Gene expression profiling in RAS oncogene-transformed cell lines and in solid tumors using subtractive suppression hybridization and cDNA arrays

Selection of optimal control samples is crucial in expression profiling tumor samples. To address this issue, we performed microarray expression profiling of control samples routinely used in head and neck squamous cell carcinoma studies: human bronchial and tracheal epithelial cells, squamous cells obtained by laser uvulopalatoplasty and tumor surgical margins. We compared the results using multidimensional scaling and hierarchical clustering versus tumor samples and laryngeal squamous cell carcinoma cell lines. A general observation from our study is that the analyzed cohorts separated according to two dominant factors: “malignancy”, which separated controls from malignant samples and “cell culture-microenvironment” which reflected the differences between cultured and non-cultured samples. In conclusion, we advocate the use of cultured epithelial cells as controls for gene expression profiling of cancer cell lines. In contrast, comparisons of gene expression profiles of cancer cell lines versus surgical margin controls should be treated with caution, whereas fresh frozen surgical margins seem to be appropriate for gene expression profiling of tumor samples.

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Gene Expression Profiling on Global cDNA Arrays Gives Hints Concerning Potential Signal Transduction Pathways Involved in Cardiac Fibrosis of Renal Failure

Comparative and Functional Genomics ◽

10.1002/cfg.347 ◽

2003 ◽

Vol 4 (6) ◽

pp. 571-583 ◽

Cited By ~ 2

Author(s):

Kerstin Amann ◽

Heidrun Ridinger ◽

Christiane Rutenberg ◽

Eberhard Ritz ◽

Gerhard Mall ◽

...

Keyword(s):

Gene Expression ◽

Renal Failure ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Cardiac Remodelling ◽

Cardiomyocyte Hypertrophy ◽

Specific Gene ◽

Interstitial Tissue ◽

Sham Operation ◽

Cdna Arrays

Cardiac remodelling with interstitial fibrosis in renal failure, which so far is only poorly understood on the molecular level, was investigated in the rat model by a global gene expression profiling analysis. Sprague–Dawley rats were subjected to subtotal nephrectomy (SNX) or sham operation (sham) and followed for 2 and 12 weeks, respectively. Heart-specific gene expression profiling, with RZPD Rat Unigene-1 cDNA arrays containing about 27 000 gene and EST sequences revealed substantial changes in gene expression in SNX compared to sham animals. Motor protein genes, growth and differentiation markers, and extracellular matrix genes were upregulated in SNX rats. Obviously, not only genes involved in cardiomyocyte hypertrophy, but also genes involved in the expansion of non-vascular interstitial tissue are activated very early in animals with renal failure. Together with earlier findings in the SNX model, the present data suggest the hypothesis that the local renin–angiotensin system (RAS) may be activated by at least two pathways: (a) via second messengers and Gproteins (short-term signalling); and (b) via motor proteins, actins and integrins (longterm signalling). The study documents that complex hybridization analysis yields reproducible and promising results of patterns of gene activation pointing to signalling pathways involved in cardiac remodelling in renal failure. The complete array data are available via http://www.rzpd.de/cgi-bin/services/exp/viewExpressionData.pl.cgi

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