Gene Chip Analysis for Detection of Potential Tumor Suppressor Genes in Colorectal Cancer Cell Lines
Michael C. Gock*1, Dirk Koczan2, Ernst Klar1, Michael Linnebacher1
1Department of General Surgery, University of Rostock, Rostock, Germany; 2Institute of Immunology, University of Rostock, Rostock, Germany
Background
Anomalies within the chromosomal structure are fundamentally involved in tumorigenesis of colorectal cancer (CRC). Actual generations of gene chips provide very high resolution to study phenomena like loss of heterozygoty (LOH) or total losses that are known to cause inactivation of tumor suppressor genes (TSG). In this study we use the latest generation of gene chips to reveal recurrent LOH and total losses in coding regions of CRC cell genome and thereby to reveal unknown TSGs.
Methods
The genome of 7 established human CRC cell lines was analyzed using latest gene chip technology (1.800k Genome Wide SNP 6.0 chip by Affymetrix). Results were compared in selected cases with conventional cytogenetic (mFISH analysis). After selecting potential TSGs their expression profile on mRNA level was analyzed using end point and real time PCR. cDNA cloning with subsequent sequencing was performed to reveal possible mutations as well as alternative splice variants.
Results
Gene chip results were basically congruent to those of mFISH analysis but provided a major improvement in terms of resolution. In this initial analysis we limited us to examine a microsatellite unstable cell line. We found four genes as candidate TSGs, two of them turned out to be described as TSG for CRC (FHIT und WWOX).
Conclusion
We discovered two genes as potential, so far unknown, TSGs for CRC. These genes need further investigation. Additionally gene chip analysis proved to be a simple and useful technique detection of possible TSGs in tumor cell lines.
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