IMMUNE_HIERARCHY
Primary Lane
Lane 2 — Programmable Immune Instruction
Secondary Lane
Lane 1 — Mechanistic Pathogenesis
Person
One-Sentence Thesis
Selective miRNA-based silencing of influenza open reading frames can be used as a perturbation system to test how antigen abundance, antigen acquisition, and infection context shape antibody quality, CD8 T-cell profiles, and peptide presentation.
Central Scientific Question
Can engineered influenza constructs that selectively silence different viral open reading frames control the quality and hierarchy of antibody and CD8 responses, while also revealing fundamental rules of antigen capture and immune engagement?
Construct Panel
Leon compares three miRNA-targeted influenza constructs to the wild-type counterpart:
| Construct | Meaning | Silenced targets | Primary use |
|---|---|---|---|
| HANA | HA/NA | HA and NA | Tests effects of reduced surface antigen expression on antibody and CD8 outcomes. |
| PAM | PA/M | PA and M | Tests how targeting internal or polymerase-associated antigens affects CD8 hierarchy. |
| PANA / NAPA | PA/NA or NA/PA | PA and NA | Alternate combinatorial perturbation of antigen expression and immune readout. |
Established Observations
- HA surface depletion reduces the level and quality of HA-directed antibody responses.
- The miRNA-targeted constructs generate antibody and CD8 profiles that differ from the wild-type PR8 counterpart.
- CD8 sequencing data show an APC-associated signature in the three miRNA-targeted constructs relative to PR8.
- TCR profiling suggests a more diverse T-cell receptor repertoire after vaccination with the miRNA-targeted constructs.
- The CD8 response is less predictable than the antibody response: despite canonical NP and PA dominance in influenza CD8 immunity, PA targeting does not simply collapse or redirect the response as expected.
- Across the three targeted constructs, CD8 profiles may be more similar than different, with major differences relating more strongly to NP.
Working Model
This project began as a tool-building and vaccine-design effort, but the immunology has become the central story.
The current working model is that replication-defective or miRNA-silenced viruses alter the context of antigen acquisition. When the virus is not killing cells and spreading in the usual way, antigen-presenting cells may sample viral material more comprehensively and in a less inflammatory context. The relevant antigen source may shift toward direct sampling of virions rather than sampling from productively infected or dying cells.
This model reframes the project from “which antigen is silenced?” toward “what source of antigen is being captured, by which APCs, under what inflammatory context?”
Narrative Evolution
- Initial frame: use miRNA silencing to build vaccine tools and bias immune output.
- Current frame: use engineered replication-defective influenza variants to uncover basic rules of antigen capture, peptide presentation, APC engagement, and adaptive immune hierarchy.
Scientific Importance
The project may support vaccine-design logic, but its strongest near-term manuscript identity is likely a discovery paper about antigen acquisition and immune engagement rather than a technology paper about miRNA targeting.
Linked Programs
- Universal Flu Vaccine Egg Farmers Canada
- ADAR LICENSING
- VECTOR DELIVERY
- Single Cell Analysis
- DATASET REGISTRY
- VECTOR REGISTRY
- NEGATIVE RESULTS AND ABANDONED IDEAS
Manuscript Triage
Likely paper type: Discovery paper.
The paper should be able to state a biological principle about antigen capture or immune hierarchy without relying on miRNA targeting as the novelty.
Open Questions
- What directly explains the APC-associated signature in CD8 sequencing data?
- Why does PA targeting not produce a simple PA-dependent shift in CD8 outcome?
- Is NP immunodominance or NP-associated antigen capture the key driver of the observed differences?
- Which APC populations acquire antigen from these constructs?
- Is antigen sampled primarily from virions, infected cells, dying cells, or a mixed source?
- Which validation experiment most directly tests the antigen-capture model?
TODO
- Add exact construct maps, miRNA target sites, rescue history, and naming conventions.
- Add mouse model, dose, route, timing, assays, and readouts.
- Add antibody profiling details and figure links.
- Add CD8 sequencing and TCR repertoire dataset locations.
- Add current manuscript outline and figure logic when ready.