Development and applications of a beta-catenin oligonucleotide microarray: beta-catenin mutations are dominantly found in the proximal colon cancers with microsatellite instability.

beta-catenin mutations have been identified in a variety of human malignancies; most of these are missense mutations restricted at hot-spot areas in exon 3. beta-catenin mutations are known to be highly associated with colorectal cancers with microsatellite instability (MSI). More than 70 beta-catenin mutations have been reported in colorectal cancers, and approximately 90% of beta-catenin mutations have been found in 11 codons (codons 29, 31, 32, 33, 34, 35, 37, 38, 41, 45, and 48) as missense mutations or in-frame deletions. We have developed an oligonucleotide microarray for detecting beta-catenin mutations at these 11 codons. The developed oligonucleotide microarray can detect a total of 110 types of beta-catenin mutations, including the 60 mutations reported previously. Nine beta-catenin mutations were identified in this study by five different methods, i.e., PCR- single-strand conformational polymorphism, denaturing high performance liquid chromatography, direct sequencing, cloning-sequencing, and with an oligonucleotide microarray. All nine of the mutations were identified by denaturing high performance liquid chromatography, cloning-sequencing, and by the oligonucleotide microarray. However, PCR-single-strand conformational polymorphism missed 1 beta-catenin mutation and direct sequencing missed 2. Five beta-catenin mutations from 74 colorectal carcinomas (34 proximal colon cancers and 40 distal colorectal cancers) and 4 beta-catenin mutations from 31 colorectal cancer cell lines (7 from the proximal colon, 6 from the distal colorectum, and 18 unknown) were identified. In colorectal carcinomas, all 5 of the beta-catenin mutations were found in proximal colon tumors. In colorectal cancer cell lines, 2 of 4 cell lines with beta-catenin mutations originated from the proximal colon, and the remaining 2 cell lines were simply described as having originated from the colon. Considering the relationships among beta-catenin mutations, MSI, and tumor location, the frequency of beta-catenin mutations was found to be meaningfully higher in colorectal carcinomas with MSI than in those with microsatellite stability (P < 0.001); moreover, MSI was found to be more frequent in proximal colon tumors (P < 0.01). In addition, beta-catenin mutations were also found to be associated with proximal colon cancer (P = 0.017).