This therapeutic strategy targets spliceosome dysregulation—a hallmark of multiple neurodegenerative diseases—to restore proper mRNA splicing patterns and rescue neuronal function. Small molecule splice modulators can correct aberrant splicing events that produce toxic protein isoforms or disrupt essential neuronal gene expression.
- Primary Target: Spliceosome complex (U1 snRNP, SF3B1, SRSF2, hnRNPs)
- Target Type: Small molecule splice modulator / RNA-binding oligonucleotide
- Expression: Ubiquitous spliceosome machinery with neuron-specific vulnerability to splice dysregulation
Spliceosome dysfunction is increasingly recognized as a key contributor to neurodegeneration:
- TDP-43 pathology disrupts splicing of thousands of transcripts
- C9orf72 hexanucleotide repeat produces toxic DPR proteins through aberrant splicing
- STMN2 splicing disruption causes axonal degeneration
- Correction of splice patterns can restore neuronal viability
- APOE splicing isoform imbalances affect lipid metabolism
- ** tau isoform ratios** influence aggregation propensity
- Synaptic protein mis-splicing impairs neurotransmission
- SNCA exon skipping produces aggregation-resistant isoforms
- LRRK2 splice variants affect kinase activity
- GBA1 splicing impacts lysosomal function
- Splice-switching oligonucleotides (SSOs): Antisense oligonucleotides that block splicing enhancers/suppressors to redirect splicing
- Small molecule modulators: Drugs like E7107, H3B-8800 (currently in cancer trials) that modulate spliceosome activity
- U1 snRNP restoration: Enhance U1 function to correct 5' splice site recognition
- hnRNP modulation: Target hnRNP A1/A2 to restore splicing balance
flowchart TD
A["Spliceosome Dysregulation"] --> B["Mis-spliced mRNA"]
B --> C["Toxic Protein Isoforms"]
C --> D["Dominant-Negative Effects"]
D --> E["Neuronal Dysfunction"]
F["SSO or Small Molecule"] --> G["Correct Splice Pattern"]
G --> H["Restored Protein Isoform Balance"]
H --> I["Neuronal Function Recovery"]
G --> J["Reduced Toxic Load"]
J --> K["Neuroprotection"]
- Oligonucleotides: Require CNS delivery via intrathecal or intranasal routes; LNP or AAV delivery under development
- Small molecules: Blood-brain barrier penetration varies by compound; E7107 has limited BBB crossing
- Novel approaches: Splice-modulating ASO conjugates with brain-targeting peptides
- On-target toxicity: Broad splice modulation affects essential genes
- Therapeutic window: Selective modulation of disease-relevant splicing events required
- Off-target effects: Careful sequence design needed for SSOs
- + Autophagy inducers: Enhanced clearance of misfolded proteins from corrected splicing
- + Proteostasis modulators: Synergistic restoration of protein homeostasis
- + Gene therapy: Direct delivery of corrected splice isoforms
- Direct: mRNA-seq to quantify splice event correction
- Indirect: Protein isoform ratios in CSF (e.g., tau 3R/4R ratio)
- Clinical: Neurofilament light chain (NfL) for disease progression
| Dimension |
Score |
Rationale |
| Novelty |
9 |
Novel therapeutic approach not yet in clinical trials for neurodegeneration |
| Mechanistic Rationale |
8 |
Strong evidence for splice dysregulation across AD, PD, ALS, FTD |
| Root-Cause Coverage |
7 |
Addresses upstream dysregulation rather than downstream aggregation |
| Delivery Feasibility |
5 |
BBB remains challenge; intrathecal feasible but invasive |
| Safety Plausibility |
6 |
On-target risks require precise targeting |
| Combinability |
8 |
Synergistic with proteostasis and autophagy approaches |
| Biomarker Availability |
7 |
mRNA-seq enables direct measurement of splice correction |
| De-risking Path |
5 |
Cancer trials provide initial safety data; CNS-specific data needed |
| Multi-disease Potential |
9 |
Applicable to ALS, FTD, AD, PD |
| Patient Impact |
8 |
High unmet need in genetic forms (C9orf72, TARDBP) |
| Total |
72/100 |
|
-
iPSC Neuron Validation
- Obtain iPSC lines from C9orf72, TARDBP, and sporadic ALS/FTD patients
- Differentiate to motor neurons and cortical neurons
- Measure: splice patterns (RNA-seq), TDP-43 localization, STMN2 splicing, neuronal viability
- Test SSO delivery via lipid nanoparticles or AAV9
- Timeline: 4-6 months
- Estimated cost: $150,000-200,000
-
SSO Lead Optimization
- Design splice-switching oligonucleotides targeting disease-relevant exons:
- C9orf72 intron 1b (reduce toxic DPR translation)
- STMN2 exon 2a (restore axonal stability)
- Tau exon 10 (balance 3R/4R ratio for AD)
- In vitro screening in patient-derived neurons
- Timeline: 6-9 months
- Estimated cost: $300,000-500,000
-
Small Molecule Modulator Repurposing
- Screen FDA-approved drugs for splice-modulating activity
- Focus on CNS-penetrant compounds
- Test in ALS/FTD model systems
- Timeline: 3-4 months
- Estimated cost: $100,000-150,000
-
First-in-Human Study Design
- Phase 1: Dose escalation in healthy volunteers (if SSO) or cancer patients (if small molecule)
- Phase 1b: Patients with confirmed TDP-43 pathology (CSF biomarker positive)
- Key biomarkers: CSF splice junction reads, NfL, phosphorylated TDP-43
- Timeline: 24-36 months for Phase 1/2
- Estimated cost: $5-10M
-
Patient Population
- Genetically confirmed C9orf72 carriers (early symptomatic)
- TARDBP mutation carriers
- Sporadic ALS/FTD with TDP-43 pathology
- Target enrollment: 30-50 patients
-
Regulatory Strategy
- Orphan drug designation for rare genetic forms
- Fast track for life-threatening indication
- Parallel consultation with FDA/EMA
| Partner Type |
Target Organization |
Rationale |
| Pharma |
Biogen, Ionis |
Existing ASO platform and ALS pipeline |
| Pharma |
Roche, PTC |
Small molecule CNS capabilities |
| Biotech |
Wave Life Sciences |
Stereopure ASO technology |
| Academic |
University of Miami Brain Bank |
C9orf72 patient tissue |
| Academic |
NIH RAID program |
Preclinical screening resources |
| VC |
ARCH, Polaris, Third Rock |
Neurodegeneration-focused |
| Dimension |
Score |
Rationale |
| Novelty |
8/10/10 |
Splice-modulating therapies are novel; antisense oligonucleotides for splicing in CNS emerging |
| Mechanistic Rationale |
7/10/10 |
Can correct splice defects, restore protein isoforms; precise mechanism for neurodegeneration |
| Addresses Root Cause |
7/10/10 |
Addresses genetic regulation; can target disease-causing splice variants |
| Delivery Feasibility |
5/10/10 |
ASO delivery to brain challenging; intrathecal administration needed |
| Safety Plausibility |
6/10/10 |
Off-target splicing effects possible; requires careful design |
| Combinability |
6/10/10 |
Combines with gene therapy and traditional small molecules |
| Biomarker Availability |
6/10/10 |
Splice products measurable via RNA sequencing; biomarker development ongoing |
| De-risking Path |
7/10/10 |
ASO platform established; several CNS trials ongoing |
| Multi-disease Potential |
7/10/10 |
Relevant for genetic forms of AD, PD, ALS, Huntington disease |
| Patient Impact |
7/10/10 |
Could provide disease-modifying effects for genetically predisposed patients |
| Total |
66/100 |
|
| Phase |
Duration |
Key Milestones |
| Lead Optimization |
6-12 months |
Screen candidates, optimize PK/PD |
| Preclinical (IND-enabling) |
18-24 months |
GLP toxicology, efficacy in models, GMP manufacturing |
| IND-enabling studies |
12-18 months |
GLP toxicology, CMC, regulatory meetings |
| Phase I |
12-18 months |
Safety, dose-ranging in patients |
- Lead optimization: $3-6M
- Preclinical development: $10-18M
- IND-enabling studies: $8-15M
- Phase I trials: $15-25M
- Total to Phase I: $36-64M
- University of Pennsylvania — Dr. John Trojanowski
- Stanford University — Dr. Marion Buckwalter
- UCLA — Dr. Varghese John
- University of Michigan — Dr. Henry Paulsen
- Karolinska Institutet — Dr. Tomas M barek
- Biogen — Neuroscience pipeline
- Roche — CNS portfolio
- Merck — Neuroscience division
- Takeda — Neuroscience acquisitions
- AbbVie — CNS programs
| Risk |
Likelihood |
Impact |
Mitigation |
| Brain penetration failure |
Medium |
High |
Early PK/PD screening |
| Off-target effects |
Low |
Medium |
Selectivity profiling |
| Clinical trial recruitment |
Low |
Medium |
Multi-center design |
- Fast Track Designation: Possible
- Biomarker Development: Relevant biomarkers
- Accelerated Approval: Possible with biomarker endpoint