Differences in expression between transcripts using alternative promoters of hMLH1 gene and their correlation with microsatellite instability

Abstract

hMLH1 is involved in DNA mismatch repair and its defects cause hereditary non-polyposis colorectal cancer (HNPCC) as well as other types of cancer. A defective DNA mismatch repair system results in genetic instability, also referred to as microsatellite instability (MSI), which is a good indicator of HNPCC. Using in silico analysis of oligocapping cDNA sequences, we initially identified a splicing (variant type 2) whose second exon is 5 bp shorter than that of a genuine hMLH1 transcript (variant type 1) and a transcript using alternative promoter (variant type 3) whose transcription starts about 300 bases downstream of variant type 1. We then compared the expression level of variant types 1 and 3 among six colorectal cancer cell lines using real-time PCR. As a result, we found that the cell lines that completely suppress the expression of variant type 1 by hypermethylation expressed variant type 3 to a certain extent. This result suggests that the expression of variant types 1 and 3 did not completely follow the same transcription mechanism. We also found that the cell lines showing MSI to be positive either expressed variant type 3 more than type 1 or expressed only variant type 3. These results showed the potential applicability of mRNA expression analysis to molecular diagnostic tests of MSI-positive cancer types.