Macrodissection versus Microdissection of Rectal Carcinoma: Minor Influence of Stroma to Tumor Gene Profiles

Background: The molecular determinants of carcinogenesis, tumor progression and patient prognosis can be deduced from simultaneous comparison of thousands of genes by microarray analysis. However, the presence of stroma cells in surgically excised carcinoma tissues might obscure the tumor cell-specific gene expression profiles of these samples. To circumvent this complication, laser microdissection can be performed to separate tumor epithelium from the surrounding stroma and healthy tissue. In this report, we compared RNAs isolated from macrodissected, of which only surrounding healthy tissue had been removed, and microdissected rectal carcinoma samples by microarray analysis in order to determine the most reliable approach to detect the expression of tumor cell-derived genes by microarray analysis. Results: As microdissection yielded low tissue and RNA quantities, extra rounds of mRNA amplification were necessary to obtain sufficient RNA for microarray experiments. These second rounds of amplification influenced the gene expression profiles. Moreover, the presence of stroma cells in macrodissected samples had a minor contribution to the tumor cell gene expression profiles, which can be explained by the observation that more RNA is extracted from tumor epithelial cells than from stroma. Conclusion: These data demonstrate that the more convenient procedure of macrodissection can be adequately used and yields reliable data regarding the identification of tumor cell-specific gene expression profiles. Keywords: macrodissection, microdissection, RNA amplification, stroma, rectal carcinoma Fresh frozen rectal carcinoma samples were obtained from 14 different rectal carcinoma patients. All 14 rectal carcinoma samples are macrodissected or microdissected for tumor epithelium. Six macrodissected samples were in addition amplified a second round and of four samples the stroma was microdissected as well. Six samples were replicated, of which one sample was an amplification duplicate experiment and the other five samples were labelling replicates.