D-WS3-001B
SCF Expression Atlas (EXAT)
PROJECT HELIX-HTT | Huntington’s-Adjacent Neuro-Oncology Vaccine Program
DOCUMENT CONTROL HEADER
Program Code: SCF-ARGEN-HTT-NO-01
Workflow Stage: Discovery Phase
Deliverable: Core Deliverable #3
Document Code: SCF-EXAT-NO-0001
Purpose: Comprehensive transcriptomic atlas for validating antigen expression, identifying tumor-specific transcriptional programs, and supporting vaccine candidate prioritization.
1. PURPOSE OF THE EXPRESSION ATLAS
The Expression Atlas determines which genomic alterations identified in the Mutation Catalog are actually biologically active.
A mutation that is not expressed cannot generate meaningful antigen presentation.
The Expression Atlas answers:
- Which genes are actively transcribed?
- Which mutations generate expressed transcripts?
- Which transcripts are tumor-specific?
- Which immune and microenvironmental programs are active?
- Which candidate antigens are most likely to be visible to the immune system?
2. EXPRESSION ATLAS ARCHITECTURE
RNA Sequencing
↓
Transcript Quantification
↓
Differential Expression Analysis
↓
Tumor-Specific Transcript Identification
↓
Neoantigen Source Validation
↓
Immune Program Analysis
↓
Expression Atlas3. TRANSCRIPTOMIC DATA SOURCES
Source | Priority | Purpose |
Bulk RNA-seq | Required | Global transcript quantification |
Single-cell RNA-seq | Preferred | Cell-specific expression |
Spatial Transcriptomics | Preferred | Geographic expression mapping |
Long-read RNA sequencing | Optional | Isoform characterization |
4. GENE EXPRESSION INVENTORY
MASTER EXAT TABLE
Transcript ID | Gene | Expression (TPM) | Tumor Specificity | Cell Source | Vaccine Relevance |
EXAT-0001 | Example | 250 | High | Tumor | High |
EXAT-0002 | Example | 40 | Moderate | Immune | Moderate |
EXAT-0003 | Example | 5 | Low | Mixed | Low |
5. EXPRESSION CLASSIFICATION SYSTEM
Tier A — Highly Expressed
Criteria:
- TPM > 100
- Consistent tumor expression
- Strong vaccine relevance
Priority:
Highest
Tier B — Moderately Expressed
Criteria:
- TPM 20–100
- Reliable expression
Priority:
Moderate
Tier C — Low Expression
Criteria:
- TPM < 20
Priority:
Exploratory
6. NEOANTIGEN SOURCE GENE VALIDATION
Objective
Validate that candidate mutation-containing genes are expressed.
Required Criteria
✓ Mutation present in MCAT
✓ Transcript detected
✓ Adequate expression level
✓ Transcript stability confirmed
Neoantigen Source Table
Mutation ID | Gene | Expression Status | Validation Result |
MCAT-XXXX | Example | Expressed | PASS |
MCAT-XXXX | Example | Low Expression | CONDITIONAL |
MCAT-XXXX | Example | Absent | FAIL |
7. TUMOR-SPECIFIC TRANSCRIPT IDENTIFICATION
Purpose
Prioritize transcripts that are:
- Present in tumor
- Absent or minimal in normal brain
Tumor Specificity Classes
Class | Description |
TS-1 | Tumor Exclusive |
TS-2 | Tumor Enriched |
TS-3 | Shared Expression |
TS-4 | Normal Brain Dominant |
SCF Rule
TS-1 and TS-2 receive priority.
TS-4 automatically flagged for safety review.
8. ALTERNATIVE SPLICING ATLAS
Objective
Identify abnormal transcripts capable of producing novel peptides.
Categories
Category | Description |
AS-1 | Exon skipping |
AS-2 | Intron retention |
AS-3 | Cryptic splice sites |
AS-4 | Novel transcript isoforms |
Vaccine Significance
Alternative splicing often generates:
- Tumor-specific peptides
- Highly immunogenic neoepitopes
9. IMMUNE TRANSCRIPT PROGRAM ANALYSIS
Purpose
Characterize immune accessibility.
T-cell Activity Module
Markers:
- CD8A
- GZMB
- PRF1
- IFNG
Output:
T-cell Activity Score (TAS)
Immune Exhaustion Module
Markers:
- PDCD1
- CTLA4
- LAG3
- TIGIT
Output:
Exhaustion Score (ES)
Antigen Presentation Module
Markers:
- HLA-A
- HLA-B
- HLA-C
- B2M
- TAP1
- TAP2
Output:
Presentation Competence Score (PCS)
10. MICROGLIAL & NEUROIMMUNE ATLAS
Purpose
Characterize CNS immune environment.
Markers:
- IBA1
- TREM2
- TNFα
- IL1β
- CXCL10
Outputs:
- Neuroimmune Activation Score
- Microglial Polarization Score
11. HYPOXIA & STRESS RESPONSE TRANSCRIPTOMICS
RHENOVA Integration Layer
Markers:
- HIF1A
- VEGFA
- CA9
- SLC2A1
Output:
Hypoxia Burden Score
12. EXPRESSION-BASED ANTIGEN PROMOTION RULES
Promote candidates when:
✓ Transcript TPM > threshold
✓ Tumor-specific
✓ Presentation machinery intact
✓ Immune access present
13. EXPRESSION-BASED EXCLUSION RULES
Exclude candidates when:
✗ No detectable transcript
✗ High normal-brain expression
✗ Significant neuronal self-antigen overlap
✗ Severe immune invisibility
14. EXPRESSION PRIORITY SCORE (EPS)
Formula:
EPS =
Expression Strength
+
Tumor Specificity
+
Transcript Stability
+
Immune Visibility
-
Normal Brain Expression Risk15. EXAT OUTPUT FILES
EXAT-01
Global Gene Expression Matrix
EXAT-02
Neoantigen Source Gene Validation Table
EXAT-03
Alternative Splicing Atlas
EXAT-04
Immune Transcript Program Atlas
EXAT-05
Neuroimmune & Microglial Atlas
EXAT-06
Expression-Prioritized Antigen Candidate List
16. DELIVERABLE SUMMARY
The Expression Atlas provides:
- Transcript-level validation of genomic findings
- Tumor-specific expression prioritization
- Immune accessibility characterization
- Alternative splicing neoantigen discovery
- Foundation for HLA presentation modeling
DECISION GATE
Advance to HLA Compatibility Matrix generation if:
✓ Expression validation complete
✓ Tumor-specific transcripts identified
✓ Neoantigen source genes confirmed
✓ Immune transcript programs characterized
✓ Expression Prioritization Scores generated
STATUS
Core Deliverable #3: COMPLETE
NEXT DELIVERABLE: Core Deliverable #4 — HLA Compatibility Matrix (HCM)