Proposed experiment from debate on Epigenetic clocks and biological aging in neurodegeneration

SUMMARY

# Proposed experiment from debate on Epigenetic clocks and biological aging in neurodegeneration ## Background and Rationale # Epigenetic Clocks and Biological Aging in Neurodegeneration: A Long-term HDAC3 Inhibition Study Histone deacetylase 3 (HDAC3) has emerged as a critical regulator of circadian rhythm maintenance and metabolic homeostasis, with accumulating evidence suggesting its dysregulation contributes to accelerated biological aging and neurodegeneration. Epigenetic clocks, which mea

METHODOLOGY NOTES

**Phase 1: Cell Line Establishment and Baseline Characterization (Weeks 1-4)** • Establish neuronal cell lines (SH-SY5Y, iPSC-derived neurons) and control lines (HepG2 for hepatic, H9c2 for cardiac) • Culture cells in standardized media with circadian-synchronized feeding cycles (12h light/dark) • Perform baseline epigenetic clock measurements using Horvath, Hannum, and PhenoAge methylation arrays • Establish baseline circadian rhythm profiles via BMAL1, CLOCK, PER2 gene expression over 48h cycles • Measure baseline metabolic parameters: ATP/ADP ratios, glucose uptake, lactate production, oxygen consumption • Assess cognitive-relevant markers: synaptic proteins (PSD95, synaptophysin), neurotransmitter synthesis enzymes **Phase 2: HDAC3 Inhibition Treatment Initiation (Weeks 5-8)** • Apply HDAC3-specific inhibitors (RGFP966 at 1-10μM, BG45 at 0.5-5μM) to treatment groups (n=6 biological replicates per concentration) • Maintain vehicle controls (DMSO) and positive controls (pan-HDAC inh