This experiment proposes a comprehensive investigation of epigenetic dysregulation in neurodegenerative diseases, focusing on DNA methylation patterns, histone modifications, and non-coding RNA expression in patient brain tissue and iPSC-derived neurons. The study will identify novel epigenetic biomarkers and therapeutic targets.
Epigenetic dysregulation—including aberrant DNA methylation, altered histone marks, and dysregulated microRNAs—plays a causal role in neurodegeneration rather than being merely a consequence. Reversing these changes will mitigate pathological protein aggregation and neuronal loss.
- Characterize the epigenome of AD and PD patient brains vs. age-matched controls
- Identify disease-specific epigenetic signatures distinguishing AD from PD
- Validate functional relevance using iPSC-derived neurons with epigenetic editing
- Screen epigenetic drugs for therapeutic potential
- Samples: 50 AD brains, 50 PD brains, 50 age-matched controls (from brain banks)
- Assays:
- Reduced Representation Bisulfite Sequencing (RRBS) for DNA methylome
- ChIP-seq for H3K9ac, H3K27ac, H3K4me3, H3K27me3
- RNA-seq for mRNA and miRNA
- Brain regions: prefrontal cortex, hippocampus, substantia nigra, cerebellum
- Analysis: Differential methylation analysis, histone mark enrichment, co-expression networks
- Cell lines: 3 AD-iPSC lines, 3 PD-iPSC lines, 3 controls
- Differentiation: Dopaminergic neurons (PD), cortical neurons (AD)
- Epigenetic profiling: Match Phase 1 assays in differentiated neurons
- Functional assays: Neuronal survival, neurite outgrowth, protein aggregation markers
- Tools: dCas9-DNMT3A for DNA methylation targeting
- Tools: dCas9-LSD1 for H3K4me1 demethylation
- Targets: Top 10 differentially methylated regions from Phase 1
- Readouts: Gene expression changes, protein aggregation, neuronal viability
- Compound library: 200 FDA-approved epigenetic drugs (HDAC inhibitors, DNMT inhibitors, BET inhibitors)
- Screening platform: Automated microscopy in iPSC-derived neurons
- Hits: 10 compounds for further validation in mouse models
¶ Reagents and Costs
| Item |
Cost |
| Human brain tissue (50 AD + 50 PD + 50 controls) |
$150,000 |
| RRBS library prep (300 samples) |
$90,000 |
| ChIP-seq (1200 samples: 300 × 4 marks) |
$180,000 |
| RNA-seq (300 samples) |
$75,000 |
| iPSC lines (9 lines) |
$45,000 |
| Neuron differentiation reagents |
$60,000 |
| CRISPR epigenetic editing constructs |
$40,000 |
| Drug library screening |
$35,000 |
| Bioinformatics analysis |
$50,000 |
| Personnel (2 postdocs, 1 bioinformatician, 24 months) |
$360,000 |
| Total |
$1,085,000 |
- Dr. Shelley Berger — Epigenetics, University of Pennsylvania (DNA methylation)
- Dr. Li-Huei Tsai — HDAC inhibitors, MIT ( epigenetic drugs)
- Dr. Enrico Tongiorgi — iPSC neurons, Italy (neuronal differentiation)
- Dr. Jonathan Mill — Epigenomics, King's College London (brain epigenetics)
- Dr. Amanda Link — DNA methylation in PD, University of Florida
- Total: 28 months
- Phase 1: Months 1-8 (epigenomic mapping)
- Phase 2: Months 9-16 (iPSC validation)
- Phase 3: Months 17-22 (CRISPR editing)
- Phase 4: Months 23-28 (drug screening)
- Publication: Month 30
| Dimension |
Score |
Rationale |
| Scientific Value |
10 |
Addresses fundamental mechanism of epigenetic dysregulation in neurodegeneration |
| Feasibility |
7 |
Technically complex but builds on established epigenomics methods |
| Novelty |
10 |
First comprehensive epigenomic comparison across AD and PD |
| Disease Impact |
10 |
Could identify novel therapeutic targets and biomarkers |
| Reach |
8 |
Findings applicable to multiple neurodegenerative diseases |
| Cost Efficiency |
7 |
High cost but broad impact across many disease areas |
| Time Efficiency |
6 |
28 months is moderate for comprehensive study |
| Evidence Base |
7 |
Some preliminary data exists but large gaps remain |
| Addresses Uncertainty |
10 |
Directly tests whether epigenetic changes are causal |
| Translation Potential |
10 |
Epigenetic drugs are clinically tractable |
Raw Score: 81/100
Weighted Score: 116.5/140