Transcriptome and methylome analysis of periodontitis and peri-implantitis with tobacco use.

Peri-implantitis is similar to periodontitis in both symptoms and treatment; however, their level of similarity remains controversial. Here, we compared multiple cases of periodontitis and peri-implantitis through transcriptome and methylome profiling, and analyzed the effects of smoking as a typical risk factor. Human gingival tissues were obtained from 20 patients with periodontitis or peri-implantitis via periodontal surgical procedures. Total RNA and genomic DNA were isolated, and transcriptome and methylome datasets were generated. Comprehensive analysis of differential gene expression, DNA methylation, and protein-protein interactions indicated that periodontitis and peri-implantitis share biological similarities; however, hierarchical clustering between the two disease groups revealed distinct molecular characteristics. These differences might be related to structural differences in natural tooth-bone and implant-bone. Additionally, smoking differentially affected periodontitis and peri-implantitis in terms of host-defense mechanism impairment. Within the limitations of this study, the results provide evidence that peri-implantitis is distinct from periodontitis and that smoking potentially affects disease progression. Our study provides a foundation for the rational design of a large-scale study in the future for a more comprehensive analysis that includes microbiome and clinical data.