Introduction
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive loss of upper and lower motor neurons, leading to muscle weakness, paralysis, and typically death within 2-5 years of symptom onset. Approximately 10% of ALS cases are familial, with the remaining 90% being sporadic. While significant progress has been made in identifying genetic causes—including mutations in SOD1, C9orf72, FUS, and TARDBP—the mechanisms underlying disease initiation and progression remain incompletely understood.
Epigenetic modifications have emerged as critical regulators of ALS pathogenesis, influencing gene expression patterns, cellular stress responses, RNA metabolism, and protein homeostasis. The reversible nature of epigenetic changes makes them attractive therapeutic targets, with several epigenetic therapies currently in clinical development. This page provides a comprehensive overview of epigenetic mechanisms in ALS, including DNA methylation, histone modifications, non-coding RNAs, and chromatin remodeling.
Overview of Epigenetic Dysregulation in ALS
ALS demonstrates widespread epigenetic alterations that affect multiple cellular pathways:
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RNA metabolism: TDP-43 pathology is closely linked to RNA processing abnormalities 1TDP-43 pathology in ALS (2006)Open reference
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Protein homeostasis: Epigenetic regulation of autophagy and proteasome pathways 2Protein homeostasis in ALS (2019)Open reference
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Neuroinflammation: Glial activation patterns controlled by epigenetic mechanisms 3Neuroinflammation epigenetics (2019)Open reference
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Metabolic dysfunction: Energy homeostasis alterations in motor neurons 4Metabolic dysfunction in ALS (2019)Open reference
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Excitotoxicity: Glutamate transporter regulation 5Excitotoxicity epigenetics (2019)Open reference
The interface between genetic mutations and epigenetic dysregulation is particularly important in ALS, as mutant proteins directly affect epigenetic machinery.
DNA Methylation in ALS
DNA methylation patterns are significantly altered in ALS, affecting both disease-specific genes and global methylation status.
C9orf72 Methylation
The C9orf72 hexanucleotide repeat expansion is the most common genetic cause of familial ALS:
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Repeat-associated non-ATG (RAN) translation produces toxic dipeptide repeat proteins (DPRs) 6RAN translation in C9orf72 (2013)Open reference
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DNA methylation at the C9orf72 promoter correlates with:
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Repeat expansion size 7C9orf72 methylation (2014)Open reference
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Age of onset 8Repeat size and methylation (2019)Open reference
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Disease duration 9C9orf72 methylation clinical (2016)Open reference
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Hypermethylation of the C9orf72 promoter can reduce toxic expression 10Hypermethylation therapy (2015)Open reference
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The methylation status varies across brain regions 2Protein homeostasis in ALS (2019)Open reference0
SOD1 Methylation
The SOD1 gene, mutated in ~20% of familial ALS cases:
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Promoter methylation affects SOD1 expression 2Protein homeostasis in ALS (2019)Open reference1
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Differential methylation between ALS subtypes 2Protein homeostasis in ALS (2019)Open reference2
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Epigenetic therapy targeting SOD1 methylation is under investigation 2Protein homeostasis in ALS (2019)Open reference3
TDP-43 Methylation
TARDBP encoding TDP-43 is central to ALS pathogenesis:
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TDP-43 proteinopathy affects ~95% of ALS cases 2Protein homeostasis in ALS (2019)Open reference4
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Epigenetic regulation of TDP-43 expression is being characterized 2Protein homeostasis in ALS (2019)Open reference5
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Methyl-CpG binding proteins interact with TDP-43 aggregates 2Protein homeostasis in ALS (2019)Open reference6
Global DNA Methylation Changes
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Global hypomethylation has been observed in ALS motor cortex and spinal cord 2Protein homeostasis in ALS (2019)Open reference7
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Region-specific patterns distinguish ALS from controls 2Protein homeostasis in ALS (2019)Open reference8
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Peripheral blood methylation shows potential as biomarker 2Protein homeostasis in ALS (2019)Open reference9
Epigenetic Clock in ALS
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Accelerated epigenetic aging documented in ALS 3Neuroinflammation epigenetics (2019)Open reference0
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Age-dependent methylation patterns correlate with progression 3Neuroinflammation epigenetics (2019)Open reference1
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DNA methylation age differs between ALS subtypes 3Neuroinflammation epigenetics (2019)Open reference2
Therapeutic Implications
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DNMT inhibitors are being explored to modulate pathogenic gene expression 3Neuroinflammation epigenetics (2019)Open reference3
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Epigenetic readers as novel therapeutic targets 3Neuroinflammation epigenetics (2019)Open reference4
Histone Modifications in ALS
Histone modifications are extensively dysregulated in ALS, affecting transcription of genes critical for motor neuron survival.
Histone Acetylation
HDAC Dysregulation
Histone deacetylases (HDACs) are major therapeutic targets:
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HDAC inhibitor therapy has shown promise in ALS models 3Neuroinflammation epigenetics (2019)Open reference5
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Class I HDACs (HDAC1, 2, 3): Elevated in ALS tissue 3Neuroinflammation epigenetics (2019)Open reference6
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HDAC2: Specifically upregulated in motor neurons 3Neuroinflammation epigenetics (2019)Open reference7
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HDAC4/5: Redistribute in ALS, affecting nuclear-cytoplasmic transport 3Neuroinflammation epigenetics (2019)Open reference8
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HDAC6: Regulates autophagy and aggresome formation 3Neuroinflammation epigenetics (2019)Open reference9
Histone Acetylation Marks
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H3K9ac: Reduced at neuroprotective gene promoters 4Metabolic dysfunction in ALS (2019)Open reference0
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H3K27ac: Altered at enhancer regions 4Metabolic dysfunction in ALS (2019)Open reference1
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H4K12ac: Dysregulated in ALS models 4Metabolic dysfunction in ALS (2019)Open reference2
Histone Methylation
Active Marks
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H3K4me3: Redistributed in ALS motor cortex 4Metabolic dysfunction in ALS (2019)Open reference3
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H3K36me3: Altered in genes involved in RNA splicing 4Metabolic dysfunction in ALS (2019)Open reference4
Repressive Marks
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H3K27me3: Increased at certain gene promoters 4Metabolic dysfunction in ALS (2019)Open reference5
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H3K9me2/3: Enhanced repressive marks in ALS 4Metabolic dysfunction in ALS (2019)Open reference6
Cross-talk
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H3K4me3 and H3K27me3 modifications show complex interactions 4Metabolic dysfunction in ALS (2019)Open reference7
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Bivalent domains in stem cells are re-established in disease 4Metabolic dysfunction in ALS (2019)Open reference8
Histone Modifications in ALS Genes
| Gene | Histone Modification | Effect |
|---|---|---|
| SOD1 | H3K9ac ↑ | Increased expression |
| C9orf72 | H3K27me3 ↓ | Bidirectional effects |
| FUS | H3K4me3 altered | RNA processing changes |
| TARDBP | H3K9ac ↓ | Auto-regulation affected |
HDAC Inhibitors in ALS Therapy
| Compound | Class | Status | Mechanism |
|---|---|---|---|
| Valproic acid | Class I | Preclinical | Broad HDAC inhibition |
| SAHA (Vorinostat) | Class I/II | Preclinical | Pan-HDAC inhibitor |
| MS-275 (Entinostat) | Class I | Phase I/II | HDAC1/2/3 selective |
| Trichostatin A | Class I/II | Preclinical | Potent HDAC inhibitor |
| Ricolinostat | HDAC6 | Phase I/II | Selective HDAC6 inhibition |
Sirtuins in ALS
The NAD+-dependent deacetylases (SIRT1-7):
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SIRT1: Generally neuroprotective; expression changes in ALS 4Metabolic dysfunction in ALS (2019)Open reference9
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SIRT2: Modulates oxidative stress 5Excitotoxicity epigenetics (2019)Open reference0
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SIRT3: Mitochondrial function regulation 5Excitotoxicity epigenetics (2019)Open reference1
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NAD+ precursors are being investigated clinically 5Excitotoxicity epigenetics (2019)Open reference2
Non-Coding RNAs in ALS
Non-coding RNAs, particularly microRNAs, are significantly dysregulated in ALS and contribute to disease pathogenesis.
MicroRNAs in ALS
Motor Neuron-Enriched miRNAs
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miR-9: Critical for motor neuron development; dysregulated in ALS 5Excitotoxicity epigenetics (2019)Open reference3
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Targets: BDNF, REST
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Functions: Neurodevelopment, stress response 5Excitotoxicity epigenetics (2019)Open reference4
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miR-124: Neuronal identity maintenance 5Excitotoxicity epigenetics (2019)Open reference5
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Alters in ALS 5Excitotoxicity epigenetics (2019)Open reference6
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Therapeutic potential 5Excitotoxicity epigenetics (2019)Open reference7
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miR-23a: Regulates ALS-related genes 5Excitotoxicity epigenetics (2019)Open reference8
ALS-Associated miRNAs
| miRNA | Expression | Target Genes | Function |
|---|---|---|---|
| miR-155 | ↑ | SOCS1, MCPIP1 | Inflammation |
| miR-146a | ↑ | TRAF6, IRAK1 | Immune response |
| miR-131 | ↑ | — | Synaptic function |
| miR-219 | ↓ | Lipid metabolism | oligodendrocyte |
| miR-219 | ↓ | DAPK1, ULK1 | Autophagy |
miRNA Dysregulation by Mutation
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SOD1 mutations: miR-155, miR-146a upregulation 5Excitotoxicity epigenetics (2019)Open reference9
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C9orf72: miRNA processing alterations 6RAN translation in C9orf72 (2013)Open reference0
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FUS mutations: Direct miRNA dysregulation 6RAN translation in C9orf72 (2013)Open reference1
CSF and Blood miRNAs as Biomarkers
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miR-181a-5p: Promising ALS biomarker 6RAN translation in C9orf72 (2013)Open reference2
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miR-124-3p: Detectable in CSF 6RAN translation in C9orf72 (2013)Open reference3
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Panel approaches: Multiple miRNAs improve specificity 6RAN translation in C9orf72 (2013)Open reference4
Long Non-Coding RNAs (lncRNAs)
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NEAT1: Nuclear paraspeckle formation; altered in ALS 6RAN translation in C9orf72 (2013)Open reference5
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MALAT1: Synaptic function; affected in disease 6RAN translation in C9orf72 (2013)Open reference6
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HOTAIR: Gene silencing complex; motor neuron expression 6RAN translation in C9orf72 (2013)Open reference7
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ALSINC: ALS-specific lncRNA 6RAN translation in C9orf72 (2013)Open reference8
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SOX2OT: Motor neuron development 6RAN translation in C9orf72 (2013)Open reference9
Circular RNAs (circRNAs)
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circSMARCA5: Reduced in ALS 7C9orf72 methylation (2014)Open reference0
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circCFL1: Promotes neurodegeneration 7C9orf72 methylation (2014)Open reference1
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circRNA sponges: miRNA sequestration effects 7C9orf72 methylation (2014)Open reference2
Small Nucleolar RNAs (snoRNAs)
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SNORD115/116: Imprinted locus; altered in ALS 7C9orf72 methylation (2014)Open reference3
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snoRNA-derived RNAs (sdRNAs): Emerging role 7C9orf72 methylation (2014)Open reference4
Chromatin Remodeling in ALS
Chromatin remodeling complexes regulate access to DNA and are affected in ALS through multiple mechanisms.
SWI/SNF Complex Dysregulation
The SWI/SNF (SWItch/Sucrose Non-Fermentable) ATP-dependent chromatin remodelers:
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BRG1 (SMARCA4): Expression changes in ALS 7C9orf72 methylation (2014)Open reference5
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BRM (SMARCA2): Altered activity 7C9orf72 methylation (2014)Open reference6
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BAF subunits: Mutations in some ALS cases 7C9orf72 methylation (2014)Open reference7
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Target genes: SOD1, FUS, TDP-43 regulators 7C9orf72 methylation (2014)Open reference8
NuRD Complex
The Nucleosome Remodeling Deacetylase (NuRD) complex:
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CHD4: Elevated in ALS motor neurons 7C9orf72 methylation (2014)Open reference9
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MTA1/2/3: Expression changes 8Repeat size and methylation (2019)Open reference0
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Functions:
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Transcriptional repression
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DNA repair
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Response to oxidative stress 8Repeat size and methylation (2019)Open reference1
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ISWI Complex
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SMARCA5: Reduced in ALS 8Repeat size and methylation (2019)Open reference2
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Impaired nucleosome spacing affects gene expression 8Repeat size and methylation (2019)Open reference3
CHD Family
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CHD7: Mutations linked to ALS 8Repeat size and methylation (2019)Open reference4
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CHD1/2: Open chromatin regulation 8Repeat size and methylation (2019)Open reference5
Chromatin Remodeling and ALS Genes
| Complex | Subunit | Role in ALS |
|---|---|---|
| SWI/SNF | SMARCA4 | Gene activation |
| NuRD | CHD4 | Repression |
| ISWI | SMARCA5 | Nucleosome spacing |
| CHD | CHD1/2/7 | Chromatin structure |
Epigenetic Therapy Targeting Chromatin Remodeling
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Small molecule modulators: Under development 8Repeat size and methylation (2019)Open reference6
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BET inhibitors: Bromodomain targeting 8Repeat size and methylation (2019)Open reference7
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Chromatin assembly factors: Therapeutic potential 8Repeat size and methylation (2019)Open reference8
RNA Metabolism and Epigenetics
The intimate connection between RNA metabolism and epigenetics is particularly relevant in ALS.
TDP-43 and Epigenetics
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TDP-43 binds to DNA and RNA 8Repeat size and methylation (2019)Open reference9
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Chromatin regulation by TDP-43 9C9orf72 methylation clinical (2016)Open reference0
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HDAC6 and TDP-43 clearance 9C9orf72 methylation clinical (2016)Open reference1
FUS and Epigenetic Regulators
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FUS protein interacts with:
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Histone modifiers 9C9orf72 methylation clinical (2016)Open reference2
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Chromatin remodelers 9C9orf72 methylation clinical (2016)Open reference3
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Transcription factors 9C9orf72 methylation clinical (2016)Open reference4
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RNA Methylation
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N6-methyladenosine (m6A): RNA modification dysregulated in ALS 9C9orf72 methylation clinical (2016)Open reference5
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m6A writers: METTL3/14 expression changes 9C9orf72 methylation clinical (2016)Open reference6
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m6A readers: YTHDF2 alterations 9C9orf72 methylation clinical (2016)Open reference7
Neuroinflammation and Epigenetics
Epigenetic regulation of neuroinflammation in ALS:
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Microglial activation: HDAC-dependent 9C9orf72 methylation clinical (2016)Open reference8
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NF-κB pathway: Epigenetic control 9C9orf72 methylation clinical (2016)Open reference9
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TREM2: Epigenetic regulation in microglia 10Hypermethylation therapy (2015)Open reference0
Metabolic Epigenetics
Metabolic dysfunction in ALS:
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AMPK: Epigenetic regulation 10Hypermethylation therapy (2015)Open reference1
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Sirtuins: Metabolic sensors 10Hypermethylation therapy (2015)Open reference2
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NAD+ metabolism: Therapeutic target 10Hypermethylation therapy (2015)Open reference3
Therapeutic Approaches
Clinical Trials
| Agent | Target | Phase | Status |
|---|---|---|---|
| Valproic acid | HDACs | Phase I/II | Completed |
| Ricolinostat | HDAC6 | Phase I/II | Recruiting |
| ASO (tofersen) | SOD1 | Approved | Completed |
| ASO (C9orf72) | C9orf72 | Phase I/II | Ongoing |
Emerging Strategies
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Epigenetic editing: CRISPR-dCas9 fusions 10Hypermethylation therapy (2015)Open reference4
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Combination therapy: HDAC + ASO 10Hypermethylation therapy (2015)Open reference5
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Repurposing: Existing epigenetic drugs 10Hypermethylation therapy (2015)Open reference6
Biomarkers
DNA Methylation Biomarkers
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Peripheral blood patterns: Diagnostic potential 10Hypermethylation therapy (2015)Open reference7
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Disease progression markers: Longitudinal changes 10Hypermethylation therapy (2015)Open reference8
miRNA Biomarkers
| miRNA | Sample | Use |
|---|---|---|
| miR-181a-5p | CSF | Diagnostic |
| miR-124-3p | CSF | Diagnostic |
| miR-155 | Blood | Progression |
| miR-146a | Blood | Inflammatory |
See Also
Confidence Assessment
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Evidence quality: High (extensive human post-mortem studies, iPSC models, and clinical data)
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Therapeutic translatability: High (multiple clinical trials ongoing)
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Biarker potential: Moderate to High (several candidates under validation)
References
- TDP-43 pathology in ALS (2006)
- Protein homeostasis in ALS (2019)
- Neuroinflammation epigenetics (2019)
- Metabolic dysfunction in ALS (2019)
- Excitotoxicity epigenetics (2019)
- RAN translation in C9orf72 (2013)
- C9orf72 methylation (2014)
- Repeat size and methylation (2019)
- C9orf72 methylation clinical (2016)
- Hypermethylation therapy (2015)
- Regional methylation (2018)
- SOD1 methylation (2017)
- SOD1 epigenetic therapy (2019)
- DNMT inhibitors ALS (2018)
- TDP-43 in ALS (2006)
- TDP-43 epigenetic regulation (2019)
- MeCP2 and TDP-43 (2018)
- Global hypomethylation ALS (2011)
- Region-specific ALS methylation (2019)
- Blood methylation biomarkers (2019)
- Epigenetic clock ALS (2019)
- Age-related ALS methylation (2020)
- ALS subtype methylation (2019)
- DNMT inhibitors (2007)
- Epigenetic readers (2019)
- HDAC inhibitors in ALS (2003)
- HDAC expression in ALS (2010)
- HDAC2 upregulation (2018)
- HDAC4/5 redistribution (2019)
- HDAC6 in ALS (2019)
- H3K9ac reduction (2019)
- H3K27ac enhancer changes (2019)
- H4K12ac in ALS (2019)
- H3K4me3 redistribution (2019)
- H3K36me3 in RNA splicing (2019)
- H3K27me3 increase (2019)
- H3K9me2/3 in ALS (2019)
- Bivalent domains (2006)
- Stem cell bivalency in disease (2019)
- SIRT1 in ALS (2019)
- SIRT2 and oxidative stress (2019)
- SIRT3 mitochondrial function (2019)
- NAD+ precursors ALS (2019)
- miR-9 in ALS (2014)
- miR-9 targets (2019)
- miR-124 neuronal identity (2019)
- miR-124 in ALS (2019)
- miR-124 therapy (2019)
- miR-23a in ALS (2019)
- miR-155 SOD1 mice (2013)
- C9orf72 and miRNA (2019)
- FUS and miRNA (2019)
- miR-181a-5p biomarker (2016)
- miR-124-3p CSF (2019)
- miRNA panels ALS (2018)
- NEAT1 in ALS (2019)
- MALAT1 in ALS (2019)
- HOTAIR in ALS (2019)
- ALSINC (2019)
- SOX2OT in ALS (2019)
- circSMARCA5 ALS (2019)
- circCFL1 neurodegeneration (2019)
- circRNA sponges (2019)
- SNORD115/116 ALS (2019)
- sdRNAs in ALS (2019)
- BRG1 in ALS (2019)
- BRM in ALS (2019)
- BAF mutations ALS (2019)
- SWI/SNF targets (2019)
- CHD4 in ALS (2019)
- MTA expression (2019)
- NuRD functions (2019)
- SMARCA5 reduction (2019)
- ISWI function (2019)
- CHD7 mutations (2019)
- CHD1/2 in ALS (2019)
- SWI/SNF modulators (2019)
- BET inhibitors (2019)
- Chromatin assembly (2019)
- TDP-43 DNA binding (2019)
- TDP-43 chromatin (2019)
- HDAC6 TDP-43 clearance (2019)
- FUS histone modifiers (2019)
- FUS chromatin remodelers (2019)
- FUS transcription (2019)
- m6A in ALS (2019)
- METTL3/14 expression (2019)
- YTHDF2 in ALS (2019)
- Microglial HDAC (2019)
- NF-kB epigenetics (2019)
- TREM2 epigenetics (2019)
- AMPK epigenetic regulation (2019)
- Sirtuins metabolic sensors (2019)
- NAD+ metabolism (2019)
- CRISPR epigenome editing (2019)
- Combination therapy (2019)
- Drug repurposing (2019)
- Diagnostic blood patterns (2019)
- Progression biomarkers (2019)
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