Journal: PLoS ONE

Article Title: The Transcriptional Response to Oxidative Stress during Vertebrate Development: Effects of tert -Butylhydroquinone and 2,3,7,8-Tetrachlorodibenzo- p -Dioxin

doi: 10.1371/journal.pone.0113158

Figure Lengend Snippet: Zebrafish embryos, eleutheroembryos, or larvae were exposed to DMSO, tBHQ (10 µM), or TCDD (2 nM) at 1, 2, 3, 4, 5, or 6-dpf for 6 hr (4 groups per compound per time point), and sampled immediately followed exposure for isolation of RNA as described in Materials and Methods . The yellow shading indicates the time-point chosen for the microarray analysis. Phases of zebrafish development are not absolute but are categorized here as embryos (1, 2, and 3-dpf), eleutheroembryos (4 and 5-dpf), and larvae (6-dpf) following the nomenclature of others , ).

Article Snippet: The loaded microarray was incubated at 60°C for 17 hours with rotation in an Agilent DNA Microarray Hybridization Oven.

Techniques: Isolation, Microarray

Journal: Oncotarget

Article Title: Increased PTP1B expression and phosphatase activity in colorectal cancer results in a more invasive phenotype and worse patient outcome

doi: 10.18632/oncotarget.7829

Figure Lengend Snippet: A. Oncomine analysis of the colorectal cancer datasets reporting on PTPN1 expression shows that in 8 out of 14 datasets report an overexpression of PTPN1 in cancer as compared to normal colonic tissue. B-E. Representation of individual datasets reporting on PTPN1 expression from oncomine website, analyzed using unpaired students' T-test.

Article Snippet: Pre-cleared protein extracts were incubated overnight at 4°C under rotation with antibodies against PTP1B (Santa Cruz Biotechnologies, Dallax, Tx).

Techniques: Expressing, Over Expression

Journal: Oncotarget

Article Title: Increased PTP1B expression and phosphatase activity in colorectal cancer results in a more invasive phenotype and worse patient outcome

doi: 10.18632/oncotarget.7829

Figure Lengend Snippet: Tissues of patients with inactive ulcerative colitis (Control, n=9), dysplasia (n=5), and colorectal cancer (CRC, n=7) were stained for PTP1B by immunohistochemistry. PTP1B staining was scored for percentage of positive intestinal epithelial cells A. as well as intensity of staining B. and statistical analysis was performed using Mann-Whitney t-test. (*** P >0.001). C. Representative examples (10x and 40x magnifications) of control, dysplasia, and CRC are shown. D. Western blot analysis of PTP1B expression in 6 paired freshly frozen colorectal cancer; C and normal adjacent tissues; N, with β-actin as loading control. E. Quantification of western blot represented as means or individual pairs (** P >0.01). F. Same data as in E, but individual patients shown. Bars connect CRC samples to their corresponding.

Article Snippet: Pre-cleared protein extracts were incubated overnight at 4°C under rotation with antibodies against PTP1B (Santa Cruz Biotechnologies, Dallax, Tx).

Techniques: Control, Staining, Immunohistochemistry, MANN-WHITNEY, Western Blot, Expressing

Journal: Oncotarget

Article Title: Increased PTP1B expression and phosphatase activity in colorectal cancer results in a more invasive phenotype and worse patient outcome

doi: 10.18632/oncotarget.7829

Figure Lengend Snippet: IHC analysis of PTP1B on a tissue micro array (TMA) of colorectal cancer patients (n=371) and healthy adjacent tissue (n=251) using the Allred score. A. Allred score is significantly increased in CRC compared to control. Patients are divided in two groups based on the Allred score (Low < 6; High >6). B.-F. Kaplan meier curves for overall survival, disease free survival, disease specific survival, local recurrence free survival, and distant metastasis free survival reveal. High PTP1B expression is significantly correlated to worse survival (p=logrank).

Article Snippet: Pre-cleared protein extracts were incubated overnight at 4°C under rotation with antibodies against PTP1B (Santa Cruz Biotechnologies, Dallax, Tx).

Techniques: Microarray, Control, Expressing

Journal: Oncotarget

Article Title: Increased PTP1B expression and phosphatase activity in colorectal cancer results in a more invasive phenotype and worse patient outcome

doi: 10.18632/oncotarget.7829

Figure Lengend Snippet: Patient characteristics of tissue micro array stained for PTP1B

Article Snippet: Pre-cleared protein extracts were incubated overnight at 4°C under rotation with antibodies against PTP1B (Santa Cruz Biotechnologies, Dallax, Tx).

Techniques: Microarray, Staining

Journal: Oncotarget

Article Title: Increased PTP1B expression and phosphatase activity in colorectal cancer results in a more invasive phenotype and worse patient outcome

doi: 10.18632/oncotarget.7829

Figure Lengend Snippet: Uni- and multivariate analysis for overall survival

Article Snippet: Pre-cleared protein extracts were incubated overnight at 4°C under rotation with antibodies against PTP1B (Santa Cruz Biotechnologies, Dallax, Tx).

Techniques: Adjuvant

Journal: Oncotarget

Article Title: Increased PTP1B expression and phosphatase activity in colorectal cancer results in a more invasive phenotype and worse patient outcome

doi: 10.18632/oncotarget.7829

Figure Lengend Snippet: Uni- and multivariate analysis for disease free survival

Article Snippet: Pre-cleared protein extracts were incubated overnight at 4°C under rotation with antibodies against PTP1B (Santa Cruz Biotechnologies, Dallax, Tx).

Techniques: Adjuvant

Journal: Oncotarget

Article Title: Increased PTP1B expression and phosphatase activity in colorectal cancer results in a more invasive phenotype and worse patient outcome

doi: 10.18632/oncotarget.7829

Figure Lengend Snippet: HCT116 and CACO-2 cells were lentivirally transduced with 2 different shRNAs directed against PTP1B and non-target control vector. Western blot analysis of PTP1B knockdown and control cells in HCT116 A. and CACO-2 B. cells reveals increased phosphorylation of Src Y527, and reduced phosphorylation of ERK1/2 in the knockdown cells.

Article Snippet: Pre-cleared protein extracts were incubated overnight at 4°C under rotation with antibodies against PTP1B (Santa Cruz Biotechnologies, Dallax, Tx).

Techniques: Transduction, Control, Plasmid Preparation, Western Blot, Knockdown, Phospho-proteomics

Journal: Oncotarget

Article Title: Increased PTP1B expression and phosphatase activity in colorectal cancer results in a more invasive phenotype and worse patient outcome

doi: 10.18632/oncotarget.7829

Figure Lengend Snippet: A. MTT proliferation assay of HCT116 knockdown and control cells after 96 hours reveals a slight decrease in cell numbers in the knockdown cell lines (* P >0.05; *** P >0.001). B. Cell cycle analysis using Propidium-iodine staining of HCT116 cells followed by FACS analysis shows that PTP1B induces a slight G0/G1 cell cycle arrest, however this is not significant. C. Clonogenic assay of CACO-2 control and knockdown cells shows a reduced number of colonies, which are significantly reduced in size (*** P >0.001). D, E. β-catenin reporter assay of CACO-2 and HCT116 control and knockdown cells show reduced β-catenin signaling levels upon PTP1B knockdown.

Article Snippet: Pre-cleared protein extracts were incubated overnight at 4°C under rotation with antibodies against PTP1B (Santa Cruz Biotechnologies, Dallax, Tx).

Techniques: Proliferation Assay, Knockdown, Control, Cell Cycle Assay, Staining, Clonogenic Assay, Reporter Assay

Journal: Oncotarget

Article Title: Increased PTP1B expression and phosphatase activity in colorectal cancer results in a more invasive phenotype and worse patient outcome

doi: 10.18632/oncotarget.7829

Figure Lengend Snippet: A, B. HCT116 and CACO-2 cell migration was measured by scratch assays, where simple scratch wounds were made using a pipet tip, and pictures are taken at 0h, 24h, and/or 48h. C, D. Two-dimensional migration was analyzed using a ring-barrier system. HCT116 and CACO-2 cell migration on gelatin was tracked during 24h, with locations being captured using time-lapse microscopy every 12min (x=start, line=cell track). Quantification of migrated path indicates that the total migration and velocity were significantly reduced in PTP1B knockdown cells. Effective migration is even further reduced. (D; *P<0.05; **P<0.01; ***P<0.001). E, F. Track diagrams of migrated path of individual cells (x=start, line=cell track).

Article Snippet: Pre-cleared protein extracts were incubated overnight at 4°C under rotation with antibodies against PTP1B (Santa Cruz Biotechnologies, Dallax, Tx).

Techniques: Migration, Time-lapse Microscopy, Knockdown

Journal: Oncotarget

Article Title: Increased PTP1B expression and phosphatase activity in colorectal cancer results in a more invasive phenotype and worse patient outcome

doi: 10.18632/oncotarget.7829

Figure Lengend Snippet: A, B. CRC cell adhesion was determined by MTT assay of adherent cells after indicated time points, with fibronectin (FN) coating serving as control. HCT116 and CACO-2 PTP1B knockdown cells adhere less than control cells (*P<0.05; **P<0.01; ***P<0.001). C. Soft-agar colony formation of HCT116 cells shows reduced ability for knockdown cells to form colonies as shown by a reduced number in colonies (*P<0.05; **P<0.01). D, E. Anoikis resistance assay by plating cells on poly-HEMA coated plates, showing significantly reduced cell numbers after 24 hours of culturing on these plates (**P<0.01; ***P<0.001).

Article Snippet: Pre-cleared protein extracts were incubated overnight at 4°C under rotation with antibodies against PTP1B (Santa Cruz Biotechnologies, Dallax, Tx).

Techniques: MTT Assay, Control, Knockdown

Journal: Molecular Cancer

Article Title: The lncRNA CASC15 regulates SOX4 expression in RUNX1-rearranged acute leukemia

doi: 10.1186/s12943-017-0692-x

Figure Lengend Snippet: CASC15 knockdown leads to enrichment for the transcriptional program of SOX4 and YY1 . a Unsupervised hierarchical gene clustering of differentially expressed genes upon CASC15 siRNA mediated knockdown in RS4;11 cells (PPDE >99%, fold change >2). b - g RT-qPCR confirmation of differentially expressed genes from the microarray in RS4;11 ( b - d ) and REH ( e - g ) cell lines. h To narrow down transcription factors that might be responsible for the observed changes in gene expression, we overlapped transcription factors that were associated with the differentially expressed gene sets in CASC15 KD RS4;11 cells as well as CASC15 KO REH cells. Shown are the numbers of genes in the differentially expressed gene set for each transcription factor that showed an association. i - j Enrichment plots from gene set enrichment analysis (GSEA). The differentially regulated gene set from CASC15 KD RS4;11 cells showed a positive enrichment score when compared to genes up-regulated in ACC3 cells with SOX4 knockdown ( i ; Enrichment Score = 0.5, FDRq = 0.0 and P value = 0.0), and showed a negative enrichment score when compared to genes downregulated in ACC3 cells with SOX4 knockdown ( j ; Enrichment Score = −0.38,FDRq = .017 and P value = 0.01). k - l Enrichment plots from gene set enrichment analysis (GSEA) showing that the differentially regulated gene set showed a positive enrichment score when compared with upregulated genes upon YY1 knockdown ( k ; Enrichment Score = 0.5, FDRq = 0 and P value = 0.0) and a negative enrichment score with downregulated genes upon YY1 knockdown ( l ; Enrichment Score = -0.39, FDRq = 0 and P value = 0.0)

Article Snippet: Pre-cleared lysate was divided into two and incubated overnight with gentle rotation at 4 °C with the YY1 antibody (Rabbit mAb #2185: Cell signaling) and the normal IgG.

Techniques: Knockdown, Quantitative RT-PCR, Microarray, Gene Expression

Journal: Molecular Cancer

Article Title: The lncRNA CASC15 regulates SOX4 expression in RUNX1-rearranged acute leukemia

doi: 10.1186/s12943-017-0692-x

Figure Lengend Snippet: CASC15 regulates the activity of YY1 on the SOX4 promoter. a Transcriptional activity of SOX4 promoter upon CASC15 (L) and/or YY1 overexpression, as measured by dual luciferase assay. Luciferase values are normalized to the empty vector. b - d RT-qPCR with primers directed against SOX 4 (b) CASC15 ( c ) and YY1 ( d ) and Western blot for YY1 ( e ) in 293 T cells transiently transfected with YY1 and CASC15 . All qPCR analyses for CASC15 were performed with primer set #1 and normalized to GAPDH or actin, except where otherwise noted. Experiments were repeated three times for validation

Article Snippet: Pre-cleared lysate was divided into two and incubated overnight with gentle rotation at 4 °C with the YY1 antibody (Rabbit mAb #2185: Cell signaling) and the normal IgG.

Techniques: Activity Assay, Over Expression, Luciferase, Plasmid Preparation, Quantitative RT-PCR, Western Blot, Transfection, Biomarker Discovery

Journal: Non-Coding RNA

Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

doi: 10.3390/ncrna10020025

Figure Lengend Snippet: Top ten upregulated lncRNAs and mRNAs and their respective fold-changes and p -values based on the cDNA microarray dataset. The transcripts were statistically analyzed in the Agilent GeneSpring GX (v14.9.1) software using moderated t -test and Benjamin–Hochberg multiple testing corrections and had satisfied the p -value of <0.05 and fold-change cutoff of ±2.00. Data shown are from four independent experiments.

Article Snippet: After fragmentation steps following the manufacturer’s protocol, the cRNAs were immediately hybridized into the Agilent SurePrint G3 Human Gene Expression v3 8x60K for 17 h at 65 °C in a rotating microarray hybridization oven (Agilent, Santa Clara, CA, USA) prior to washing.

Techniques: Microarray, Software

Journal: Non-Coding RNA

Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

doi: 10.3390/ncrna10020025

Figure Lengend Snippet: Top ten downregulated lncRNAs and mRNAs and their respective fold-changes and p -values based on the cDNA microarray dataset. The transcripts were statistically analyzed in the Agilent GeneSpring GX (v14.9.1) software using moderated t -test and Benjamin–Hochberg multiple testing corrections and had satisfied the p -value of <0.05 and fold-change cutoff of ±2.00. Data shown are from four independent experiments.

Article Snippet: After fragmentation steps following the manufacturer’s protocol, the cRNAs were immediately hybridized into the Agilent SurePrint G3 Human Gene Expression v3 8x60K for 17 h at 65 °C in a rotating microarray hybridization oven (Agilent, Santa Clara, CA, USA) prior to washing.

Techniques: Microarray, Software

Journal: Non-Coding RNA

Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

doi: 10.3390/ncrna10020025

Figure Lengend Snippet: Difference in lncRNA and mRNA fold-changes between the cDNA microarray and in-house RT-qPCR experiments. Data shown are from three independent experiments (in triplicates) with calculated SD values to represent error bars and their statistical analyses were conducted using one-way ANOVA.

Article Snippet: After fragmentation steps following the manufacturer’s protocol, the cRNAs were immediately hybridized into the Agilent SurePrint G3 Human Gene Expression v3 8x60K for 17 h at 65 °C in a rotating microarray hybridization oven (Agilent, Santa Clara, CA, USA) prior to washing.

Techniques: Microarray, Quantitative RT-PCR

Journal: Non-Coding RNA

Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

doi: 10.3390/ncrna10020025

Figure Lengend Snippet: ( A ) LncRNA-mRNA interaction network was constructed based on the ten selected candidate lncRNAs from the cDNA microarray dataset. The resulting mRNA interactions were predicted using the “rtool” database with −20 kcal as the minimum energy threshold and were filtered to show only mRNAs that were also dysregulated in the dataset. Data were visualized using Cytoscape v3.8.2. (Pink diamond = candidate lncRNA, blue circle = predicted putative mRNA targets). ( B ) A total of nine mRNAs were identified as both responsible in the “regulated exocytosis” hit as well as highly likely to be regulated by the candidate lncRNAs listed in ( A ). Data were visualized using Cytoscape v3.8.2. (pink diamond = candidate regulator lncRNA, blue circle = mRNA predicted involved in the biological process).

Article Snippet: After fragmentation steps following the manufacturer’s protocol, the cRNAs were immediately hybridized into the Agilent SurePrint G3 Human Gene Expression v3 8x60K for 17 h at 65 °C in a rotating microarray hybridization oven (Agilent, Santa Clara, CA, USA) prior to washing.

Techniques: Construct, Microarray