Background: Epigenetic modifications, particularly DNA methylation, play a critical role in regulating gene expression under stress conditions. This study investigates the methylation landscape of mitochondrial stress response genes in retinal pigment epithelium (RPE) cells exposed to oxidative stress, focusing on how these changes may drive pathophysiological alterations linked to retinal degenerative diseases.

Methods: Human RPE cells were treated with N-retinylidene-N-retinylethanolamine adduct (A2E) to induce oxidative stress. Whole-genome bisulfite sequencing (WGBS) was employed to profile methylation patterns. Differentially methylated regions (DMRs) were identified and analyzed for enrichment in mitochondrial stress-related pathways using bioinformatic tools, including Bismark, MethylKit, and ClueGO.

Results: Analysis revealed significant methylation changes in key mitochondrial stress pathway genes: 1) Hypomethylation of PGC1α and NRF1, genes essential for mitochondrial biogenesis and repair, indicating an adaptive response. 2) Hypermethylation of BCL2 and HSP70, associated with decreased anti-apoptotic signaling and impaired mitochondrial protein folding capacity. 3) Identification of novel DMRs in regulatory regions of genes involved in oxidative phosphorylation (e.g., ND5, COX2) and antioxidant defense mechanisms (SOD2, GPX1). Lastly, 4) clustering analysis of DMRs highlighted enrichment in pathways linked to mitochondrial unfolded protein response (UPRmt) and oxidative stress mitigation.

Conclusion: Oxidative stress induces significant alterations in the methylation profiles of mitochondrial stress pathway genes in RPE cells. These changes likely contribute to mitochondrial dysfunction and cellular apoptosis, underpinning the pathophysiology of retinal degenerative conditions. The identification of key methylation markers provides novel insights into the epigenetic regulation of mitochondrial function and potential therapeutic targets for restoring retinal allostasis.