DNA methylation profiles of gingival tissues in periodontal disease

Objective: We have recently reported that periodontal pathogens can alter DNA methylation patterns of host genomic DNA. DNA methylation is an epigenetic phenomenon that controls gene expression without a change in DNA sequence. Changes in DNA methylation generally remain stable following cell division to permanently alter the tissue gene expression and response to challenge. The goal of this study was to determine whether the biofilm was inducing local alterations in host DNA methylation patterns that could potentially modulate gene expression.

Material and Methods: Genome-wide alterations in DNA methylation patterns were performed by analyses using CpG island microarrays. Diseased gingival tissues collected from patients with severe periodontal disease were compared with healthy gingival tissues from either healthy or diseased patients. Genomic DNA was isolated and restrictively digested with MseI, ligated to linkers and subjected to restrictive digestion by two methylation-sensitive restrictive enzymes, BstUI and HpaII. Following PCR amplification, products were labeled by Cy5 for test samples and Cy3 for control samples, hybridized to a 12K Human CpG-island microarray and analyzed for differences in CpG methylation patterns comparing health to disease.

Results: Altered DNA methylation patterns were found in samples from patients with periodontal disease suggesting a local epigenetic modulation of host DNA structure. Preliminary results suggest that many genes are differentially methylated at sites of periodontal disease compared to health. Hypermethylation, which is usually associated with gene silencing, was observed for many genes including SOCS3, VDR, MMP25 and BMP4.

Conclusion: Chronic infection and underlying inflammation in gingival tissue is associated with altered DNA methylation of multiple genes. Such modification may significantly contribute to permanent alteration of the local environment to further enhance the inflammatory tissue phenotype.