Journal: Anticancer research

Article Title: ROCK I Has More Accurate Prognostic Value than MET in Predicting Patient Survival in Colorectal Cancer

doi:

Figure Lengend Snippet: ROCK I and MET proteins are over-expressed in colorectal cancer. Following immunostaining intensity scoring of the tissue microarray slides, the scoring data obtained from four to eight available cores per patient for ROCK I (Panel A) and MET (Panel B) expression, were analyzed. Both proteins were significantly over-expressed in colorectal cancer tissues compared to the normal, adjacent control tissues.

Article Snippet: Anti-ROCK I antibody (C-19; catalog number: SC-6055) and anti-MET antibody (C-12; catalog number: SC-10) were purchased from Santa Cruz Biotechnology (Dallas, Texas, USA).

Techniques: Immunostaining, Microarray, Expressing, Control

Journal: Anticancer research

Article Title: ROCK I Has More Accurate Prognostic Value than MET in Predicting Patient Survival in Colorectal Cancer

doi:

Figure Lengend Snippet: Specific immunostaining for ROCK I and MET proteins in colorectal cancer. Tissue microarray slides were prepared with primary antibodies specific for ROCK I and MET. Representative images of the immunohistochemistry results for ROCK I (Panel A) and MET (Panel B) are shown. Intensity of staining is labeled as 0 (no staining detected), 1, 2 or 3 (high intensity) on the upper part of each picture.

Article Snippet: Anti-ROCK I antibody (C-19; catalog number: SC-6055) and anti-MET antibody (C-12; catalog number: SC-10) were purchased from Santa Cruz Biotechnology (Dallas, Texas, USA).

Techniques: Immunostaining, Microarray, Immunohistochemistry, Staining, Labeling

Journal: Anticancer research

Article Title: ROCK I Has More Accurate Prognostic Value than MET in Predicting Patient Survival in Colorectal Cancer

doi:

Figure Lengend Snippet: Stratification of ROCK I and MET expression in different stages of colorectal cancer. According to the protein expression levels determined through evaluation of cancer tissue staining, each patient was assigned to one of three groups: low, medium or high expression level. Panel A shows tumor stage (I, II, III and IV) stratification of ROCK I expression groups. Panel C displays MET expression groups, while Panels B and D present the mean expression data per tumor stage of ROCK I and MET, respectively. The asterisk indicates a significant mean expression difference as determined by the Student’s t-test.

Article Snippet: Anti-ROCK I antibody (C-19; catalog number: SC-6055) and anti-MET antibody (C-12; catalog number: SC-10) were purchased from Santa Cruz Biotechnology (Dallas, Texas, USA).

Techniques: Expressing, Staining

Journal: Anticancer research

Article Title: ROCK I Has More Accurate Prognostic Value than MET in Predicting Patient Survival in Colorectal Cancer

doi:

Figure Lengend Snippet: Correlation of five-year survival of colorectal cancer patients with protein expression levels. Kaplan-Meier plots show the results of the five-year survival of 108 colorectal cancer patients, stratified by protein expression levels. The correlation of expression levels (low, medium and high) of ROCK I (Panel A) and MET (Panel B) with 5-year colon cancer survival are shown. The asterisk denotes a significant difference between ROCK I high expression and low expression levels of 5-year survival. The p-values are generated from the comparisons of the low or medium with the high expression group.

Article Snippet: Anti-ROCK I antibody (C-19; catalog number: SC-6055) and anti-MET antibody (C-12; catalog number: SC-10) were purchased from Santa Cruz Biotechnology (Dallas, Texas, USA).

Techniques: Expressing, Generated

Journal: Anticancer research

Article Title: ROCK I Has More Accurate Prognostic Value than MET in Predicting Patient Survival in Colorectal Cancer

doi:

Figure Lengend Snippet: Cox proportional hazards model (multivariate) analysis of protein expression levels, tumor stage and patient survival.

Article Snippet: Anti-ROCK I antibody (C-19; catalog number: SC-6055) and anti-MET antibody (C-12; catalog number: SC-10) were purchased from Santa Cruz Biotechnology (Dallas, Texas, USA).

Techniques: Expressing

Journal: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

Article Title: Reparameterization of PAM50 expression identifies novel breast tumor dimensions and leads to discovery of a genomewide significant breast cancer locus at 12q15

doi: 10.1158/1055-9965.EPI-17-0887

Figure Lengend Snippet: Example Utah high-risk breast cancer pedigree 1817. a. Confirmed and sampled breast cancer cases are indicated in black (55 sampled out of 138 total confirmed UCR cases). Star, triangle and hexagon symbols indicate pedigree branches. b. shows only those cases from (a) with tumor expression data available and indicates PAM50 intrinsic subtype by color. Cases whose tumors are extreme for PC3 are indicated by ‘3’; extreme for PC5 are indicated by ‘5’. c. shows only the PC3-extreme cases from (b). A ‘+’ indicates those cases that share the genomewide significant region at 12q15.

Article Snippet: Gene expression data was generated using the PAM50 RT-qPCR research assay( 12 ) in the Bernard Lab at the Huntsman Cancer Institute( 15 ).

Techniques: Expressing

Journal: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

Article Title: Reparameterization of PAM50 expression identifies novel breast tumor dimensions and leads to discovery of a genomewide significant breast cancer locus at 12q15

doi: 10.1158/1055-9965.EPI-17-0887

Figure Lengend Snippet: Summary of the 11 high-risk Utah pedigrees Tumor count by intrinsic subtype per pedigree.

Article Snippet: Gene expression data was generated using the PAM50 RT-qPCR research assay( 12 ) in the Bernard Lab at the Huntsman Cancer Institute( 15 ).

Techniques:

Journal: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

Article Title: Reparameterization of PAM50 expression identifies novel breast tumor dimensions and leads to discovery of a genomewide significant breast cancer locus at 12q15

doi: 10.1158/1055-9965.EPI-17-0887

Figure Lengend Snippet: A slice from a three-dimensional scatterplot of PC1, PC2, and PC4 shows that they recapitulate the PAM50 intrinsic subtypes. Reinforcing the constrasts illustrated in Figure 2, PC1 here clearly distinguishes Basal-like from Luminal A tumors. PC2 and PC4 aid in distinguishing HER2-enriched from Luminal B tumors. Combined, these three components define clusters corresponding to the intrinsic subtypes.

Article Snippet: Gene expression data was generated using the PAM50 RT-qPCR research assay( 12 ) in the Bernard Lab at the Huntsman Cancer Institute( 15 ).

Techniques:

Journal: eLife

Article Title: Evidence that synthetic lethality underlies the mutual exclusivity of oncogenic KRAS and EGFR mutations in lung adenocarcinoma

doi: 10.7554/eLife.06907

Figure Lengend Snippet: ( A ) Induced expression of transduced genes in human lung cancer cell lines. PC9 and H358 cell lines were transduced with the indicated tetracycline-responsive plasmids. Lysates of cells cultured in the presence or absence of doxycycline (Dox) for 24 hr were prepared and assayed for the indicated protein expression by western blotting, as described in Materials and Methods. ( B ) Co-expression of mutant KRAS and EGFR reduces cell viability. Cells were grown in the presence or absence of Dox for up to 7 days and tested for viability by alamar blue. Averaged values from three independent experiments were normalized and plotted for each cell line relative to untreated cells (no Dox) at the indicated time points. Error bars represent ± standard deviation (SD) for each point. p-values were calculated between the + and − Dox states of individual cell lines at each time point using a two-tailed, unpaired t test with Welch's correction. *, ** and *** represent significance values <0.01, <0.001 and <0.0001, respectively. ( C ) Co-expression of mutant KRAS and EGFR reduces cell number. Cells were grown as in panel B and counted on day 7. Average cell number from three independent experiments were normalized and plotted for each cell line relative to cells expressing TetO-GFP in the absence of Dox. Error bars represent ± standard error of the mean (SEM) and p-values were calculated between the + and − Dox states as described in A . ( D ) Erlotinib protects PC9- TetO-KRASG12V cells from the toxic effects of oncogene co-expression. Cells were grown with or without erlotinib (Erl) and/or Dox for 7 days and cell viability determined by alamar blue. Results from three independent experiments were normalized and plotted for each cell line relative to untreated cells (no Dox) with error bars representing ± SEM. p-values were calculated between the groups indicated as in A . DOI: http://dx.doi.org/10.7554/eLife.06907.005

Article Snippet: Co-expression of mutant KRAS and EGFR increases MAP kinase (MAPK) signaling. ( A ) Modified PC9 and H358 lung adenocarcinoma cells (see ) were cultured in the presence or absence of doxycycline (Dox) for 24 hr and analyzed for global gene expression changes using Affymetrix microarrays (see ‘Materials and methods’ for details).

Techniques: Expressing, Transduction, Cell Culture, Western Blot, Mutagenesis, Standard Deviation, Two Tailed Test

Journal: eLife

Article Title: Evidence that synthetic lethality underlies the mutual exclusivity of oncogenic KRAS and EGFR mutations in lung adenocarcinoma

doi: 10.7554/eLife.06907

Figure Lengend Snippet: ( A ) Modified PC9 and H358 lung adenocarcinoma cells (see ) were cultured in the presence or absence of doxycycline (Dox) for 24 hr and analyzed for global gene expression changes using Affymetrix microarrays (see ‘Materials and methods’ for details). Microarray probes differentially expressed in each TetO cell line upon the addition of Dox were identified (corrected p < 0.01, compared to control without Dox), and those genes specifically induced by Dox in either TetO-KRAS or TetO-EGFR cells and not the TetO-GFP control cells were determined. The Venn diagram indicates the resulting number of gene probes identified in each cell line, including the 152 unique probes specifically modulated by expression of mutant KRAS and EGFR in both PC9 and H358 cells. ( B ) Gene Set Enrichment Analysis (GSEA) of the genes specifically regulated upon mutant KRAS and EGFR co-expression in both PC9 and H358 lung adenocarcinoma cells identified three oncogenic signatures that were significantly upregulated (FDR q-value <0.01) upon co-expression; the top two are indicative of KRAS signaling (see ‘Materials and methods’ and ). The displayed enrichment plot is for the most significant gene set (q-value = 0, Normalized Enrichment Score = 2.29) demonstrating enrichment for genes related to the upregulation of mutant KRAS . ( C ) Ingenuity Pathway Analysis (IPA) of the KRAS + EGFR induced gene set was performed and the top ten significantly regulated canonical pathways in which these genes are involved are displayed (see ‘Materials and methods’). P38 MAPK signaling was identified as the most significant upregulated pathway from this analysis; ERK/MAPK signaling was the second. ( D ) A highly simplified diagram of the EGFR/RAS signaling pathway is illustrated; the components assessed by western blot highlighted in blue. ( E ) Increased MAPK signaling in cells co-expressing mutant oncogenes. The indicated cells were cultured for 3 days with or without Dox; lysates were assayed by western blotting for the indicated proteins and phospho-proteins. Where relevant, the phosphorylated Tyrosine (Y) or Threonine (T) residue being measured is shown. Data are representative of three independent experiments. DOI: http://dx.doi.org/10.7554/eLife.06907.008

Article Snippet: Co-expression of mutant KRAS and EGFR increases MAP kinase (MAPK) signaling. ( A ) Modified PC9 and H358 lung adenocarcinoma cells (see ) were cultured in the presence or absence of doxycycline (Dox) for 24 hr and analyzed for global gene expression changes using Affymetrix microarrays (see ‘Materials and methods’ for details).

Techniques: Modification, Cell Culture, Gene Expression, Microarray, Control, Expressing, Mutagenesis, Western Blot, Residue