RNA base-modification and A-to-I editing landscapes of oxidatively stressed human retinal pigment epithelium under Quantum Molecular Resonance electrotherapy and blood-derived secretome

Chemical modifications of RNA bases and adenosine-to-inosine (A-to-I) editing are regulatory layers essentially unexplored in the retinal pigment epithelium (RPE), whose oxidative dysfunction underlies age-related macular degeneration. We mapped both layers in ARPE-19 cells exposed to tert-butyl hydroperoxide under two non-pharmacological interventions, Quantum Molecular Resonance (QMR) electrotherapy and a patient blood-derived secretome, across 56 libraries spanning four arms, three time points and matched stressed and stress-free conditions (GEO: GSE328981). Base modifications were called with HARMLNC and A-to-I editing screened with a transition-signal caller, then re-analysed with REDItools3, JACUSA2 and LoDEI. The high-confidence set comprised 241 calls at 15 sites, all of classes canonical to tRNA and rRNA. The most prevalent was an adenosine modification at chrM:2617 in mitochondrial 16S rRNA (MT-RNR2), detected in 51 of 56 libraries and in every arm. Two positions 1 bp apart lie in an EZR/SYTL3 overlap region, whereas a third chromosome 6 site maps to HLA-C, 127.5 Mb away. No position of either layer differed between treatment arms: 7 testable modification sites (minimum p = 0.19) and, at single-nucleotide resolution under dedicated callers agreeing to r = 0.975–0.992, 15 curated editing positions (minimum q = 0.169). Two one-sided tests bound any change in substitution composition within 1.4% and in mean editing frequency within 10% for secretome and combination and 20% for QMR. Against a stress-free baseline internal to the cohort, only chrM:13710 (MT-ND5) changed detectably (q = 0.03). These layers are therefore small, largely constitutive and quantifiably undisturbed by either intervention at the resolution available.