MD, United States), which contains 13,617 human circRNA probes.

Techniques: Expressing, Diagnostic Assay

Journal: Discover Oncology

Article Title: Hsa_circ_0072732 enhances sunitinib resistance of renal cell carcinoma by inhibiting ferroptosis

doi: 10.1007/s12672-024-01580-2

Figure Lengend Snippet: Hsa_circ_0072732 was upregulated in RCC. A The upregulated circRNAs analysis in GSE108735 and GSE100186. GSE100186: eight renal celar cell carcinoma tissues from CCRCC surgery were distributed into two experimental groups: tumor tissue group and normal tissue group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar). GSE108735:seven paired frozen carcinoma tissues as well as normal tissues from patients with renal cell carcinoma were used for circRNA profiling by second generation of RNA sequencing. B The expressions of Hsa_circ_0072732 were detected using qRT-PCR in RCC and normal renal epithelial cell line KiMA. C , D Actinomycin D assays were performed in 786-O and Caki-1. qRT-PCR was used for detection. E , F RNase R assays were performed in 786-O and Caki-1. qRT-PCR was used for detection. *P < 0.05; **P < 0.01; ***P < 0.001

Article Snippet: GSE100186: eight renal celar cell carcinoma tissues from CCRCC surgery were distributed into two experimental groups: tumor tissue group and normal tissue group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar).

Techniques: RNA Sequencing Assay, Quantitative RT-PCR

Journal: Molecular Cancer

Article Title: A novel protein encoded by a circular RNA circPPP1R12A promotes tumor pathogenesis and metastasis of colon cancer via Hippo-YAP signaling

doi: 10.1186/s12943-019-1010-6

Figure Lengend Snippet: CircRNA expression profile in CC and characterization of circPPP1R12A. a Heatmap of the differentially expressed circRNAs in 10 pairs of human CC tissues and matched non-tumor tissues. b Classification of dysregulated circRNAs. c CircPPP1R12A was back-spliced by exons 24 and 25 of PPP1R12A gene located at 12q21.2. d The expression level of circPPP1R12A in CC and matched non-tumor tissue samples from 20 patients was analyzed by real-time PCR. e The expression level of circPPP1R12A in a series of cultured CC cell lines (HT-29, HCT-116, SW480, SW620, LoVo, SW48, DLD-1, Caco2 and HCT-15) was analyzed by real-time PCR. *** P < 0.001

Article Snippet: The circRNA microarray (Arraystar Human circRNAs chip, ArrayStar) consisting of more than 5000 probes specific to splicing sites of human circRNAs was used.

Techniques: Expressing, Real-time Polymerase Chain Reaction, Cell Culture

Journal: Molecular Cancer

Article Title: A novel protein encoded by a circular RNA circPPP1R12A promotes tumor pathogenesis and metastasis of colon cancer via Hippo-YAP signaling

doi: 10.1186/s12943-019-1010-6

Figure Lengend Snippet: Characterization the existence and subcellular distribution of circPPP1R12A in CC cells and tissues. a The divergent primers detected circPPP1R12A in cDNA but not in gDNA. b Real-time PCR analysis of circPPP1R12A and linear PPP1R12A mRNA after treatment with RNase R in HCT-116 cells showed that circPPP1R12A was resistant to RNase R treatment. The sub-cellular distribution of circPPP1R12A was mostly present in the cytoplasm by the nuclear mass separation assay ( c ) and FISH ( d ). e The level of circPPP1R12A was analyzed by in situ hybridization on CC tissue microarray, showing that circPPP1R12A was up-regulated in CC tissues compared with normal tissues, and such up-regulation was positively correlated with larger tumors and a higher TNM stage. f Kaplan–Meier analysis of the correlation between circPPP1R12A expression and overall survival showed that patients with higher levels of circPPP1R12A had a significantly shorter overall survival. *** P < 0.001

Article Snippet: The circRNA microarray (Arraystar Human circRNAs chip, ArrayStar) consisting of more than 5000 probes specific to splicing sites of human circRNAs was used.

Techniques: Real-time Polymerase Chain Reaction, In Situ Hybridization, Microarray, Expressing

Journal: Molecular Cancer

Article Title: A novel protein encoded by a circular RNA circPPP1R12A promotes tumor pathogenesis and metastasis of colon cancer via Hippo-YAP signaling

doi: 10.1186/s12943-019-1010-6

Figure Lengend Snippet: CircRNA circPPP1R12A encodes a small unchartered protein circPPP1R12A-73aa. a The 1138-nt circPPP1R12A was potentially translated into a 73-aa (~ 10 kDa) protein (circPPP1R12A-73aa). b To establish a detectable PPP1R12A-C expression vector, flag-labeled circPPP1R12A sequence was cloned into a CMV-induced expression vector (Lv-flag-circPPP1R12A). For the circPPP1R12A-73aa deleted circPPP1R12A expression vector, flag-labeled circPPP1R12A sequence with start codon mutant (ATG/ACG) was cloned into a CMV-induced expression vector (Lv-flag-circPPP1R12A-Mut). For the circPPP1R12A-73aa positive control, the flag-labeled circPPP1R12A-73aa sequence was cloned into a CMV-induced expression vector (Lv- circPPP1R12A-73aa). The schematic structure of these vectors was shown. c The expression level of circPPP1R12A was analyzed by real-time PCR. d The expression level of flag-indicated circPPP1R12A-73aa was detected by Western blotting analysis. e The pulldown cell lysates from indicated groups were separated by SDS-PAGE. Protein bands at 10 kDa were manually excised and submitted for identification by LC-MS/MS. f LC-MS/MS-identified sequences covered 76% of the aa sequences of circPPP1R12A-73aa. Unique aa sequences of spectrum (GRLRHVNCLSPGVQD) formed by circular junction of circPPP1R12A-73aa are shown. The data are represented as the means ± SEM; * P < 0.05, ** P < 0.01, *** P < 0.001

Article Snippet: The circRNA microarray (Arraystar Human circRNAs chip, ArrayStar) consisting of more than 5000 probes specific to splicing sites of human circRNAs was used.

Techniques: Expressing, Plasmid Preparation, Labeling, Sequencing, Clone Assay, Mutagenesis, Positive Control, Real-time Polymerase Chain Reaction, Western Blot, SDS Page, Liquid Chromatography with Mass Spectroscopy

Journal: Molecular Cancer

Article Title: A novel protein encoded by a circular RNA circPPP1R12A promotes tumor pathogenesis and metastasis of colon cancer via Hippo-YAP signaling

doi: 10.1186/s12943-019-1010-6

Figure Lengend Snippet: CircRNA circPPP1R12A promotes the cell proliferation, but not migration and invasion abilities of CC cells. a Schematic illustration and real-time PCR confirmation showing circPPP1R12A overexpression in DLD-1 and Caco-2 cells. b CircPPP1R12A promoted the proliferation of DLD-1 and Caco-2 cells shown by CCK8 assay. c CircPPP1R12A promoted the proliferation of DLD-1 and Caco-2 cells shown by colony formation assay. d CircPPP1R12A did not affect the migration of DLD-1 and Caco-2 cells shown by wound healing assay. e CircPPP1R12A did not affect the invasion of DLD-1 and Caco-2 cells shown by matrigel assay. The data are represented as the means ± SEM; * P < 0.05

Article Snippet: The circRNA microarray (Arraystar Human circRNAs chip, ArrayStar) consisting of more than 5000 probes specific to splicing sites of human circRNAs was used.

Techniques: Migration, Real-time Polymerase Chain Reaction, Over Expression, CCK-8 Assay, Colony Assay, Wound Healing Assay, Matrigel Assay

Journal: Frontiers in Oncology

Article Title: CircRNA_036186 mediates HNSCC progression by regulating 14-3-3ζ

doi: 10.3389/fonc.2024.1498139

Figure Lengend Snippet: Identification of circRNA_036186-miR-193b-3p-14-3-3ζ-regulatory axis. (A) The heatmap illustrates the expression profiles of 287 circRNAs, of which 146 exhibited increased expression and 141 exhibited decreased expression. The colouration gradually transitions from blue to red, indicating increased expression. (B) The five most highly ranked circRNAs and their target miRNAs, each corresponding to a node, are shown with two interacting genes based on base sequence pairing connected by a solid line. (C) The intersection results of the HNSCC occurrence and development group, the prognosis group, and the competing endogenous RNA networks in OncomiR. (D) The predicted target mRNAs from three databases—Wayne ’ s map, miR-193b-3pmicroT-CDS, Tarbase, and TargetScan—were taken as intersections. (E) A search of the Tarbase database revealed that miR-193b-3p has a base sequence that binds and interacts with the 14-3-3ζ target. (F, G) The results of the RT-PCR experiments indicated that circRNA_036186 and miR-193b-3p exhibited elevated expression in HNSCC tissues relative to paracancerous tissues in five pairs of HNSCC and paracancerous tissue samples. (H, I) The results of RT-PCR experiments indicated that the mRNA expression of circRNA_036186 and miR-193b-3p was markedly elevated in all three HNSCC cell lines relative to HOK. (n=3, * p <0.05, ** p <0.01, *** p <0.001, **** p <0.0001).

Article Snippet: We used the Arratstar Super RNA Labeling Kit to amplify the enriched circRNA, which was then transcribed into fluorescent cRNA.The labelled cRNA was hybridised to the Arraystar Human circRNA V2 chip.

Techniques: Expressing, Sequencing, Reverse Transcription Polymerase Chain Reaction

Journal: Frontiers in Oncology

Article Title: CircRNA_036186 mediates HNSCC progression by regulating 14-3-3ζ

doi: 10.3389/fonc.2024.1498139

Figure Lengend Snippet: Top 5 circRNA.

Article Snippet: We used the Arratstar Super RNA Labeling Kit to amplify the enriched circRNA, which was then transcribed into fluorescent cRNA.The labelled cRNA was hybridised to the Arraystar Human circRNA V2 chip.

Techniques:

Journal: Frontiers in Oncology

Article Title: CircRNA_036186 mediates HNSCC progression by regulating 14-3-3ζ

doi: 10.3389/fonc.2024.1498139

Figure Lengend Snippet: Effect of down-regulation of circRNA_0361863p and miR-193b-3p on 14-3-3ζ in HSC2. (A) The results of the RT-PCR experiment indicated that si-circ_0036186 had been successfully transfected into HSC2. (B) The results of the RT-PCR experiments indicated that miR-193b-3p had been successfully transfected into HSC2. (C) Reverse transcription polymerase chain reaction (RT-PCR) experiments were conducted to ascertain the impact of transfection on 14-3-3ζ mRNA expression. (D, E) Western blotting experiments were conducted to ascertain the impact of transfection on 14-3-3ζ protein expression. (n=3, * p <0.05, *** p <0.001, **** p <0.0001).

Article Snippet: We used the Arratstar Super RNA Labeling Kit to amplify the enriched circRNA, which was then transcribed into fluorescent cRNA.The labelled cRNA was hybridised to the Arraystar Human circRNA V2 chip.

Techniques: Reverse Transcription Polymerase Chain Reaction, Transfection, Reverse Transcription, Polymerase Chain Reaction, Expressing, Western Blot

Journal: Frontiers in Oncology

Article Title: CircRNA_036186 mediates HNSCC progression by regulating 14-3-3ζ

doi: 10.3389/fonc.2024.1498139

Figure Lengend Snippet: Effect of down-regulation of circRNA_0361863p and miR-193b-3p on the proliferation, migration, invasion, and scratch healing rate of HSC2 cells. (A–D) The Transwell assay assessed the impact of circRNA_0361863p and miR-193b-3p down-regulation on cell migration and invasion of HSC2. (E, F) The Scratch test assessed the scratch healing rate of HSC2 after the down-regulation of circRNA_0361863p and miR-193b-3p. (G) The cell activity of HSC2 was evaluated after the down-regulation of circRNA_0361863p and miR-193b-3p through CCK-8 experiments. (n=3, **** p <0.0001).

Article Snippet: We used the Arratstar Super RNA Labeling Kit to amplify the enriched circRNA, which was then transcribed into fluorescent cRNA.The labelled cRNA was hybridised to the Arraystar Human circRNA V2 chip.

Techniques: Migration, Transwell Assay, Activity Assay, CCK-8 Assay

Journal: Molecular Therapy. Nucleic Acids

Article Title: The circular RNA Ataxia Telangiectasia Mutated regulates oxidative stress in smooth muscle cells in expanding abdominal aortic aneurysms

doi: 10.1016/j.omtn.2023.08.017

Figure Lengend Snippet: Circular RNAs are deregulated in human abdominal aortic aneurysm (A) Volcano plot depicting downregulated (51, blue) and upregulated (40, red). Circular RNAs (circRNAs) in human elective human abdominal aortic aneurysm (eAAA, n = 11) vs . control (CTRL, n = 6) aorta specimens, as resulted by array experiments. Log2 fold change and -log10 p value are plotted on the x and y axes, respectively. IDs of circRNAs meant for a first round of validation are highlighted. Statistics: unpaired t test; p values <0.05 are considered significant. (B) Pie chart illustrating the proportion of exonic (89.8%), intronic (5.7%), sense overlapping (3.4%), and antisense (1.1%) array-identified differentially expressed circRNAs. Absolute numbers are further indicated for each group. (C) Real-time quantitative PCR (qPCR) validation of hsa_circ_0005660 (c NFIX ), hsa_circ_0003641 (c ATM ), hsa_circ0042103 (c MYOCD ), hsa_circ003218 (c BMPR2 ), hsa_circ0004771 (c NRIP1 ), and hsa_circ0005615 (c NFATC3 ) differential expression in human eAAA (N = 8) and CTRL (N = 4) aortas. 2 –ddCT was calculated by normalizing on RPLPO . Data are represented as mean ± SEM. Statistics: unpaired t test; p values <0.05 are considered significant. NS, not significant; eAAA, elective AAA.

Article Snippet: The resulting labeled cDNA was then purified and 1 μg was fragmented, heated, and subsequently hybridized with an 8 × 15k commercially available array chip displaying 13,617 human circRNAs (Arraystar, no. AS-S-CR-H-V2.0) for 17 h at 65°C in an Agilent Hybridization Oven.

Techniques: Control, Biomarker Discovery, Real-time Polymerase Chain Reaction, Quantitative Proteomics

Journal: Cancer Cell International

Article Title: A 3-circular RNA signature as a noninvasive biomarker for diagnosis of colorectal cancer

doi: 10.1186/s12935-019-0995-7

Figure Lengend Snippet: Profiling of circRNAs in the plasmas from GC patients CRC and normal plasma and the biological structure of circRNAs. a Volcano plot displays the circRNAs differentially expressed (fold change > 2) between CRC and normal plasma (P < 0.05). b Heat map shows the top 20 dysregulated circRNAs between CRC and normal plasma. c Schematics shows the biological structure of hsa_circ¬_0082182, hsa_circ¬_0000370, and hsa_circ¬_0035445

Article Snippet: The Arraystar human circular RNAs array chips (Arraystar Human circRNAs chip; AS-S-CR-H-V2.0, ArrayStar Inc., Rockville, MD, USA), which contains 13, 617 circRNAs and 5261 probes for circRNAs specific splicing sites were applied.

Techniques: Clinical Proteomics

Journal: Cancer Cell International

Article Title: A 3-circular RNA signature as a noninvasive biomarker for diagnosis of colorectal cancer

doi: 10.1186/s12935-019-0995-7

Figure Lengend Snippet: ROC curves analysis of hsa_circ_0082182, hsa_circ_0000370, hsa_circ-_0035445, and mixture of these three circRNAs ( a – d )

Article Snippet: The Arraystar human circular RNAs array chips (Arraystar Human circRNAs chip; AS-S-CR-H-V2.0, ArrayStar Inc., Rockville, MD, USA), which contains 13, 617 circRNAs and 5261 probes for circRNAs specific splicing sites were applied.

Techniques:

Journal: Cancer Cell International

Article Title: A 3-circular RNA signature as a noninvasive biomarker for diagnosis of colorectal cancer

doi: 10.1186/s12935-019-0995-7

Figure Lengend Snippet: The expression of circRNAs (hsa_circ_0082182, hsa_circ_0000370, and hsa_circ_0035445) in the plasma of CRC patients before and after surgery ( a – c )

Article Snippet: The Arraystar human circular RNAs array chips (Arraystar Human circRNAs chip; AS-S-CR-H-V2.0, ArrayStar Inc., Rockville, MD, USA), which contains 13, 617 circRNAs and 5261 probes for circRNAs specific splicing sites were applied.

Techniques: Expressing, Clinical Proteomics

Journal: Cancer Cell International

Article Title: A 3-circular RNA signature as a noninvasive biomarker for diagnosis of colorectal cancer

doi: 10.1186/s12935-019-0995-7

Figure Lengend Snippet: Functional analysis for three circRNAs. a GO and KEGG analysis of hsa_circ_0082182 based on the ceRNA network. b GO and KEGG analysis of hsa_circ_0000370 based on the ceRNA network. c GO and KEGG analysis of hsa_circ_0035445 based on the ceRNA network

Article Snippet: The Arraystar human circular RNAs array chips (Arraystar Human circRNAs chip; AS-S-CR-H-V2.0, ArrayStar Inc., Rockville, MD, USA), which contains 13, 617 circRNAs and 5261 probes for circRNAs specific splicing sites were applied.

Techniques: Functional Assay

Journal: Journal of Cancer

Article Title: Emerging roles of circRNA in formation and progression of cancer

doi: 10.7150/jca.30828

Figure Lengend Snippet: Overview of deregulated circRNAs in HCC

Article Snippet: The circRNAs chip (Arraystar Human circRNAs chip, ArrayStar) containing 5396 probes specific for human circular RNAs splicing sites can be used to investigate different expressions of circRNAs between tumor tissues and normal tissues.

Techniques: Expressing

Journal: Journal of Cancer

Article Title: Emerging roles of circRNA in formation and progression of cancer

doi: 10.7150/jca.30828

Figure Lengend Snippet: Overview of deregulated circRNAs in GC

Article Snippet: The circRNAs chip (Arraystar Human circRNAs chip, ArrayStar) containing 5396 probes specific for human circular RNAs splicing sites can be used to investigate different expressions of circRNAs between tumor tissues and normal tissues.

Techniques: Expressing

Journal: Journal of Cancer

Article Title: Emerging roles of circRNA in formation and progression of cancer

doi: 10.7150/jca.30828

Figure Lengend Snippet: Overview of deregulated circRNAs in CRC

Article Snippet: The circRNAs chip (Arraystar Human circRNAs chip, ArrayStar) containing 5396 probes specific for human circular RNAs splicing sites can be used to investigate different expressions of circRNAs between tumor tissues and normal tissues.

Techniques: Expressing

Journal: Discover Oncology

Article Title: Hsa_circ_0072732 enhances sunitinib resistance of renal cell carcinoma by inhibiting ferroptosis

doi: 10.1007/s12672-024-01580-2

Figure Lengend Snippet: Hsa_circ_0072732 was upregulated in RCC. A The upregulated circRNAs analysis in GSE108735 and GSE100186. GSE100186: eight renal celar cell carcinoma tissues from CCRCC surgery were distributed into two experimental groups: tumor tissue group and normal tissue group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar). GSE108735:seven paired frozen carcinoma tissues as well as normal tissues from patients with renal cell carcinoma were used for circRNA profiling by second generation of RNA sequencing. B The expressions of Hsa_circ_0072732 were detected using qRT-PCR in RCC and normal renal epithelial cell line KiMA. C , D Actinomycin D assays were performed in 786-O and Caki-1. qRT-PCR was used for detection. E , F RNase R assays were performed in 786-O and Caki-1. qRT-PCR was used for detection. *P < 0.05; **P < 0.01; ***P < 0.001

Article Snippet: GSE100186: eight renal celar cell carcinoma tissues from CCRCC surgery were distributed into two experimental groups: tumor tissue group and normal tissue group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar).

Techniques: RNA Sequencing, Quantitative RT-PCR