PROJECT HELIX-HTT | Huntington’s-Adjacent Neuro-Oncology Vaccine Program | Construct Design Blueprint

DV02-01 — Construct Design Blueprint

HELIX-VAX-01 / HELIX-VAX-02

PROJECT HELIX-HTT | Huntington’s-Adjacent Neuro-Oncology Vaccine Program

1. Construct Design Purpose

The Construct Design Blueprint defines how validated antigens from the Validated Antigen Master Inventory (VAMI) are assembled into vaccine-ready therapeutic constructs.

The design goal is to create a vaccine that can:

Present multiple tumor antigens
Activate CD8 cytotoxic T cells
Support CD4 helper T-cell memory
Reduce immune escape
Preserve CNS safety
Remain manufacturable for preclinical and IND development

2. Lead Construct Overview

HELIX-VAX-01

Field	Specification
Platform	Multi-antigen mRNA vaccine
Development Role	Lead construct
Antigen Count	8–12
Primary Function	Personalized anti-tumor immunity
Target Setting	Huntington’s-adjacent neuro-oncology
Development Status	Advance

3. Backup Construct Overview

HELIX-VAX-02

Field	Specification
Platform	Synthetic long peptide vaccine
Development Role	Backup construct
Antigen Count	5–8
Primary Function	Manufacturing-risk mitigation
Target Setting	Same antigen universe as HELIX-VAX-01
Development Status	Parallel backup

4. HELIX-VAX-01 Construct Architecture

Antigen Composition

Antigen Class	Target Allocation	Role
Personalized neoantigens	60–70%	Tumor-specific core
Fusion antigens	10–20%	High-specificity junction targets
Tumor-associated antigens	10–20%	Breadth and redundancy
SCF stress antigens	0% clinical construct	Research-only reserve

Reference Antigen Layout

5' Cap
↓
UTR Optimization Region
↓
Signal / Trafficking Optimization Region
↓
Neoantigen A1
↓
Processing Linker
↓
Neoantigen A2
↓
Processing Linker
↓
Fusion Antigen F1
↓
Processing Linker
↓
Neoantigen A3
↓
Processing Linker
↓
Neoantigen A4
↓
Processing Linker
↓
Tumor-Associated Antigen B1
↓
Processing Linker
↓
Neoantigen A5
↓
Poly(A) Tail

5. HELIX-VAX-02 Construct Architecture

Synthetic Long Peptide Backup Design

Design Feature	Specification
Peptide Length	Long peptide format
Antigen Count	5–8
Priority	Highest-confidence antigens only
Use Case	Backup / confirmatory platform
Immune Goal	APC uptake + broad presentation

Reference Peptide Set

SLP-1: Neoantigen A1
SLP-2: Neoantigen A2
SLP-3: Fusion Antigen F1
SLP-4: Neoantigen A3
SLP-5: Tumor-Associated Antigen B1
SLP-6: Backup Neoantigen A4

6. Antigen Ordering Logic

Antigens are ordered according to SCF ranking hierarchy:

Clonal Neoantigen
↓
Confirmed Presented Neoantigen
↓
Fusion Antigen
↓
Secondary Neoantigen
↓
Tumor-Associated Antigen
↓
Exploratory / Backup Antigen

Ordering Rules

Rule	Purpose
Place clonal neoantigens early	Maximize core tumor coverage
Include fusion antigen near front-middle	Preserve high-specificity junction visibility
Place TAAs later	Reduce dominance over personalized antigens
Exclude SCF stress antigens from clinical construct	Maintain first-generation safety
Avoid repeated similar peptide motifs	Reduce processing competition

7. Linker Design Strategy

Purpose of Linkers

Processing linkers separate antigen units so immune-processing machinery can generate individual peptides efficiently.

Linker Requirements

Requirement	Rationale
Flexible	Supports proper processing
Non-immunodominant	Avoids immune distraction
Cleavable	Enables antigen release
Non-toxic	Maintains safety
Low homology to CNS proteins	Reduces autoimmune risk

8. Immune Activation Design

CD8 Cytotoxic Layer

Purpose:

Activate tumor-killing T cells
Prioritize HLA-I antigens
Maximize class I presentation

CD4 Helper Layer

Purpose:

Improve immune memory
Support sustained CD8 activity
Reduce short-lived response failure

Construct Balance Target

Immune Layer	Target Role
CD8	Primary tumor killing
CD4	Immune durability
Innate activation	Adjuvant-dependent

9. Immune Escape Resistance Design

Escape Prevention Features

Feature	Function
Multi-antigen loading	Prevents single-antigen escape
Clonal antigen preference	Targets broad tumor population
Fusion antigen inclusion	Targets tumor-specific junctions
Backup antigen set	Enables rapid construct revision
TAA support	Adds breadth if neoantigens are lost

10. CNS Safety Architecture

Because this vaccine targets neuro-oncology, CNS safety is mandatory.

Required Exclusion Filters

Reject antigens with:

High similarity to essential neuronal proteins
High expression in normal brain
Predicted autoimmune neurotoxicity
Strong microglial hyperactivation risk
Poor SCF neuroimmune compatibility

CNS Compatibility Requirement

Safety Status	Action
Green	Include
Yellow	Backup / review
Red	Exclude

11. SCF Microenvironment Integration

Construct engineering is adjusted by the SCF-MES score.

MES Domain	Construct Impact
High immune access	Proceed with standard antigen load
Low immune access	Favor stronger adjuvant support
High hypoxia	Pair with RHENOVA conditioning strategy
High redox burden	Monitor oxidative immune suppression
High immune suppression	Consider combination immunotherapy
Neuroimmune activation	Tighten CNS safety threshold

12. Construct Quality Attributes

CQA	Definition
Identity	Correct antigen sequence
Purity	Minimal contaminants
Potency	Ability to induce antigen-specific immunity
Stability	Maintains integrity during storage
Safety	No unacceptable CNS cross-reactivity
Manufacturability	Reproducible production pathway

13. Construct Scoring

Construct Development Score

CDS =
Antigen Quality
+ Presentation Strength
+ Immune Breadth
+ Escape Resistance
+ Manufacturability
- CNS Risk
- Immune Escape Risk

Advancement Thresholds

CDS Range	Decision
≥85	Advance as lead
70–84	Advance as backup
55–69	Optimize
<55	Redesign

14. Final Construct Recommendation

Lead Candidate

HELIX-VAX-01

Platform: Multi-antigen mRNA

Reason: highest adaptability, broad antigen inclusion, personalized redesign capacity.

Backup Candidate

HELIX-VAX-02

Platform: Synthetic long peptide

Reason: manufacturing simplicity and regulatory familiarity.

15. Immediate Next Steps

Generate antigen ordering map
Finalize linker architecture plan
Conduct manufacturability assessment
Complete CNS safety engineering report
Advance to adjuvant selection and optimization package

Status

DV02-01 Construct Design Blueprint: Complete

Next Sub-Deliverable: DV02-02 Antigen Ordering Map