IF a multi-epitope mRNA–lipid nanoparticle (LNP) neoantigen vaccine — encoding a concatenated polyepitope construct of (a) 9–15-mer peptides spanning the DNMT3A R882H substitution optimized for both MHC class I (e.g., HLA-A*02:01) and MHC class II presentation, and (b) novel open-reading-frame (neoORF) peptides derived from the most recurrent TET2 frameshift/nonsense truncations — formulated with a TLR4 agonist adjuvant (MPLA) and administered intramuscularly (prime × 2, boost × 1 over 6 weeks) to aged (18–22 month), male and female C57BL/6 mice bearing confirmed high-variant-allele-frequency (VAF ≥ 10%) somatic Dnmt3a hotspot or Tet2 loss-of-function CHIP clones (induced by retroviral transduction or aged naturally),

THEN a ≥ 30% reduction in CHIP clone VAF in bone marrow and peripheral blood (measured by droplet digital PCR at 12 and 24 weeks post-vaccination), suppressed progression to myelodysplastic phenotype, reduced IL-1β/IL-6 systemic inflammatory burden, and emergence of mutation-specific tetramer-positive CD4⁺ and CD8⁺ T cell populations will be observed,

BECAUSE of the following mechanistic chain:

1. CHIP-derived CD14⁺ monocytes carrying DNMT3A and TET2 mutations constitutively upregulate MHC class II HLA genes relative to wild-type controls, making them intrinsically superior professional antigen-presenting cells for their own mutant-derived peptides — thereby creating a pre-existing, exploitable immunological vulnerability on the surface of the very clones to be eliminated. (Mutated cells mediate distinct inflammatory responses in clonal hematopoiesis)[https://doi.org/10.1101/2022.12.01.518580]

2. The DNMT3A R882H single-nucleotide variant generates peptide sequences with altered anchor residues relative to the wild-type arginine-containing peptide; computational pipelines (NetMHCpan, pVACseq) predict that R882H-spanning 9-mers achieve strong predicted MHC-I binding (IC₅₀ < 500 nM) to HLA-A*02:01 and HLA-A*24:02 while retaining differential affinity over wild-type, supporting selective recognition as a genuine neoantigen rather than a self-peptide, as summarized in the computational neoantigen literature of the Evidence Set.

3. TET2 frameshift and nonsense mutations generate neoORF-derived peptides that are entirely non-self — lacking central immune tolerance — and thus produce a broader and higher-affinity neoantigen candidate pool than single-residue substitutions, as supported by the neoantigen prediction literature summarized in the Evidence Set; mRNA-LNP delivery enables simultaneous priming against both mutation types within a single formulation.

4. mRNA-LNP vaccination, proven by COVID-19 vaccine precedent to robustly prime de novo CD4⁺ and CD8⁺ T cell responses in aged individuals, will generate mutation-specific effector and memory T cell populations; the MHC-II upregulation uniquely present on CHIP monocytes (Finding 1 above) means these cells will act as direct targets for cytotoxic CD4⁺ T cells (Th1-polar...

SENS category: OncoSENS

Key references: • doi.org/10.1101/2022.12.01.518580] • doi.org/10.1101/2023.11.08.23298270]