Bacterial lipopolysaccharide alters DNA methylation in colorectal cancer cells

Colorectal cancer (CRC) is commonly associated with epigenetic modifications, including altered DNA methylation. Recent studies suggest that tumour-resident bacteria may influence CRC development, yet the impact of bacteria on epigenetic regulation is not understood. This study investigates the effect of lipopolysaccharide (LPS) from Fusobacterium periodonticum and Bacteroides fragilis, bacteria that are abundant in CRC tumours with high CpG island methylator phenotype (CIMP), on DNA methylation in HT29 colorectal cancer cells. HT29 cells were treated with LPS from F. periodonticum, B. fragilis, or a combination of both. DNA methylation was assessed using reduced representation bisulfite sequencing (RRBS), followed by bioinformatic analysis to identify differentially methylated CpG sites. RT-qPCR was used to analyse the expression of selected genes with altered CpG promoter methylation. F. periodonticum LPS treatment induced both hypermethylation and hypomethylation in HT29 cells, with significant hypermethylation observed near specific promoter regions, including PEPD and VAV3, with associated decrease in gene expression of these genes. B. fragilis LPS treatment predominantly induced hypomethylation. Co-treatment with both LPS molecules resulted in distinct methylation patterns, with B. fragilis LPS attenuating F. periodonticum LPS-induced hypermethylation. Bacterial LPS can induce dynamic alterations in DNA methylation profiles in HT29 colorectal cancer cells, leading to changes in gene expression. These findings suggest a novel link between tumour-resident bacteria and DNA methylation in colorectal cancer, highlighting, for the first time, a potential mechanism by which bacteria may influence colorectal carcinogenesis.