ID: h-a976bf02b0
Hypothesis

Structured Intronic Scaffold Regions in Enhancer-dilncRNAs Enable Cell-Type Selective Targeting

Structured Intronic Scaffold Regions in Enhancer-dilncRNAs Enable Cell-Type Selective Targeting starts from the claim that modulating ECEPs (PAX6-AS1, KCNC2-AS1) within the disease context of molecular biology can redirect a disease-rele.
🧬 ECEPs (PAX6-AS1, KCNC2-AS1)🩺 molecular-biology🎯 Composite 49%💱 $0.52▲5.5%proposed
molecular biology
EvidencePending (0%)📖 0 cit🗣 1 debates 6 support 2 oppose
✓ All Quality Gates Passed
Mechanistic 0.45 (15%) Evidence 0.42 (15%) Novelty 0.82 (12%) Feasibility 0.38 (12%) Impact 0.55 (12%) Druggability 0.48 (10%) Safety 0.52 (8%) Competition 0.70 (6%) Data Avail. 0.35 (5%) Reproducible 0.42 (5%) KG Connect 0.50 (8%) 0.489 composite

🧪 Overview

Mechanistic Overview


Structured Intronic Scaffold Regions in Enhancer-dilncRNAs Enable Cell-Type Selective Targeting starts from the claim that modulating ECEPs (PAX6-AS1, KCNC2-AS1) within the disease context of molecular biology can redirect a disease-relevant process. The original description reads: "## Mechanistic Overview Structured Intronic Scaffold Regions in Enhancer-dilncRNAs Enable Cell-Type Selective Targeting starts from the claim that modulating ECEPs (PAX6-AS1, KCNC2-AS1) within the disease context of molecular biology can redirect a disease-relevant process. The original description reads: "## Mechanistic Overview Structured Intronic Scaffold Regions in Enhancer-dilncRNAs Enable Cell-Type Selective Targeting starts from the claim that Cancer-specific enhancer-associated dilncRNAs (ECEPs) such as PAX6-AS1 and KCNC2-AS1 contain conserved intronic stem-loop structures absent in non-cancer cells due to alternative splicing. ASOs targeting these conserved structured regions would preferentially disrupt oncogenic enhancer function (BET proteins, Mediator complex scaffolding) and reduce BRD4 occupancy at MYC enhancers.

...

🧬 Mechanism

🧬 Curated Mechanism Pathway

Curated pathway from expert analysis

flowchart TD
    A["ECEPs Enhancer-Linked lncRNA<br/>PAX6-AS1 and KCNC2-AS1"]
    B["Structured Intronic Scaffold<br/>RNA Secondary Structure Element"]
    C["Cell-Type Selective Expression<br/>Neuron and Glia Specificity"]
    D["Enhancer-Promoter Loop<br/>Topological Domain Regulation"]
    E["Target Gene Activation<br/>PAX6 or KCNC2 Transcription"]
    F["ECEP Dysregulation<br/>Altered Enhancer Activity"]
    G["Neuronal Identity Loss<br/>Ion Channel and TF Misregulation"]
    A --> B
    B --> C
    C --> D
    D --> E
    F -.->|"disrupts"| D
    F --> G
    style A fill:#1a237e,stroke:#4fc3f7,color:#4fc3f7
    style E fill:#7b1fa2,stroke:#ce93d8,color:#ce93d8
    style F fill:#b71c1c,stroke:#ef9a9a,color:#ef9a9a
    style G fill:#b71c1c,stroke:#ef9a9a,color:#ef9a9a

⚖️ Evidence

⚖️ Evidence Matrix6 supports2 contradicts
Supports
EPE lncRNAs are dynamically regulated and conserved
Supports
Pathogenicity and virulence of Japanese encephalitis virus: Neuroinflammation and neuronal cell damage.
Virulence2021PMID:33724154
Supports
Human herpesvirus-associated transposable element activation in human aging brains with Alzheimer's disease.
Alzheimers Dement2025PMID:39985481
Supports
SPI1-mediated MIR222HG transcription promotes proneural-to-mesenchymal transition of glioma stem cells and immunosuppressive polarization of macrophages.
Theranostics2023PMID:37351164
Supports
Chromatin remodeling effects on enhancer activity.
Cell Mol Life Sci2016PMID:27026300
Supports
Sex Differences in Brain Cell Type-Specific Chromatin Accessibility in Schizophrenia.
Biol Psychiatry2026PMID:41072639
Contradicts
Incomplete structural characterization and mechanism
Contradicts
Cell-type selectivity dependent on unknown splicing patterns
📖 Linked Papers

No linked papers recorded for this hypothesis yet.

🏥 Translation

🧬 3D Protein Structure — ECEPS

No curated PDB or AlphaFold mapping for ECEPS yet. Search RCSB →

🧠 GTEx v10 Brain ExpressionJSON

Median TPM across 13 brain regions for ECEPs (PAX6-AS1, KCNC2-AS1) from GTEx v10.

Cerebellar Hemisphere40.6 Cerebellum37.3 Cortex3.5 Caudate basal ganglia3.3 Anterior cingulate cortex BA243.3 Frontal Cortex BA93.1 Amygdala3.1 Putamen basal ganglia2.7 Nucleus accumbens basal ganglia2.5 Hippocampus1.8 Spinal cord cervical c-11.3 Hypothalamus1.0 Substantia nigra1.0median TPM (GTEx v10)

💉 Clinical Trials

No clinical trials data linked to this hypothesis yet.

No curated ClinVar variants loaded for this hypothesis.

Run scripts/backfill_clinvar_variants.py to fetch P/LP/VUS variants.

🔍 Search ClinVar for ECEPs (PAX6-AS1, KCNC2-AS1) →

No DepMap CRISPR Chronos data found for ECEPs (PAX6-AS1, KCNC2-AS1).

Run python3 scripts/backfill_hypothesis_depmap.py to populate.

💰 Estimated Development
Cost
$0
Timeline

🏆 Tournament

🏆 Arenas / Elo

No arena matches recorded yet. Browse Arenas →

📊 Market Indicators

7d Trend
Stable
7d Momentum
▼ 0.2%
Volatility
Low
0.0078
Events (7d)
2
Price History
▲5.5%

💾 Resource Usage

LLM Tokens
12,828
$0.0385
Total Cost
$0.0385

🔮 Predictions

🔎 Predictions vs Observations2 predictions · 0 with recorded observations
PredictionPredictedObservedStatusConf
IF RNA structure mapping (icSHAPE) is performed on PAX6-AS1 and KCNC2-AS1 introns in matched tumor (n=20) vs adjacent normal (n=20) samples from TCGA breast cancer cohort, THEN cancer samples will shoConserved stem-loop structures retained in >70% of cancer transcripts vs <30% of normal transcripts, with structural divergence score (Shannon entropy of paired— no observation —pending0.42
IF ASOs (15-18nt gapmer) targeting the conserved intronic stem-loop region (nt 200-400) of PAX6-AS1 are delivered to MDA-MB-231 breast cancer cells at 50nM for 48 hours, THEN BRD4 ChIP-seq signal at tBRD4 occupancy at MYC enhancer reduced by ≥50% with corresponding ≥40% decrease in MYC nascent transcription (EU incorporation assay) and no toxicity (>90% cell— no observation —pending0.38
🔮 Falsifiable Predictions (2)
pendingconf 42%
IF RNA structure mapping (icSHAPE) is performed on PAX6-AS1 and KCNC2-AS1 introns in matched tumor (n=20) vs adjacent normal (n=20) samples from TCGA breast cancer cohort, THEN cancer samples will show ≥2-fold higher frequency of conserved intronic stem-loop retention (>85% base pairing) compared to
Predicted outcome: Conserved stem-loop structures retained in >70% of cancer transcripts vs <30% of normal transcripts, with structural divergence score (Shannon entropy
Falsification: Normal tissue samples show equivalent or greater conservation of intronic stem-loop structures as cancer samples, or cancer samples show no structured region enrichment, disproving the claim that thes
pendingconf 38%
IF ASOs (15-18nt gapmer) targeting the conserved intronic stem-loop region (nt 200-400) of PAX6-AS1 are delivered to MDA-MB-231 breast cancer cells at 50nM for 48 hours, THEN BRD4 ChIP-seq signal at the MYC enhancer (chr8:128,748,000-128,752,000) will decrease by >50% compared to ASO-control treated
Predicted outcome: BRD4 occupancy at MYC enhancer reduced by ≥50% with corresponding ≥40% decrease in MYC nascent transcription (EU incorporation assay) and no toxicity
Falsification: BRD4 occupancy at MYC enhancer does not change (change <20%) or increases following ASO treatment, indicating the structured intronic region does not functionally scaffold BET protein engagement.
Metadatasource: v1_phase_c_backfill · origin_type: debate_synthesizer
sourcev1_phase_c_backfill
origin_typedebate_synthesizer
_schema_version1
📊 Evidence Profile
Evidence Balance
+0%
Certainty
0%
Debates
0
Incoming
0
Outgoing
0
0 supporting 0 contradicting 0 neutral
Public annotations (0)Annotate on Hypothes.is →
No public annotations yet.