Chemically induced DNA hypomethylation in breast carcinoma cells detected by the amplification of intermethylated sites.
BACKGROUND
Compromised patterns of gene expression result in genomic instability, altered patterns of gene expression and tumour formation. Specifically, aberrant DNA hypermethylation in gene promoter regions leads to gene silencing, whereas global hypomethylation events can result in chromosomal instability and oncogene activation. Potential links exist between environmental agents and DNA methylation, but the destabilizing effects of environmental exposures on the DNA methylation machinery are not understood within the context of breast cancer aetiology.


METHODS
We assessed genome-wide changes in methylation patterns using a unique methylation profiling technique called amplification of intermethylated sites (AIMS). This method generates easily readable fingerprints that represent the investigated cell line's methylation profile, based on the differential cleavage of DNA with methylation-specific isoschisomeric restriction endonucleases.


RESULTS
We validated this approach by demonstrating both unique and reoccurring sites of genomic hypomethylation in four breast carcinoma cell lines treated with the cytosine analogue 5-azacytidine. Comparison of treated with control samples revealed individual bands that exhibited methylation changes, and these bands were excized and cloned, and the precise genomic location individually identified. In most cases, these regions of hypomethylation coincided with susceptible target regions previously associated with chromosome breakage, rearrangement and gene amplification. Similarly, we observed that acute benzopyrene exposure is associated with altered methylation patterns in these cell lines.


CONCLUSIONS
These results reinforce the link between environmental exposures, DNA methylation and breast cancer, and support a role for AIMS as a rapid, affordable screening method to identify environmentally induced DNA methylation changes that occur in tumourigenesis.
Sadikovic
Bekim
B
The London Regional Cancer Centre, Child Health Research Institute, and the Department of Biochemistry, Paediatrics and Oncology, at the University of Western Ontario, London, Ontario, Canada. bsadikov@uwo.ca
Haines
Thomas R
TR
Butcher
Darci T
DT
Rodenhiser
David I
DI
D001374:Azacitidine / Q000494:pharmacology; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D002277:Carcinoma / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000037:antagonists & inhibitors / Q000378:metabolism; D019175:DNA Methylation / Q000187:drug effects*; D004273:DNA, Neoplasm / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D011401:Promoter Regions, Genetic / Q000235:genetics
D004273:DNA, Neoplasm; D004248:DNA (Cytosine-5-)-Methyltransferases; D001374:Azacitidine