Journal: Translational Cancer Research

Article Title: Screening of significant oncogenic changes in air pollution-related lung cancer in Chinese population

doi: 10.21037/tcr-19-1314

Figure Lengend Snippet: Primer information for RT-PCR in this study

Article Snippet: To facilitate an enhanced amplification of CD74-ROS1 , a Taq PCR kit (cat. No., E5000S; New England Biolabs, Ipswich, MA, USA) was used, with a reaction volume of 25 µL comprising 1.5 µL cDNA template and 0.5 µL (10 µM) each of forward and reverse primers.

Techniques: Sequencing

Journal: Translational Cancer Research

Article Title: Screening of significant oncogenic changes in air pollution-related lung cancer in Chinese population

doi: 10.21037/tcr-19-1314

Figure Lengend Snippet: Association of HER2 overexpression, as well as EML4-ALK and CD74-ROS1 fusion with clinical features

Article Snippet: To facilitate an enhanced amplification of CD74-ROS1 , a Taq PCR kit (cat. No., E5000S; New England Biolabs, Ipswich, MA, USA) was used, with a reaction volume of 25 µL comprising 1.5 µL cDNA template and 0.5 µL (10 µM) each of forward and reverse primers.

Techniques: Over Expression

Journal: Translational Cancer Research

Article Title: Screening of significant oncogenic changes in air pollution-related lung cancer in Chinese population

doi: 10.21037/tcr-19-1314

Figure Lengend Snippet: Association of HER2 overexpression, and EML4-ALK and CD74-ROS1 fusion genes with air pollution (A), smoking (B), and total exposure (C). Low air pollution, living in relatively clean region C (Bap concentration, <60 ng/m 3 ); High air pollution, living in heavily polluted regions A (Bap concentration, >170 ng/m 3 )/B (Bap concentration, 60–170 ng/m 3 ). Low total exposure, living in relatively clean region C and also non-smoking; high total exposure, living in heavily polluted regions A/B or smoking. HER2 , human epidermal growth factor receptor; EML4-ALK , echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase; CD74-ROS1 , cluster of differentiation 74-ROS proto-oncogene 1; Bap, benzo(a)pyrene.

Article Snippet: To facilitate an enhanced amplification of CD74-ROS1 , a Taq PCR kit (cat. No., E5000S; New England Biolabs, Ipswich, MA, USA) was used, with a reaction volume of 25 µL comprising 1.5 µL cDNA template and 0.5 µL (10 µM) each of forward and reverse primers.

Techniques: Over Expression, Concentration Assay

Journal: Translational Cancer Research

Article Title: Screening of significant oncogenic changes in air pollution-related lung cancer in Chinese population

doi: 10.21037/tcr-19-1314

Figure Lengend Snippet: Oncogenic alterations of cell lines included in the study

Article Snippet: To facilitate an enhanced amplification of CD74-ROS1 , a Taq PCR kit (cat. No., E5000S; New England Biolabs, Ipswich, MA, USA) was used, with a reaction volume of 25 µL comprising 1.5 µL cDNA template and 0.5 µL (10 µM) each of forward and reverse primers.

Techniques: Over Expression

Journal: Translational Cancer Research

Article Title: Screening of significant oncogenic changes in air pollution-related lung cancer in Chinese population

doi: 10.21037/tcr-19-1314

Figure Lengend Snippet: RT-PCR analysis of EML4-ALK and CD74-ROS1 fusion genes. (A) Graphical representation of EML4-ALK fusion gene; (B) electrophoresis results of EML4-ALK fusion gene in tumor tissue samples and cell line. Fragment size of 550 bp represent variant 5b in EML4 -E2+ ALK -E20, whereas fragment size of 1,100 bp represent variant 2 in EML4 -E13+ ALK -E20; (C) graphical representation of CD74-ROS1 fusion gene; (D) electrophoresis results of CD74-ROS1 fusion gene in tumor samples. RT-PCR, reverse transcription polymerase chain reaction; EML4-ALK , echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase; CD74-ROS1 , cluster of differentiation 74-ROS proto-oncogene 1. E, exon. P45, P50, P11, P22, P37, P71, P41, and P66 represent sample numbers.

Article Snippet: To facilitate an enhanced amplification of CD74-ROS1 , a Taq PCR kit (cat. No., E5000S; New England Biolabs, Ipswich, MA, USA) was used, with a reaction volume of 25 µL comprising 1.5 µL cDNA template and 0.5 µL (10 µM) each of forward and reverse primers.

Techniques: Reverse Transcription Polymerase Chain Reaction, Electrophoresis, Variant Assay

Journal: PLoS ONE

Article Title: Preclinical Activity of ARQ 087, a Novel Inhibitor Targeting FGFR Dysregulation

doi: 10.1371/journal.pone.0162594

Figure Lengend Snippet: (A) ARQ 069. (B) ARQ 087. (C) Enzyme kinetic analysis was performed to determine the mode of inhibition of ARQ 087 with FGFR1 and FGFR2. Concentrations of ATP [ATP] and ARQ 087 [I] are indicated on the graphs. The rate plotted is the AlphaScreen ™ signal obtained from the plate reader with background correction. The experiments were conducted in triplicates and the means and the standard deviations were plotted. The number of parameter ( n p ), the sum of squares rel ( SS rel ), Akaike information criterion ( AIC ), weight of AIC ( w (AIC) ), Bayesian information criterion ( BIC ) and the weight of BIC ( w (BIC) ) for each binding mode were determined by the DynaFit software and are summarized below the plots. The dissociation constant ( K i) of ARQ 087 for FGFR1 and FGFR2 are shown. (D) The effect of ARQ 087 on the activation of FGFR1 and FGFR2 was examined in a continuous autophosphorylation assay.

Article Snippet: Kinase inhibitory activity of ARQ 087 was determined for the recombinant FGFR1 (Cat#08133, Carna BioScience, Kobe, Japan) or FGFR2 proteins (Cat#08134, Carna BioScience, Kobe, Japan), utilizing a biotinylated PYK2 peptide substrate (biotin-AGAGSIESDIYAEIPDETC-NH2, Biopeptide, San Diego, CA), and ATP (Cat#12215226, Roche, Indianapolis, IN), with AlphaScreen ™ technology (PerkinElmer, Waltham, MA).

Techniques: Inhibition, Amplified Luminescent Proximity Homogenous Assay, Binding Assay, Software, Activation Assay

Journal: PLoS ONE

Article Title: Preclinical Activity of ARQ 087, a Novel Inhibitor Targeting FGFR Dysregulation

doi: 10.1371/journal.pone.0162594

Figure Lengend Snippet: ARQ 087 biochemical activity.

Article Snippet: Kinase inhibitory activity of ARQ 087 was determined for the recombinant FGFR1 (Cat#08133, Carna BioScience, Kobe, Japan) or FGFR2 proteins (Cat#08134, Carna BioScience, Kobe, Japan), utilizing a biotinylated PYK2 peptide substrate (biotin-AGAGSIESDIYAEIPDETC-NH2, Biopeptide, San Diego, CA), and ATP (Cat#12215226, Roche, Indianapolis, IN), with AlphaScreen ™ technology (PerkinElmer, Waltham, MA).

Techniques: Activity Assay

Journal: PLoS ONE

Article Title: Preclinical Activity of ARQ 087, a Novel Inhibitor Targeting FGFR Dysregulation

doi: 10.1371/journal.pone.0162594

Figure Lengend Snippet: COS-1 cells ectopically expressing FGFR1, FGFR2, FGFR3 or FGFR4 were treated with the indicated concentrations of ARQ 087 for 2 hours followed by stimulation with 100 pM of FGF1/2/7 for 15 minutes. Total and phospho-FGFR was assessed by Western blot analyses. β-Actin was used as a loading control. The EC 50 values of individual FGFR family members are shown.

Article Snippet: Kinase inhibitory activity of ARQ 087 was determined for the recombinant FGFR1 (Cat#08133, Carna BioScience, Kobe, Japan) or FGFR2 proteins (Cat#08134, Carna BioScience, Kobe, Japan), utilizing a biotinylated PYK2 peptide substrate (biotin-AGAGSIESDIYAEIPDETC-NH2, Biopeptide, San Diego, CA), and ATP (Cat#12215226, Roche, Indianapolis, IN), with AlphaScreen ™ technology (PerkinElmer, Waltham, MA).

Techniques: Expressing, Western Blot

Journal: PLoS ONE

Article Title: Preclinical Activity of ARQ 087, a Novel Inhibitor Targeting FGFR Dysregulation

doi: 10.1371/journal.pone.0162594

Figure Lengend Snippet: ARQ 087 GI 50 in Ba/F3 transfected cell lines.

Article Snippet: Kinase inhibitory activity of ARQ 087 was determined for the recombinant FGFR1 (Cat#08133, Carna BioScience, Kobe, Japan) or FGFR2 proteins (Cat#08134, Carna BioScience, Kobe, Japan), utilizing a biotinylated PYK2 peptide substrate (biotin-AGAGSIESDIYAEIPDETC-NH2, Biopeptide, San Diego, CA), and ATP (Cat#12215226, Roche, Indianapolis, IN), with AlphaScreen ™ technology (PerkinElmer, Waltham, MA).

Techniques: Transfection

Journal: PLoS ONE

Article Title: Preclinical Activity of ARQ 087, a Novel Inhibitor Targeting FGFR Dysregulation

doi: 10.1371/journal.pone.0162594

Figure Lengend Snippet: ARQ 087 activity in FGFR dysregulated cell lines.

Article Snippet: Kinase inhibitory activity of ARQ 087 was determined for the recombinant FGFR1 (Cat#08133, Carna BioScience, Kobe, Japan) or FGFR2 proteins (Cat#08134, Carna BioScience, Kobe, Japan), utilizing a biotinylated PYK2 peptide substrate (biotin-AGAGSIESDIYAEIPDETC-NH2, Biopeptide, San Diego, CA), and ATP (Cat#12215226, Roche, Indianapolis, IN), with AlphaScreen ™ technology (PerkinElmer, Waltham, MA).

Techniques: Activity Assay, Amplification, Over Expression

Journal: Diagnostics

Article Title: A Highly Sensitive XNA-Based RT-qPCR Assay for the Identification of ALK, RET, and ROS1 Fusions in Lung Cancer

doi: 10.3390/diagnostics14050488

Figure Lengend Snippet: ( a ) Analytical sensitivity of the Qfusion TM ALK fusion detection assay. ( b ) Analytical sensitivity of the Qfusion TM RET fusion detection assay. ( c ) Analytical sensitivity of the Qfusion TM ROS1 fusion detection assay.

Article Snippet: The total RNA from each cell line underwent serial dilution with normal lung tissue RNA (Biochain) and then was checked using the Qfusion TM ALK fusion detection kit, the Qfusion TM RET fusion detection kit, or the Qfusion TM ROS1 fusion detection kit (DiaCarta Inc.).

Techniques: Detection Assay

Journal: Diagnostics

Article Title: A Highly Sensitive XNA-Based RT-qPCR Assay for the Identification of ALK, RET, and ROS1 Fusions in Lung Cancer

doi: 10.3390/diagnostics14050488

Figure Lengend Snippet: Evaluating Qfusion TM assay performance. ( a ) Each Qfusion TM assay was tested with the corresponding cell lines: A549, H2228 (EML4-ALK), LC-2/ad (CCDC6-RET), and HCC78 (SLC45A-ROS1). The A549 was a fusion-negative cell line and Cq was not determined (ND). ( b , c ) FFPE RNA reference standard was diluted with normal FFPE RNA and analyzed with each Qfusion TM assay. The x-axis represents the logarithm base 10 value of tumor percentage. Cq values were determined for 15% of tumor samples.

Article Snippet: The total RNA from each cell line underwent serial dilution with normal lung tissue RNA (Biochain) and then was checked using the Qfusion TM ALK fusion detection kit, the Qfusion TM RET fusion detection kit, or the Qfusion TM ROS1 fusion detection kit (DiaCarta Inc.).

Techniques:

Journal: Diagnostics

Article Title: A Highly Sensitive XNA-Based RT-qPCR Assay for the Identification of ALK, RET, and ROS1 Fusions in Lung Cancer

doi: 10.3390/diagnostics14050488

Figure Lengend Snippet: Consistency between OptiSeq TM lung cancer fusion NGS panel and Qfusion TM ALK, RET, or ROS1 fusion detection assay results. ( a ) Analysis of twenty FFPE samples using the OptiSeq TM lung cancer fusion NGS panel revealed the presence of SLC34A2-ROS1 fusion in two patient samples. The Y-axis represents normalized reads, and the error bars indicate the standard deviations of three replicates. ( b ) The same twenty FFPE samples were subjected to analysis using Qfusion TM assays. The results confirmed ROS1 fusion positivity in two patients with SLC34A2-ROS1 fusion. Qfusion TM ALK and RET fusion detection assays showed no ALK and RET fusions. The error bars depict the standard deviations of three replicates.

Article Snippet: The total RNA from each cell line underwent serial dilution with normal lung tissue RNA (Biochain) and then was checked using the Qfusion TM ALK fusion detection kit, the Qfusion TM RET fusion detection kit, or the Qfusion TM ROS1 fusion detection kit (DiaCarta Inc.).

Techniques: Detection Assay

Journal: Diagnostics

Article Title: A Highly Sensitive XNA-Based RT-qPCR Assay for the Identification of ALK, RET, and ROS1 Fusions in Lung Cancer

doi: 10.3390/diagnostics14050488

Figure Lengend Snippet: Assessment of Qfusion TM assays’ performance utilizing clinical samples. ( a ) Results from the analysis of 57 FFPE lung cancer patient samples using the Qfusion TM ALK, RET, or ROS1 fusion detection assay. The data reveals the identification of one patient with ALK and RET fusions and one patient with ROS1 fusion. ( b ) Validation of distinct fusion events through singleplex RT-qPCR. The identified ALK fusions included EML4-ALK V1/V7, while the RET fusion involved CCDC6-RET. Additionally, a single ROS1 fusion event, CD74-ROS1, was confirmed.

Article Snippet: The total RNA from each cell line underwent serial dilution with normal lung tissue RNA (Biochain) and then was checked using the Qfusion TM ALK fusion detection kit, the Qfusion TM RET fusion detection kit, or the Qfusion TM ROS1 fusion detection kit (DiaCarta Inc.).

Techniques: Detection Assay, Biomarker Discovery, Quantitative RT-PCR