Mesothelioma differential expression

To investigate the molecular events controlling malignant transformation of human pleural cells, we compared constitutive gene expression of mesothelioma cells to that of pleural cells. Using cDNA microarray and high-density filter array, we assessed expression levels of > 6500 genes. Most of the highly expressed transcripts were common to both cell lines and included genes associated with stress response and DNA repair, outcomes consistent with the radio- and chemo-resistance of mesothelioma. Interestingly, of the fewer than 300 genes that differed between cell lines, most functioned in (i) macromolecule stability, (ii) cell adhesion and recognition, (iii) cell migration (invasiveness), and (iv) extended cell division Keywords: c-DNA array from Incyte Pharmaceuticals™, cell line comparison Target cDNA was generated from 1 μg polyadenylated mRNA that was reverse transcribed to produce cDNA and labeled either with Cy3 (MSTO-211H) or Cy5 (Met-5A) dUTP. The average intensity of the Cy3 fluorescence divided by the average intensity of the Cy5 fluorescence equaled 0.97 (balance coefficient), indicating similar labeling efficiency for each set of target cDNAs. Target cDNA was hybridized on Incyte Pharmaceuticals™ arrays containing 6356 probes with sequences complementary to 4311 human genes and 2045 human expressed sequence tags (ESTs) (Unigem V™, Genome Systems Inc., St Louis, MO, USA). Dye-swaps were performed. More than 600 probes were internal and external controls. Inclusion criteria were derived from an image recognition algorithm for each cDNA in the analysis and included a fluorescent signal from the cDNA exceeding a signal to background ratio of 2.5 and the cDNA covering its grid location on the microarray for >40%. In this study, genes were considered differentially expressed (DE) if the change was >2.0-fold. The cDNAs corresponding to genes of known function were sorted by enzyme, function or pathway cluster analysis using a Gemtools software (v2.4.2, Incyte Pharmaceuticals, Freemont, CA, USA).