Epigenetic Dysregulation Validation in Parkinson's Disease

SUMMARY

# Epigenetic Dysregulation Validation in Parkinson's Disease ## Background and Rationale This comprehensive clinical validation study examines genome-wide epigenetic modifications in Parkinson's disease patients to test the hypothesis that aberrant DNA methylation and histone modifications drive disease pathogenesis. The multi-phase approach combines epigenome-wide association studies (EWAS) with functional validation in patient-derived induced pluripotent stem cell (iPSC) models. Phase 1 involv

METHODOLOGY NOTES

**Phase 1: Sample Collection and Preparation (Weeks 1-4)** • Collect post-mortem brain tissue samples from substantia nigra, striatum, and frontal cortex from 50 Parkinson's disease patients and 30 age-matched controls • Obtain patient-derived iPSCs from 40 PD patients and 25 controls, differentiate into dopaminergic neurons using established protocols • Isolate high-quality DNA, RNA, and chromatin from all samples using standardized extraction protocols • Perform quality control assessment: DNA integrity number >7.0, RNA integrity number >6.0 • Aliquot samples for methylation analysis, ChIP-seq, and RNA-seq studies **Phase 2: DNA Methylation Profiling (Weeks 5-8)** • Conduct genome-wide DNA methylation analysis using Illumina EPIC 850K arrays on all tissue and cell samples • Perform targeted bisulfite sequencing on key PD-associated gene promoters (SNCA, LRRK2, PARK2, PINK1, DJ1) • Validate differential methylation using pyrosequencing on 10 selected CpG sites • Calculate methylation