Enrichment of Genomic Pathways Based on Differential DNA Methylation Profiles Associated with Knee Osteoarthritis Pain

Abstract

Our study aimed to identify differentially methylated CpGs/regions and their enriched genomic pathways associated with knee osteoarthritis (KOA). We recruited cognitively healthy middle to older aged (age 45-85) adults with (n=182) and without (n=31) self-reported KOA pain. We also extracted DNA from peripheral blood that was analyzed using MethylationEPIC arrays. The R package minfi1 was used to perform methylation data preprocessing and quality control. To investigate biological pathways impacted by differential methylation, we performed pathway enrichment analysis using Ingenuity Pathway Analysis (IPA) to identify canonical pathways and upstream regulators. Annotated genes within ±5kb of the putative differentially methylated regions (DMRs, p<0.05) were subjected to the IPA analysis. There was no significant difference in age, sex, study site between no pain and pain group (p>0.05). Non-Hispanic black individuals were overrepresented in the pain group (p = 0.003). At raw p < 0.05 cutoff, we identified a total of 19,710 CpG probes, including 13,951 hypermethylated CpG probes, for which DNA methylation level was higher in the group with higher pain grade. We also identified 5,759 hypomethylated CpG probes for which DNA methylation level was lower in the pain group with higher pain grade. IPA revealed that pain-related DMRs were enriched across multiple pathways and upstream regulators. The top 10 canonical pathways were linked to cellular signaling processes related to immune responses (i.e., the antigen presentation, PD-1, PD-L1 cancer immunotherapy, B cell development, IL-4 signaling, Th1 and Th2 activation pathway, and phagosome maduration). Moreover, in terms of upstream regulators, NDUFAF3 was the most significant (p=8.6E-04) upstream regulator. Our findings support our previous preliminary work suggesting the importance of epigenetic regulation of the immune system in knee OA pain and the need for future work to understand the epigenetic contributions to chronic pain.

Note:

Funding Information: This work was supported by NIH/NIA Grants R01AG067757 (YCA); and R37AG033906 (RBF). A portion of this work was performed in the McKnight Brain Institute at the National High Magnetic Field Laboratory’s Advanced Magnetic Resonance Imaging and Spectroscopy (AMRIS) Facility, which is supported by National Science Foundation Cooperative Agreement No. DMR 1157490 and DMR-1644779 and the State of Florida.

Declaration of Interests: None.

Ethics Approval Statement: All procedures were reviewed and approved by the Institutional Review Boards of the UF and UAB, and all participants provided verbal and written informed consent.

Keywords: Knee osteoarthritis, DNA methylation, genomic pathways, immune signaling, older adult