Integrative Epigenomic and Targeted Protein Analysis in MRONJ: Correlating DNA Methylation with Bone Biomarkers

Medication-related osteonecrosis of the jaw (MRONJ) is a severe adverse effect of antiresorptive agents, including bisphosphonates (BPs) and denosumab (DMB). We conducted a case-control epigenome-wide association study (EWAS) of 24 cancer patients treated with BPs or BPs + DMB using the Infinium^® MethylationEPIC v2.0 to explore epigenetic differences associated with MRONJ. Differentially methylated positions (DMPs) and regions (DMRs) were assessed across three analyses: MRONJ vs. controls (main), BPs-MRONJ vs. BPs-controls, and BPs/DMB-MRONJ vs. BPs/DMB-controls. Eight plasma bone biomarkers were quantified by Luminex and correlated with top methylation sites. We identified 10 DMPs and 4 DMRs at suggestive significance (<i>p</i> < 1 × 10^-5). cg1913766 in the <i>NOP56</i> promoter was hypomethylated in the main analysis (<i>p</i> = 2.19 × 10^-7) and in BPs-MRONJ (<i>p</i> = 4.80 × 10^-6), correlating with osteocalcin (<i>p</i> = 0.02 and 0.03, respectively). <i>TNXB</i> cg21289669 was hypermethylated in the main analyses (<i>p</i> = 6.31 × 10^-6), and TNXB locus formed a DMR (<i>p</i> = 3.30 × 10^-10) in the main and BPs-MRONJ analyses (<i>p</i> = 2.76 × 10^-7). cg11392877 in <i>PDE8A</i> was hypomethylated in BPs/DMB-MRONJ (<i>p</i> = 5.35 × 10^-7). <i>TRIM15</i> was a significant DMR in BPs-MRONJ and the main analysis (<i>p</i> = 3.30 × 10^-10). <i>TRIM15</i>, <i>TNXB</i>, and <i>PDE8A</i> regulate collagen I, while <i>NOP56</i> supports ribosome biogenesis, potentially contributing to MRONJ. Given the small sample size, these findings are preliminary and validation in larger studies is warranted.