Journal: International Journal of Molecular Sciences

Article Title: Differential Expression of Peroxisomal Proteins in Distinct Types of Parotid Gland Tumors

doi: 10.3390/ijms22157872

Figure Lengend Snippet: Peroxisomal ether lipid and cholesterol synthesis in PMA. The mRNA expression by real-time PCR analysis of ( A ) Agps (** p = 0.0018), ( B ) Hmgcr (* p = 0.0235) and Pmvk (* p = 0.0478) are expressed lower while Gnpat (*** p = 0.0004) ( A ), Hmgcs, Idi (* p = 0.0155), Fdps (* p = 0.0257) and Sqs (** p = 0.0059) ( B ) are expressed higher in PMA than in healthy tissue. (Explanation of the notations: The number of asterices signifies the degree of significance of the p -value, while # means not significant.)

Article Snippet: Alkylglycerone-phosphate synthase (AGPS) , Mouse, monoclonal , 78 kDa , 1:1000 , 1:500 , Santa cruz, Cat no: sc-374201.

Techniques: Expressing, Real-time Polymerase Chain Reaction

Journal: International Journal of Molecular Sciences

Article Title: Differential Expression of Peroxisomal Proteins in Distinct Types of Parotid Gland Tumors

doi: 10.3390/ijms22157872

Figure Lengend Snippet: List of antibodies used for the detection of peroxisomal proteins in the parotid gland.

Article Snippet: Alkylglycerone-phosphate synthase (AGPS) , Mouse, monoclonal , 78 kDa , 1:1000 , 1:500 , Santa cruz, Cat no: sc-374201.

Techniques: Molecular Weight, Phospho-proteomics, Marker

Journal: International Journal of Molecular Sciences

Article Title: Differential Expression of Peroxisomal Proteins in Distinct Types of Parotid Gland Tumors

doi: 10.3390/ijms22157872

Figure Lengend Snippet: List of the human primers used for qPCR analyses.

Article Snippet: Alkylglycerone-phosphate synthase (AGPS) , Mouse, monoclonal , 78 kDa , 1:1000 , 1:500 , Santa cruz, Cat no: sc-374201.

Techniques:

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression profile of circRNAs in the human thyroid cancer cell line FRO

doi: 10.3892/ol.2018.8356

Figure Lengend Snippet: Primer sequences.

Article Snippet: FRO cells were cultured in a 6-well plate for 24 h, and then transfected with an AGPS short hairpin (sh)RNA plasmid (sc-94310-SH; Santa Cruz Biotechnology, Inc., Dallas, TX, USA) (AGPS sh group) or with an AGPS clustered regularly interspaced short palindromic repeats-associated protein-9 nuclease knockout (KO) plasmid (sc-404604; Santa Cruz Biotechnology, Inc.) (AGPS KO group), according to the manufacturer's protocol.

Techniques: Sequencing

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression profile of circRNAs in the human thyroid cancer cell line FRO

doi: 10.3892/ol.2018.8356

Figure Lengend Snippet: Expression of AGPS in thyroid cancer cell lines. AGPS expression in the thyroid cancer cell lines TPC-1, FTC-133 and FRO was evaluated using reverse transcription-quantitative polymerase chain reaction analysis. *P<0.05 vs. TPC-1. AGPS, alkylglycerone phosphate synthase.

Article Snippet: FRO cells were cultured in a 6-well plate for 24 h, and then transfected with an AGPS short hairpin (sh)RNA plasmid (sc-94310-SH; Santa Cruz Biotechnology, Inc., Dallas, TX, USA) (AGPS sh group) or with an AGPS clustered regularly interspaced short palindromic repeats-associated protein-9 nuclease knockout (KO) plasmid (sc-404604; Santa Cruz Biotechnology, Inc.) (AGPS KO group), according to the manufacturer's protocol.

Techniques: Expressing, Reverse Transcription, Real-time Polymerase Chain Reaction

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression profile of circRNAs in the human thyroid cancer cell line FRO

doi: 10.3892/ol.2018.8356

Figure Lengend Snippet: Heatmap of circRNA expression data. The different expressions of circRNAs were depicted in the heatmap. Green represents a decreased expression of circRNAs and red represents an increased expression of circRNAs. Cluster analysis demonstrated that AGPS sh and AGPS KO could induce the alteration in circRNAs expression in FRO cells. circRNA, circular RNA; AGPS, alkylglycerone phosphate synthase; sh, short hairpin; KO, knockout.

Article Snippet: FRO cells were cultured in a 6-well plate for 24 h, and then transfected with an AGPS short hairpin (sh)RNA plasmid (sc-94310-SH; Santa Cruz Biotechnology, Inc., Dallas, TX, USA) (AGPS sh group) or with an AGPS clustered regularly interspaced short palindromic repeats-associated protein-9 nuclease knockout (KO) plasmid (sc-404604; Santa Cruz Biotechnology, Inc.) (AGPS KO group), according to the manufacturer's protocol.

Techniques: Expressing, Knock-Out

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression profile of circRNAs in the human thyroid cancer cell line FRO

doi: 10.3892/ol.2018.8356

Figure Lengend Snippet: Comparison of differentially expressed circRNAs. (A) Differentially expressed circRNAs among the different groups were identified by scatter plots. The orange points represent >2-fold upregulation, whereas the blue points represent >2-fold downregulation. (B) Differences in circRNA expression among the three groups. circRNA, circular RNA; AGPS, alkylglycerone phosphate synthase; sh, short hairpin; KO, knockout.

Article Snippet: FRO cells were cultured in a 6-well plate for 24 h, and then transfected with an AGPS short hairpin (sh)RNA plasmid (sc-94310-SH; Santa Cruz Biotechnology, Inc., Dallas, TX, USA) (AGPS sh group) or with an AGPS clustered regularly interspaced short palindromic repeats-associated protein-9 nuclease knockout (KO) plasmid (sc-404604; Santa Cruz Biotechnology, Inc.) (AGPS KO group), according to the manufacturer's protocol.

Techniques: Comparison, Expressing, Knock-Out

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression profile of circRNAs in the human thyroid cancer cell line FRO

doi: 10.3892/ol.2018.8356

Figure Lengend Snippet: Venn diagrams of differentially expressed circular RNAs in the three groups. The Venn diagrams represent the shared modified genes between groups: AGPS_sh vs. control; AGPS_KO vs. control; and AGPS_sh vs. AGPS_KO, in FRO cell lines. AGPS, alkylglycerone phosphate synthase; sh, short hairpin; KO, knockout.

Article Snippet: FRO cells were cultured in a 6-well plate for 24 h, and then transfected with an AGPS short hairpin (sh)RNA plasmid (sc-94310-SH; Santa Cruz Biotechnology, Inc., Dallas, TX, USA) (AGPS sh group) or with an AGPS clustered regularly interspaced short palindromic repeats-associated protein-9 nuclease knockout (KO) plasmid (sc-404604; Santa Cruz Biotechnology, Inc.) (AGPS KO group), according to the manufacturer's protocol.

Techniques: Modification, Control, Knock-Out

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression profile of circRNAs in the human thyroid cancer cell line FRO

doi: 10.3892/ol.2018.8356

Figure Lengend Snippet: Top 50 differentially expressed circRNAs in AGPS sh and AGPS KO human thyroid cancer FRO cells.

Article Snippet: FRO cells were cultured in a 6-well plate for 24 h, and then transfected with an AGPS short hairpin (sh)RNA plasmid (sc-94310-SH; Santa Cruz Biotechnology, Inc., Dallas, TX, USA) (AGPS sh group) or with an AGPS clustered regularly interspaced short palindromic repeats-associated protein-9 nuclease knockout (KO) plasmid (sc-404604; Santa Cruz Biotechnology, Inc.) (AGPS KO group), according to the manufacturer's protocol.

Techniques: Control

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression profile of circRNAs in the human thyroid cancer cell line FRO

doi: 10.3892/ol.2018.8356

Figure Lengend Snippet: Validation of differentially expressed circRNAs using RT-qPCR. The top 10 circRNAs with increased and decreased expression in the AGPS KO group compared with the control group by RT-qPCR were identified. *P<0.05 vs. control. circRNA, circular RNA; RT-qPCR, reverse transcription-quantitative polymerase chain reaction; AGPS, alkylglycerone phosphate synthase; sh, short hairpin; KO, knockout; hsa, Homo sapiens .

Article Snippet: FRO cells were cultured in a 6-well plate for 24 h, and then transfected with an AGPS short hairpin (sh)RNA plasmid (sc-94310-SH; Santa Cruz Biotechnology, Inc., Dallas, TX, USA) (AGPS sh group) or with an AGPS clustered regularly interspaced short palindromic repeats-associated protein-9 nuclease knockout (KO) plasmid (sc-404604; Santa Cruz Biotechnology, Inc.) (AGPS KO group), according to the manufacturer's protocol.

Techniques: Biomarker Discovery, Quantitative RT-PCR, Expressing, Control, Reverse Transcription, Real-time Polymerase Chain Reaction, Knock-Out

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression profile of circRNAs in the human thyroid cancer cell line FRO

doi: 10.3892/ol.2018.8356

Figure Lengend Snippet: GO analysis of AGPS silencing in thyroid cancer FRO cells. GO analysis was performed on the up- and downregulated genes identified in the AGPS sh, AGPS KO and control thyroid cancer FRO cells. The y-axis represented gene ontology entries, the x-axis represented -log10 (P-value). -log10 (P-value) >2 was considered to indicate a significant threshold. (A) Upregulation and (B) downregulation of MF, BP and CC by GO analysis of AGPS silencing in FRO cells compared with control thyroid cancer FRO cells. (C) Upregulation and (D) downregulation of MF, BP and CC by GO analysis of AGPS silencing in FRO cells compared with AGPS KO in thyroid cancer FRO cells. (E) Upregulation and (F) downregulation of MF, BP and CC by GO analysis of AGPS KO compared with control thyroid cancer FRO cells. GO, Gene Ontology; AGPS, alkylglycerone phosphate synthase; sh, short hairpin; KO, knockout; MF, molecular function; BP, biological process; CC, cellular component.

Article Snippet: FRO cells were cultured in a 6-well plate for 24 h, and then transfected with an AGPS short hairpin (sh)RNA plasmid (sc-94310-SH; Santa Cruz Biotechnology, Inc., Dallas, TX, USA) (AGPS sh group) or with an AGPS clustered regularly interspaced short palindromic repeats-associated protein-9 nuclease knockout (KO) plasmid (sc-404604; Santa Cruz Biotechnology, Inc.) (AGPS KO group), according to the manufacturer's protocol.

Techniques: Control, Knock-Out

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression profile of circRNAs in the human thyroid cancer cell line FRO

doi: 10.3892/ol.2018.8356

Figure Lengend Snippet: KEGG pathway enrichment analysis of AGPS silencing in thyroid cancer FRO cells. KEGG pathway enrichment analysis is represented by histograms and scatter diagrams. Orange represents the pathway of upregulation gene enrichment, whereas blue represents the downregulated pathway of gene enrichment. The left and right sides of the scatter diagrams correspond to the downregulated and upregulated gene enrichment pathways, respectively. The x-axes represent the proportion of enriched genes, whereas the y-axes contain the name of the KEGG pathway. If up- or downregulated genes were enriched in a certain pathway, this pathway was represented as a point in the graph, the color of which indicated a significant P-value, whereas its size represented the number of differentially expressed genes in that particular pathway. Effect of regulatory function and signaling pathway by KEGG pathway enrichment analysis of AGPS silencing compared with (A) control and (B) KO thyroid cancer FRO cells. (C) Effect of regulatory function and signaling pathway by KEGG pathway enrichment analysis of AGPS KO compared with control thyroid cancer FRO cells. KEGG, Kyoto Encyclopedia of Genes and Genomes; AGPS, alkylglycerone phosphate synthase; KO, knockout; hsa, Homo sapiens .

Article Snippet: FRO cells were cultured in a 6-well plate for 24 h, and then transfected with an AGPS short hairpin (sh)RNA plasmid (sc-94310-SH; Santa Cruz Biotechnology, Inc., Dallas, TX, USA) (AGPS sh group) or with an AGPS clustered regularly interspaced short palindromic repeats-associated protein-9 nuclease knockout (KO) plasmid (sc-404604; Santa Cruz Biotechnology, Inc.) (AGPS KO group), according to the manufacturer's protocol.

Techniques: Control, Knock-Out

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

doi: 10.3892/ol.2020.11927

Figure Lengend Snippet: Effect of AGPS silencing on the expression levels of AGPS in glioma cells. Western blotting identified significantly downregulated expression levels of AGPS in AGPS-silenced U251 cells. n=3 *P<0.05 vs. control; # P<0.05 vs. shR-AGPS-1 group. shR, short hairpin RNA; AGPS, alkylglycerone phosphate synthase.

Article Snippet: AGPS shRNA lentiviral particles (shR-AGPS-1 and −2 groups; Santa Cruz Biotechnology, Inc.) or empty lentiviral particles used as a negative control (control group; Santa Cruz Biotechnology, Inc.) stably integrated cell lines were established following infection with 8 μg/ml lentiviruses of U251 cells using 5 μg/ml polybrene-containing RPMI-1640 medium.

Techniques: Expressing, Western Blot, Control, shRNA

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

doi: 10.3892/ol.2020.11927

Figure Lengend Snippet: Effect of AGPS silencing on the cellular morphology of U251 cells. (A) Morphological observation under the microscope in AGPS-silenced U251 cells. Magnification, ×100 or ×200. (B) BrdU assay results revealed a significant inhibition over the proliferation of AGPS-silenced U251 cells. n=10. *P<0.05 shR-2 vs. shR-1, # P<0.05 shR-1 vs. control. shR, short hairpin RNA; AGPS, alkylglycerone phosphate synthase; OD, optical density.

Article Snippet: AGPS shRNA lentiviral particles (shR-AGPS-1 and −2 groups; Santa Cruz Biotechnology, Inc.) or empty lentiviral particles used as a negative control (control group; Santa Cruz Biotechnology, Inc.) stably integrated cell lines were established following infection with 8 μg/ml lentiviruses of U251 cells using 5 μg/ml polybrene-containing RPMI-1640 medium.

Techniques: Microscopy, BrdU Staining, Inhibition, Control, shRNA

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

doi: 10.3892/ol.2020.11927

Figure Lengend Snippet: Distribution of differentially expressed lncRNAs and mRNAs identified in AGPS-silenced glioma cells. Heatmap and Venn diagrams of differentially expressed (A) lncRNAs and (B) mRNAs in AGPS-silenced U251 cells. The differential expression of lncRNAs and mRNAs were depicted in the heatmap. Green represents the downregulated expression of lncRNAs/mRNAs and red represents the upregulated expression of lncRNAs/mRNAs. The Venn diagrams represent the shared modified genes between groups. n=3. The scale bar indicates the FC, and (|FC|)>1.2 was used as a threshold. shR, short hairpin RNA; AGPS, alkylglycerone phosphate synthase; lncRNA, long non-coding RNA; FC, fold-change.

Article Snippet: AGPS shRNA lentiviral particles (shR-AGPS-1 and −2 groups; Santa Cruz Biotechnology, Inc.) or empty lentiviral particles used as a negative control (control group; Santa Cruz Biotechnology, Inc.) stably integrated cell lines were established following infection with 8 μg/ml lentiviruses of U251 cells using 5 μg/ml polybrene-containing RPMI-1640 medium.

Techniques: Quantitative Proteomics, Expressing, Modification, shRNA

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

doi: 10.3892/ol.2020.11927

Figure Lengend Snippet: Top 40 differentially expressed lncRNAs in AGPS-silenced human glioma U251 cells.

Article Snippet: AGPS shRNA lentiviral particles (shR-AGPS-1 and −2 groups; Santa Cruz Biotechnology, Inc.) or empty lentiviral particles used as a negative control (control group; Santa Cruz Biotechnology, Inc.) stably integrated cell lines were established following infection with 8 μg/ml lentiviruses of U251 cells using 5 μg/ml polybrene-containing RPMI-1640 medium.

Techniques: Control

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

doi: 10.3892/ol.2020.11927

Figure Lengend Snippet: Top 40 differentially expressed mRNAs in AGPS-silenced human glioma U251 cells.

Article Snippet: AGPS shRNA lentiviral particles (shR-AGPS-1 and −2 groups; Santa Cruz Biotechnology, Inc.) or empty lentiviral particles used as a negative control (control group; Santa Cruz Biotechnology, Inc.) stably integrated cell lines were established following infection with 8 μg/ml lentiviruses of U251 cells using 5 μg/ml polybrene-containing RPMI-1640 medium.

Techniques: Control

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

doi: 10.3892/ol.2020.11927

Figure Lengend Snippet: Functional prediction based on long non-coding RNA and mRNA co-expression in AGPS-silenced U251 cells. (A) Classification of KEGG biological functions analysis in AGPS-silenced glioma cells in Biological systems and Cellular functions. (B) Top 20 signaling pathways identified using KEGG signaling pathway enrichment analysis of AGPS-silenced U251 cells. (C) Top 20 biological process terms identified using GO enrichment analysis of AGPS-silenced U251 cells. AGPS, alkylglycerone phosphate synthase; KEGG, Kyoto Encyclopedia of Genes and Genomes; GO, Gene Ontology.

Article Snippet: AGPS shRNA lentiviral particles (shR-AGPS-1 and −2 groups; Santa Cruz Biotechnology, Inc.) or empty lentiviral particles used as a negative control (control group; Santa Cruz Biotechnology, Inc.) stably integrated cell lines were established following infection with 8 μg/ml lentiviruses of U251 cells using 5 μg/ml polybrene-containing RPMI-1640 medium.

Techniques: Functional Assay, Expressing, Protein-Protein interactions

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

doi: 10.3892/ol.2020.11927

Figure Lengend Snippet: Signaling transduction and pathway network of co-expressed lncRNAs and mRNAs in AGPS-silenced U251 cells. (A) Pathway network of co-expressed lncRNAs and mRNAs in AGPS-silenced U251 cells. (B) Global signal transduction network of co-expressed lncRNAs and mRNAs in AGPS-silenced U251 cells. The nodes represent signaling pathways, lncRNAs and mRNAs and the arrows (or edges) represent the interaction/regulation between nodes. Ex, expression; pho, phosphorylation; a, activation; ind(e), indirect effect; b(a), binding/association; ubi, ubiquitination; dep, dephosphorylation; c, compound; s(c), state change; inh, inhibition; lncRNA, long non-coding RNA; AGPS, alkylglycerone phosphate synthase.

Article Snippet: AGPS shRNA lentiviral particles (shR-AGPS-1 and −2 groups; Santa Cruz Biotechnology, Inc.) or empty lentiviral particles used as a negative control (control group; Santa Cruz Biotechnology, Inc.) stably integrated cell lines were established following infection with 8 μg/ml lentiviruses of U251 cells using 5 μg/ml polybrene-containing RPMI-1640 medium.

Techniques: Transduction, Protein-Protein interactions, Expressing, Phospho-proteomics, Activation Assay, Binding Assay, Ubiquitin Proteomics, De-Phosphorylation Assay, Inhibition

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

doi: 10.3892/ol.2020.11927

Figure Lengend Snippet: Effect of AGPS silencing on the expression levels of tumor-related mRNAs in glioma cells. Reverse transcription-quantitative PCR was used to analyze the mRNA expression levels of tumor-related mRNAs in AGPS-silenced U251 cells. *P<0.05 vs. control group; # P<0.05 vs. shR-AGPS-1 group. COL1A2, collagen I α2; COL6A3, collagen 6 α3; THBS1, thrombospondin-1; FN1, fibronectin 1; SPP1, secreted phosphoprotein 1; ITGA11, integrin subunit α11; VEGFA, vascular endothelial growth factor A; IGF1R, insulin-like growth factor 1 receptor; EGFR, epidermal growth factor receptor; TLN2, Talin 2; PXN, Paxillin; PIK3CA, phosphoinositide 3-kinase α; SHC3, Src homology 2 domain containing transforming protein 3; FGF2, fibroblast growth factor 2; ANGPT2, angiopoietin 2; CSF3, colony stimulating factor 3; IL-7R, interleukin-7 receptor subunit α; PRKAA2, protein kinase AMP-activated α2; DDIT4, DNA damage inducible transcript 4; HSP90B1, heat shock protein 90 kDa β1; CREB5, cyclic AMP-responsive element-binding protein 5; TLR3, Toll-like receptor 3; IL-1B, interleukin-1β; CXCL8, chemokine ligand 8; PTGS2, prostaglandin G/H synthase 2; SDC4, syndecan-4; shRNA, short hairpin RNA; AGPS, alkylglycerone phosphate synthase.

Article Snippet: AGPS shRNA lentiviral particles (shR-AGPS-1 and −2 groups; Santa Cruz Biotechnology, Inc.) or empty lentiviral particles used as a negative control (control group; Santa Cruz Biotechnology, Inc.) stably integrated cell lines were established following infection with 8 μg/ml lentiviruses of U251 cells using 5 μg/ml polybrene-containing RPMI-1640 medium.

Techniques: Expressing, Reverse Transcription, Real-time Polymerase Chain Reaction, Control, Binding Assay, shRNA

Journal: Oncology Letters

Article Title: Effect of alkylglycerone phosphate synthase on the expression levels of lncRNAs in glioma cells and its functional prediction

doi: 10.3892/ol.2020.11927

Figure Lengend Snippet: lncRNA target pathway network in AGPS-silenced U251 cells. The regulatory core pathways of differential lncRNAs were identified using a lncRNA-gene-pathway network, indicating the association between lncRNAs and pathways in AGPS-silenced glioma U251 cells. Red represents the higher Degree values, blue represents the lower Degree values and purple represents the middle Degree values. AGPS, alkylglycerone phosphate synthase; lncRNA, long non-coding RNA.

Article Snippet: AGPS shRNA lentiviral particles (shR-AGPS-1 and −2 groups; Santa Cruz Biotechnology, Inc.) or empty lentiviral particles used as a negative control (control group; Santa Cruz Biotechnology, Inc.) stably integrated cell lines were established following infection with 8 μg/ml lentiviruses of U251 cells using 5 μg/ml polybrene-containing RPMI-1640 medium.

Techniques: