Bioinformatic analysis reveals pancreatic cancer molecular subtypes specific to the tumor and the microenvironment

<p>Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease characterized by a dense desmoplastic reaction surrounding malignant epithelial cells. Interaction between the epithelial and stromal compartments is suggested to enhance its aggressive nature. Indeed, therapies targeting the stroma, as well as the tumor cells, may improve survival outcomes for patients. The evaluated study by Moffitt <i>et al</i>. used bioinformatic techniques to separate gene expression patterns of normal tissues from PDAC and stroma in a large cohort of samples. The researchers identified two different subtypes of PDAC (‘classical’ and ‘basal-like’) and surrounding stroma (‘normal’ and ‘activated’). The basal-like subtype was associated with worse prognosis and a trend towards better response to adjuvant therapy. Hopefully, the molecular stratification of PDAC will potentially allow more personalized treatment strategies and guide clinical decision making.</p

Representative fluorescence in situ hybridisation (FISH) images of chromosomes 2 (A, D and G), 12 (B, E and H) and 8 (C, F and I) in SK-N-AS (A-C), SK-N-ASrOALI4000(-) (D-F), and SK-N-ASrOXALI4000 (G-I) neuroblastoma cells.

<p>Scale bar represents 10μm.</p

Phosphorylation status of 49 receptor tyrosine kinases.

<p>Receptor tyrosine kinase phosphorylation was determined by a commercial kit (Proteome Profiler Human Phospho-RTK Array Kit, R&D Systems, Abingdon, UK) with subsequent densitometric analysis using ImageJ software (<a href="http://imagej.nih.gov/ij/" target="_blank">http://imagej.nih.gov/ij/</a>). A) Receptor tyrosine kinase phosphorylation status expressed as fold change spot density relative to a control membrane area. Images of the membranes are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172140#pone.0172140.s001" target="_blank">S1 Fig</a>. B) Differential phosphorylation of receptor tyrosine kinases that were found phosphorylated in at least one cell line (as indicated by a fold change spot density relative to a control membrane area >2) in SK-N-AS^rOXALI⁴⁰⁰⁰ or SK-N-AS^rOXALI^4000(-) cells relative to SK-N-AS.</p

Oxygen consumption by SK-N-AS and SK-N-AS^rOXALI⁴⁰⁰⁰ cells.

<p>Oxygen consumption was determined in intact cells in the absence of treatment (baseline), in response to oligomycin (8 μg/mL), an inhibitor of ATP synthase that causes a leak of protons resulting in inhibition of respiration (leak), and in response to FCCP (10 μM) that uncouples the electron transport chain resulting in maximum oxidative phosphorylation.</p

Effects of H1N1 influenza A virus infection on cell viability.

<p>Non-MYCN-amplified SK-N-AS neuroblastoma cells, SK-N-AS cells with acquired resistance to oxaliplatin (SK-N-AS^rOXALI⁴⁰⁰⁰), SK-N-AS^rOXALI⁴⁰⁰⁰ cells that were passaged for 10 passages in absence of oxaliplatin (SK-N-AS^rOXALI^4000(-)), or MYCN-amplified UKF-NB-3 neuroblastoma cells were infected with H1N1 influenza strain A/WSN/33 virus at different multiplicities of infection (MOIs) and cell viability was determined 48h post infection relative to non-treated control. The dotted line indicates the viability of non-infected control cells. * P < 0.05 relative to non-infected control cells.</p