Systemic Epigenome-Wide Association Study of Elk Treponeme- Associated Hoof Disease

Treponeme-associated hoof disease (TAHD) is an emerging disease of elk (Cervus canadensis) in the U.S. Pacific West. Because environmental epigenetics is the primary molecular process that mediates environmental factor impacts on a host organism and disease, the role of epigenetics in TAHD etiology was examined. The current study was designed to examine potential effects of TAHD on systemic epigenetic modifications in infected elk over a range of TAHD lesion severity. Leg tendons that contain predominantly fibroblast connective tissue cells were used to isolate fibroblast cells for epigenetic analysis in unaffected and TAHD-positive male and female Roosevelt and Rocky Mountain elk. DNA methylation in the tendon cells in the different groups was examined. Differential DNA methylation regions (DMRs) between the unaffected and TAHD-positive were identified for both female and male elk. The presence of TAHD was associated with alteration of the connective tissue cell epigenetics and DMR associated genes identified. Therefore, the infected elk were found to have a systemic epigenetic alteration that was associated with the disease despite TAHD pathology being generally limited to feet. Other cell populations with the elk are also anticipated to be affected, and if the elk germline epigenetics is altered then generational transmission of susceptibility to TAHD may impact subsequent generations through epigenetic inheritance. This first study of epigenetic changes associated with disease in elk suggests that TAHD promotes a systemic effect on the elk epigenetics which could exert health impacts on the elk. Overall design: Study samples were obtained from Rocky Mountain elk collected in Washington, Idaho, and South Dakota and from Roosevelt elk from Washington, Oregon, and California. Treponeme-associated hoof disease was confirmed present or absent for each of the samples used in the study. DNA was isolated from tendon tissue, and methylated DNA was evaluated using methylated DNA immunoprecipitation followed by next generation sequencing (MeDIP-seq). DNA methylation levels along the genome were compared between TAHD-positive and unaffected groups to determine statistically significant Differentially Methylated Regions (DMRs)