Novel genetic and epigenetic alterations in ... - Ous-research.no

Journal of Translational Medicine 2008, 6:13http://www.translational-medicine.com/content/6/1/13The "bisulphite sequence" of the MAL promoterFigure 3The "bisulphite sequence" of the MAL promoter. Representative bisulphite sequencing electropherograms of the MALpromoter in colon cancer cell lines. A subsection of the bisulphite sequence electropherogram, covering CpG sites +11 to +15relative to transcription start. Cytosines in CpG sites are indicated by a black arrow, whereas cytosines that have been convertedto thymines are underlined in red. The MAL promoter sequencing electropherograms illustrated here, are from theunmethylated V9P cell line and the hypermethylated ALA and HCT116.quency of MAL in both benign and malignant colorectaltumours (71% in adenomas and 80% in carcinomas). Thediscrepancy in methylation frequencies between thepresent report and the previous study by Mori and coworkers[31] is probably a consequence of study design.From direct bisulphite sequencing of colon cancer celllines, we have now shown that the DNA methylation ofMAL is unequally distributed within the CpG island of itspromoter (Figure 2). CpG islands often span more thanone kilobase of the gene promoter, and the methylationstatus within this region is sometimes mistakenlyassumed to be equally distributed. This is exemplified bythe MLH1 gene in which hypermethylation of a limitednumber of CpG sites approximately 200 base pairsupstream of the transcription start point invariably correlateswith the lack of gene expression, while other sites donot [32,33]. Since the results of an MSP analysis rely onthe match or mismatch of the unmethylated and methylatedprimer sequences to bisulphite treated DNA, oneshould ensure that the primers anneal to relevant CpGsites in the gene promoter. In the present study, wedesigned the MSP primers close to the transcription startpoint of the gene (-72 to +70) and found, by bisulphitesequencing, concordance between the overall methylationstatus of MAL as assessed by MSP and the methylationstatus of the individual CpG sites covered by our MSPprimer set (Figure 2). This part of the CpG island washypermethylated in the majority of colon cancer cell lines(95%). We also found that these cell lines, as well as thoseof other tissues, showed loss of MAL RNA expression fromquantitative real time analyses, and that removal of DNAhypermethylation by the combined treatment of 5-aza-2'-deoxycytidine and Trichostatin A re-induced the expressionof MAL in colon cancer cell lines (Figure 5). Furthermore,by analyzing a large series of clinicallyrepresentative samples by protein immunohistochemistrywe confirmed that the expression of MAL was lost inmalignant colorectal epithelial cells as compared to normalmucosa.We have further analyzed the same region of the MAL promoteras Mori et al., which is located -206 to -126 basepairs upstream of the transcription start point [31]. Bydirect bisulphite sequencing, we showed that only aminority of the CpG sites covered by the Mori antisenseprimer were methylated in the 19 colon cancer cell linesPage 7 of 11(page number not for citation purposes)