Additional file 1 of Identification of a robust functional subpathway signature for pancreatic ductal adenocarcinoma by comprehensive and integrated analyses

Additional file 1: Table S1. Descriptive summary of datasets used in the study. Table S2. Genes of the 00982_1 subpathway. Table S3. Predictive power of published gene signatures. Figure S1. Dataset Search strategy in GEO database. Figure S2. Flow diagram of dataset selection strategies. Figure S3. Accumulative predictive abilities of signatures. Figure S4. Genes in the path:00982_1 subpathway. Figure S5. Collision classification for GSE57495 and GSE79668 datasets. Figure S6. Prognostic capacity of path:00982_1 signature for classical subtype. by Moffitt classification. Figure S7. Association of path:00982_1 subpathway with other pathways

Additional file 1 of Identification of a robust functional subpathway signature for pancreatic ductal adenocarcinoma by comprehensive and integrated analyses

Additional file 1: Table S1. Descriptive summary of datasets used in the study. Table S2. Genes of the 00982_1 subpathway. Table S3. Predictive power of published gene signatures. Figure S1. Dataset Search strategy in GEO database. Figure S2. Flow diagram of dataset selection strategies. Figure S3. Accumulative predictive abilities of signatures. Figure S4. Genes in the path:00982_1 subpathway. Figure S5. Collision classification for GSE57495 and GSE79668 datasets. Figure S6. Prognostic capacity of path:00982_1 signature for classical subtype. by Moffitt classification. Figure S7. Association of path:00982_1 subpathway with other pathways

Effect of pristimerin on cell cycle distribution and expression of cell cycle-related proteins.

<p>(A) Effect of pristimerin on cell cycle distribution in pancreatic cancer cells. BxPC-3, PANC-1 and AsPC-1 cells were cultured in complete medium and treated with either pristimerin (200, 400 or 600 nM) or DMSO (control) for 48 h. After treatment, cells were collected by trypsinization, washed with ice-cold PBS, and digested with RNase. Cellular DNA was stained with propidium iodide and flow cytometric analysis was performed for the detection of the percentage of cells in the different phases of the cell cycle as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043826#s4" target="_blank">Materials and Methods</a>. *P<0.05, compared with control. **P<0.01, compared with control. (B) Effect of pristimerin on the protein level of cyclin D1, cyclin E, cdk 2, cdk 4, cdk 6, WAF1/p21 and KIP1/p27 in pancreatic cancer cells. As detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043826#s4" target="_blank">Materials and Methods</a>, pancreatic cancer cells (BxPC-3, PANC-1 and AsPC-1) were treated with either pristimerin (200, 400 or 600 nM) or DMSO (control) for 48 h and then harvested. Total cell lysates were prepared and subjected to SDS-PAGE followed by Western blot analysis for G1 cell cycle regulatory proteins (cyclin D1, cyclin E, cdk2, cdk4, cdk6, WAF1/p21 and KIP1/p27). β-actin was detected as protein loading control. The immunoblots shown here are representative of at least three independent experiments with similar results.</p

Effect of pristimerin on apoptosis induction in pancreatic cancer cells.

<p>(A) Effect of pristimerin on apoptosis induction assessed by Annexin V/PI method using flow cytometry. BxPC-3, PANC-1 and AsPC-1 cells were cultured in complete medium and treated with either pristimerin (200, 400 or 600 nM) or DMSO (control) for 48 h. Apoptosis rate was determined by flow cytometry on annexin V-FITC. (B) Representative dot-plots from cytometrically illustrating apoptotic status in BxPC-3 (upper panel), PANC-1 (middle panel) and AsPC-1 (lower panel) cells. (C) Effect of pristimerin on apoptosis induction assessed by fluorescence microscopy. Cells were also viewed under a fluorescence microscopy. Representative photographs were taken from Annexin V/PI-stained pancreatic cancer cells under certain treatment. (D) Effect of pristimerin on apoptosis induction assessed by caspase-3 activity assay. Cell lysates were assayed for caspase-3 activity as described in “<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043826#s4" target="_blank">Materials and methods</a>”. (E) Effect of pristimerin on cleavage of caspase-3. As detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043826#s4" target="_blank">Materials and Methods</a>, pancreatic cancer cells (BxPC-3, PANC-1 and AsPC-1) were treated with either pristimerin (200, 400 or 600 nM) or DMSO (control) for 48 h and then harvested. Total cell lysates were prepared and subjected to SDS-PAGE followed by Western blot analysis. β-actin was detected as protein loading control. The immunoblots shown here are representative of at least three independent experiments with similar results. *P<0.05, compared with control. **P<0.01, compared with control.</p

Additional file 2 of LncRNA SNHG1 contributes to sorafenib resistance by activating the Akt pathway and is positively regulated by miR-21 in hepatocellular carcinoma cells

Supplementary tables and figures. (PDF 149 kb

Additional file 1 of LncRNA SNHG1 contributes to sorafenib resistance by activating the Akt pathway and is positively regulated by miR-21 in hepatocellular carcinoma cells

Supplementary Materials and Methods. (PDF 149 kb

Chemical structure of pristimerin.

<p>Chemical structure of pristimerin.</p

The expression of COX-2 and EP2 in HCC cells and meloxicam reduces cell viability <i>in vitro</i>.

<p>(A) The expression of COX-2 in HCC cell lines SMMC-7402, Bel-7402, HepG2, SMMC-7721 and Huh-7 was detected by Western Blotting. GAPDH served as an internal control. (B) Bel-7402, HepG2 and SMMC-7721 cells that express higher levels of COX-2 were incubated with increasing concentrations of meloxicam, and the rates of viability inhibition were measured. (C) The expression of EP2 in the above five HCC cell lines was detected by Western Blotting. GAPDH served as an internal control.</p

Proposed mechanisms of pristimerin-mediated G1 arrest, apoptosis and chemosensitivity of human pancreatic cancer cells.

<p>Proposed mechanisms of pristimerin-mediated G1 arrest, apoptosis and chemosensitivity of human pancreatic cancer cells.</p

Abrogation of constitutive and gemcitabine-induced NF-κB activation by pristimerin in pancreatic cancer cells.

<p>(A) Effect of pristimerin and gemcitabine on protein levels of NF-κB/p65 in nuclear lysates and total cell lysates of pancreatic cancer cells. As detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043826#s4" target="_blank">Materials and Methods</a>, pancreatic cancer cells (BxPC-3, PANC-1 and AsPC-1) were grown in the absence or presence of pristimerin (200 nM), gemcitabine (500 nM) or their combination for 48 h and then harvested. Nuclear lysates and total cell lysates were prepared and subjected to SDS-PAGE followed by Western blot analysis for the protein level of NF-κB/p65. β-actin was detected as protein loading control. The immunoblots shown here are representative of at least three independent experiments with similar results. (B) Effect of pristimerin and gemcitabine on NF-κB/p65 DNA-binding activity in pancreatic cancer cells. As detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043826#s4" target="_blank">Materials and Methods</a>, pancreatic cancer cells (BxPC-3, PANC-1 and AsPC-1) were grown in the absence or presence of pristimerin (200 nM), gemcitabine (500 nM) or their combination for 48 h and then harvested. Nuclear lysates were prepared and the NF-κB DNA-binding activity was determined using the Trans-Am NF-κB ELISA Kit. *P<0.05, compared with control. **P<0.01, compared with control. ^#P<0.05, compared with single gemcitabine group. ^##P<0.01, compared with single gemcitabine group.</p