Professor of Internal Medicine Iowa State University Ames, IA, United States
Abstract:
Background: Recent studies indicate that dogs exposed to enteropathogens early in life are at increased risk for developing CIE as adults, suggesting that epigenetic mechanisms contribute to disease development.
Objective: To investigate DNA methylation (DNAm) in duodenal biopsies of dogs with CIE pre- versus post-treatment. Animals: Twenty dogs diagnosed with CIE.
Methods: Dogs were randomized to receive an elimination diet +/- synbiotic for 6 weeks. Endoscopic duodenal biopsies were collected pre- and post-treatment. An untargeted approach using whole genome bisulfite sequencing was used to examine methylation-specific patterns of tissue DNAm across the whole genome. Total reads were mapped to a reference Canis lupus familiaris genome, and the methylation level was calculated for each methylation site. Enrichment of DMR-involved genes was evaluated in KEGG pathways and the genomic locations of DMRs were annotated. The mucosal microbiota was investigated using FISH.
Results: Non-CG sites (CHG, CHH) exhibited distinct relationships with methylation levels compared to CG sites in synbiotic- vs. diet-treated dogs. Differentially expressed genes (DEGs, p< 0.05) included hyper-methylation genes: MAPK, Wnt, Ras, cGMP-PKG, and cAMP signaling pathways, inflammatory mediator regulation of TRP channels/MAPK signaling pathway, lysine degradation, cAMP and Rap1 pathways (CHH). Hypo-methylation genes: metabolic pathways, protein digestion and absorption, cell adhesion molecules, focal adhesion and Rap1, PI3K-Akt, TGFβ, cGMP-PKG, Ras, FoxO, AGE-RAGE, NF-κB, NOD-like receptor and AMPK pathways, pathways regulating stem cell pluripotency, endocytosis and gap junctions (CG). Conclusions and clinical importance: Genome-wide DNAm analysis identified unique functional patterns associated with hyper- and hypo-methylation and microbial imbalances in dogs with CIE.
