COLONYVAQ™, a Quantum-Classical Guided Personalized Neoantigen Vaccine for MSS Stage III Colorectal Cancer

Inclusion criteria

• \*\*Diagnosis / Histology\*\*
• Histologically confirmed adenocarcinoma of the colon or rectum.
• Pathology report available for central or sponsor review (if requested), including:
• Primary tumor site (colon vs rectum)
• Grade of differentiation
• Resection margins
• \*\*Stage and Surgical Status\*\*
• Pathologic stage III disease (any T, N1-2, M0) per AJCC 8th edition.
• R0 resection of the primary tumor documented by operative and pathology reports (no macroscopic or microscopic residual tumor at margins).
• No evidence of distant metastatic disease (M1) on staging imaging (CT chest/abdomen/pelvis ± MRI/PET per institutional standard) within a protocol-defined window (e.g., ≤8 weeks prior to enrollment).
• Enrollment and treatment initiation planned within a protocol-defined timeframe after surgery (e.g., 4-12 weeks post-resection), allowing appropriate recovery.
• \*\*Molecular Subtype (MSS/pMMR)\*\*
• Tumor confirmed MSS or pMMR by local testing using one or more of the following:
• IHC for MLH1, MSH2, MSH6, and PMS2
• PCR-based MSI panel
• NGS-based MSI/MMR assessment
• No evidence of dMMR/MSI-H status or POLE ultramutated phenotype.
• \*\*High-Risk Recurrence Profile\*\*
• At least one protocol-defined high-risk feature, including one or more of the following:
• Pathologic T4 tumor
• Pathologic N2 nodal status (≥4 positive lymph nodes)
• Positive postoperative ctDNA (MRD) by a validated tumor-informed assay within a protocol-defined window after surgery/chemotherapy initiation
• Other protocol-specified high-risk features (e.g., lymphovascular invasion, perineural invasion, poorly differentiated histology, inadequate lymph node sampling), as defined in the protocol/statistical analysis plan
• \*\*Suitability for Standard Adjuvant Chemotherapy\*\*
• Candidate for oxaliplatin-based adjuvant chemotherapy with one of the following:
• mFOLFOX6 every 14 days for \~6 months, \*\*or\*\*
• CAPOX (XELOX) every 21 days for \~3-6 months
• Chemotherapy regimen (mFOLFOX6 vs CAPOX) determined before enrollment and recorded as a stratification factor.
• No contraindications to oxaliplatin, 5-fluorouracil, leucovorin, or capecitabine (e.g., severe DPD deficiency; prior severe 5-FU/capecitabine toxicity).
• \*\*Suitability for Nivolumab\*\*
• Eligible in the investigator's judgment to receive anti-PD-1 therapy (nivolumab 3 mg/kg IV every 2 weeks), including:
• No history of severe (Grade ≥3) immune-related adverse events from prior immunotherapy
• No active autoimmune disease requiring systemic immunosuppression
• \*\*Performance Status\*\*
• ECOG performance status 0-1 at screening.
• \*\*Adequate Organ and Marrow Function\*\* (documented within 14 days prior to enrollment; no transfusions/growth factors solely to meet eligibility)
• \*\*Hematologic\*\*
• ANC ≥ 1.5 × 10⁹/L
• Platelets ≥ 100 × 10⁹/L
• Hemoglobin ≥ 9.0 g/dL (transfusions allowed if clinically indicated, but not solely to qualify)
• \*\*Hepatic\*\*
• Total bilirubin ≤ 1.5 × ULN (≤3 × ULN allowed for known Gilbert's syndrome if direct bilirubin is normal)
• AST and ALT ≤ 2.5 × ULN
• Alkaline phosphatase ≤ 2.5 × ULN (higher thresholds may be allowed for non-malignant causes per protocol)
• \*\*Renal\*\*
• Serum creatinine ≤ 1.5 × ULN \*\*or\*\* creatinine clearance ≥ 50 mL/min (Cockcroft-Gault or institutional standard)
• \*\*Biospecimen Availability (COLONYVAQ)\*\*
• Adequate tumor tissue available from resected primary tumor (and/or metastases if applicable), including one of the following:
• Fresh frozen tissue (preferred), \*\*or\*\*
• FFPE block(s), \*\*or\*\*
• ≥15 unstained slides (or equivalent) suitable for DNA/RNA extraction
• Matched normal sample (peripheral blood) available for germline DNA sequencing.
• Willingness to provide additional blood samples for ctDNA, immune monitoring, and exploratory assays per schedule.
• Pre-existing WES/RNA-seq may be accepted if meeting COLONYVAQ requirements per protocol.
• \*\*Neoantigen Suitability\*\*
• At least one predicted high-quality tumor neoantigen identified by the COLONYVAQ pipeline meeting prespecified criteria, including:
• Strong predicted binding to patient-specific HLA alleles (e.g., Kd in an established binder range)
• Evidence of tumor RNA expression of the source gene/allele
• Prioritization by multi-algorithm immunogenicity scoring and passage through COLONYVAQ quantum-geometric, thermodynamic, and immunogenicity gates
• \*\*OR\*\*
• Availability of pre-manufactured GMP-grade neoantigen peptides with demonstrated in vitro immunogenicity and acceptable safety profile.
• \*\*Life Expectancy\*\*
• Investigator-estimated life expectancy ≥ 3 years in the absence of CRC recurrence.
• \*\*Contraception and Pregnancy\*\*
• \*\*Women of childbearing potential (WOCBP)\*\*
• Negative serum or urine pregnancy test within 7 days prior to randomization
• Agreement to use highly effective contraception during treatment and for a protocol-defined period after last dose (e.g., 5 months after last nivolumab and 6 months after last chemotherapy, or per label/institutional guidance)
• \*\*Men with partners of childbearing potential\*\*
• Agreement to use effective contraception and avoid sperm donation during treatment and for the protocol-defined period after last dose
• \*\*Informed Consent and Compliance\*\*
• Able to understand and voluntarily sign written informed consent.
• Willing and able to comply with all study procedures (visits, imaging, blood draws, follow-up).

Exclusion criteria

• \*\*Residual or Metastatic Disease at Baseline\*\*
• R2 resection or indeterminate margins not clearly R0.
• Radiologic or histologic evidence of distant metastases (M1) at baseline staging (e.g., liver, lung, peritoneum).
• Gross residual disease at the primary site.
• \*\*Mismatch Repair-Deficient / MSI-High / POLE-Ultramutated Disease\*\*
• Known dMMR/MSI-H CRC or POLE ultramutated tumors for which checkpoint inhibition is standard/preferred.
• \*\*Prior Anticancer Therapy (Beyond Allowed Neoadjuvant)\*\*
• Prior systemic therapy for metastatic CRC.
• Neoadjuvant chemotherapy/chemoradiotherapy that:
• Was not completed within protocol-defined windows, \*\*or\*\*
• Led to unresolved Grade ≥2 non-hematologic toxicity (excluding alopecia or clinically insignificant neuropathy, per protocol)
• Prior tumor vaccine targeting TAAs or neoantigens (peptide, DC, viral, RNA, or DNA).
• Prior immune checkpoint inhibitor therapy (anti-PD-1, anti-PD-L1, anti-CTLA-4).
• \*\*Active or Uncontrolled Infections\*\*
• Systemic infection requiring IV or oral antimicrobials that would interfere with study treatment per investigator judgment.
• Uncontrolled HIV (e.g., CD4 below protocol threshold or unsuppressed viral load).
• Active hepatitis B with HBV DNA above predefined limit, or active hepatitis C with detectable HCV RNA not adequately treated.
• Other clinically significant infections posing excessive risk with immunotherapy, vaccine, or chemotherapy.
• \*\*Autoimmune Disease / Immunosuppression\*\*
• Severe/uncontrolled autoimmune disease requiring systemic immunosuppression (e.g., high-dose corticosteroids, biologics), including (examples):
• Systemic lupus erythematosus
• Inflammatory bowel disease with recent flares
• Rheumatoid arthritis requiring biologics
• Multiple sclerosis
• Myasthenia gravis
• Exceptions may include (per protocol):
• Stable autoimmune thyroiditis on replacement therapy
• Vitiligo
• Well-controlled type 1 diabetes
• Chronic systemic corticosteroids \>10 mg prednisone equivalent daily (or other immunosuppressants) within a protocol-defined window prior to first dose (unless physiologic/adrenal replacement).
• \*\*Transplant History\*\*
• Prior allogeneic hematopoietic stem cell transplantation.
• Prior solid organ transplantation (e.g., kidney, liver, heart).
• \*\*Hypersensitivity / Drug Intolerance\*\*
• Severe hypersensitivity (e.g., anaphylaxis) to any of the following:
• COLONYVAQ-CRC components (peptides/excipients)
• Poly I:C or similar TLR agonists
• Nivolumab or other anti-PD-1/PD-L1 agents
• Oxaliplatin, 5-FU, leucovorin, or capecitabine (including severe DPD deficiency)
• \*\*Concurrent Malignancy\*\*
• Active second primary malignancy requiring systemic therapy or expected to require systemic therapy during the trial.
• Exceptions:
• Adequately treated basal cell or squamous cell skin carcinoma
• Cervical carcinoma in situ
• Other malignancies in complete remission not expected to relapse or require systemic therapy within 5 years, per investigator judgment
• \*\*Significant Comorbidities\*\*
• Clinically significant/unstable cardiovascular disease, including:
• MI within 6 months
• Unstable angina
• Uncontrolled arrhythmias
• CHF NYHA class III-IV
• Uncontrolled hypertension despite medical therapy
• Stroke or TIA within 6 months (if risk is increased per investigator judgment).
• Severe COPD or interstitial lung disease with significant impairment, or prior pneumonitis requiring systemic steroids.
• Any other serious uncontrolled condition (e.g., poorly controlled diabetes, severe cirrhosis, advanced renal failure) that may compromise safety or adherence.
• \*\*Pregnancy / Lactation\*\*
• Pregnant at screening (positive pregnancy test).
• Breastfeeding (must discontinue lactation before first dose).
• \*\*Concurrent Investigational Agents / Confounding Therapies\*\*
• Participation in another interventional trial with systemic investigational agents (unless sponsor/IRB-approved and not confounding).
• Live attenuated vaccine within a protocol-defined period (e.g., 30 days) prior to first dose of nivolumab or COLONYVAQ-CRC, or during study treatment.
• \*\*Other Conditions Affecting Compliance or Assessment\*\*
• Psychiatric illness, cognitive impairment, substance abuse, or social situation limiting adherence to study requirements.
• Any condition that, in the investigator's opinion, makes the participant unsuitable or interferes with interpretation of safety, immunologic, or clinical outcomes.