Abstract 4441: Non-pathogenic bacteria change host DNA methylation in vivo

Abstract

Abstract Introduction: More than a thousand species of bacteria live in a normal person's gastrointestinal tract. Epigenetic effects on the colon directly caused by the commensal bacteria remain elusive. In the current study, we explore the bacterial effects on DNA methylation of the host colon. Methods: Eight non-pathogenic bacterial species were introduced to the gut of germ-free (GF) mice to make specific-pathogen free (SPF) mice. Our study consisted of the following groups (n = 6 for each): wildtype (WT) GF, WT SPF, IL-10 knockout (KO) GF, IL-10 KO SPF, and IL-10 KO GF or SPF treated with azoxymethane (AOM). We analyzed DNA methylation in genomic DNA extracted from the proximal colon using Digital Restriction Enzyme Analysis of Methylation (DREAM) and compared methylation levels at CpG sites among different groups. Results: 1) Principal component analysis (PCA) performed on methylomes of all the samples separated the mouse samples based on presence or absence of bacteria, IL-10 KO status or AOM treatment into 6 distinct groups. 2) We analyzed CpG sites differentially methylated between GF and SPF mice at p<0.05 significance level. In WT mice, there were 1871 CpG sites (11% out of 17475 analyzed sites), in IL10 KO mice, there were 5986 CpG sites (33% out of 18254 analyzed sites) and in IL10 KO AOM-treated mice there were 6755 CpG sites (31% out of 21697 analyzed sites) differentially methylated. 3) There were 756 common CpG sites differentially methylated in all SPF vs GF comparisons. Interestingly, these sites were enriched 2.6-fold for aging-related CpG sites. 4) WT SPF mice showed increased methylation at CpG sites hypomethylated in WT GF mice and, conversely, decreased methylation at CpG sites hypermethylated in WT GF mice. This pattern of DNA methylation change was also observed by comparing GF with SPF in IL-10 KO mice with or without AOM treatment. 5) Both in GF and SPF mice the DNA methylation changes were more pronounced in IL10 KO while AOM had little additional effect. 6) IL10 KO resulted in genome-wide increase of methylation. However, the introduction of bacteria in SPF mice resulted in the methylation change mainly at CpG islands. Conclusions: Non-pathogenic bacteria introduced in the colon cause methylation gains at CpG sites with low DNA methylation and methylation losses at sites with high DNA methylation in a pattern similar to the changes observed in aging and cancer. Citation Format: Ang Sun, Jaroslav Jelinek, Shinji Maegawa, Christian Jobin, Jean-Pierre Issa. Non-pathogenic bacteria change host DNA methylation in vivo. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4441.