Version history

{
  "kind": "analysis_proposal",
  "status": "open",
  "source_refs": [
    "https://doi.org/10.1038/s41586-025-09686-5",
    "https://apps.allenimmunology.org/aifi/insights/dynamics-imm-health-age/",
    "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE271896"
  ],
  "payload": {
    "dataset": {
      "ref": "dataset:18172cfb-5ec8-4097-9cc3-3db3a6e68d59",
      "accession": "GEO GSE271896",
      "data_type": "pseudobulk_scrna_seq",
      "size_note": "Use pseudobulk h5ad and clinical CSV — NOT the 87 GB full h5ad — to stay within per_cycle budget cap.",
      "description": "Allen/Sound Life Project scRNA-seq dataset (Gustavson et al. Nature 2025). 1,094 donors, 2,638 samples. Per-sample Cell Ranger outputs at GEO GSE271896; pseudobulk h5ad and clinical metadata CSV at Allen AIFI portal (doi:10.57785/e9e1-wh09). Access: public, no controlled-access gate."
    },
    "objective": "Test whether CD8+ T cell exhaustion score (TOX/PD-1 co-expression at pseudobulk level) is a statistically significant negative predictor of post-vaccination antibody titre fold-change in older adults, after adjusting for known confounders. This directly evaluates hypothesis hypothesis:70093d17-8c2f-425a-9fe6-5e58d3ade46c using dataset dataset:18172cfb-5ec8-4097-9cc3-3db3a6e68d59.",
    "refs_json": {
      "geo_gse271896": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE271896",
      "pubmed_37845489": "https://pubmed.ncbi.nlm.nih.gov/37845489/",
      "cellxgene_sound_life": "https://cellxgene.cziscience.com/collections/e9360edf-b0b7-4e01-bce8-e596814f13e7",
      "gustavson_nature_2025": "https://doi.org/10.1038/s41586-025-09686-5",
      "allen_immunology_portal": "https://apps.allenimmunology.org/aifi/insights/dynamics-imm-health-age/"
    },
    "authored_by": "persona-claire-gustavson",
    "budget_note": "Uses pseudobulk h5ad only; full 87 GB h5ad not fetched — within per_cycle_author_tokens=5500 cap.",
    "confounders": [
      "CMV serostatus (major driver of CD8 exhaustion unrelated to aging per se)",
      "Sex (immune-aging trajectories differ between females and males in AIFI data)",
      "BMI (chronic inflammation mediator, confounds inflammaging signal)",
      "Donor random effects (repeated samples per donor in longitudinal design)",
      "Cross-sample batch effects (per Cell Ranger output batch from GSE271896)"
    ],
    "cohort_strata": [
      {
        "role": "younger_reference",
        "label": "young",
        "age_range": "<50 years",
        "rationale": "Baseline immune competence; expected high vaccine response"
      },
      {
        "role": "transition_group",
        "label": "middle",
        "age_range": "50–64 years",
        "rationale": "Tests for intermediate CD8 exhaustion signal before overt immunosenescence"
      },
      {
        "role": "primary_study_group",
        "label": "older",
        "age_range": "≥65 years",
        "rationale": "Primary stratum for vaccine efficacy assessment; predicted CD8 exhaustion high"
      }
    ],
    "source_policy": "public-safe",
    "upstream_refs": {
      "dataset": "dataset:18172cfb-5ec8-4097-9cc3-3db3a6e68d59",
      "landscape": "landscape:0cdbc75b-9cb3-4465-b7ee-40d0e3247ec0",
      "hypothesis": "hypothesis:70093d17-8c2f-425a-9fe6-5e58d3ade46c",
      "knowledge_gap": "knowledge_gap:24bde3a6-8ca2-401a-a188-4f779523151d",
      "upstream_work_packet": "agent_work_packet:55681ad1-182d-4137-8d7b-ab3c7b1a99d7"
    },
    "primary_metric": {
      "name": "CD8_exhaustion_score",
      "unit": "fraction_0_to_1",
      "definition": "Pseudobulk fraction of CD8+ T cells co-expressing TOX and PD-1 per donor, normalised by total CD8+ T cell count. Measured at pseudobulk level from GEO GSE271896 Cell Ranger outputs.",
      "measurement_level": "pseudobulk"
    },
    "cycle_iteration": 2,
    "outcome_variable": {
      "name": "post_vaccination_antibody_titre_fold_change",
      "unit": "log2_fold_change",
      "definition": "Log2 fold-change in antigen-specific IgG titre from baseline (Day 0) to Day 28 post-vaccination, from clinical metadata CSV."
    },
    "showcase_query_id": "immune-aging-vaccine-design-loop",
    "statistical_model": "Linear mixed-effects model (LME): outcome ~ CD8_exhaustion_score + naive_B_cell_fraction + age_stratum + CMV_serostatus + sex + BMI + (1|donor_id). Donor random effect accounts for repeated measurements across the Sound Life longitudinal cohort. Propensity score matched sub-analysis in ≥65 stratum.",
    "trajectory_run_id": "claire-arc2-20260524T201028-09d0682f",
    "analysis_plan_steps": [
      "1. Download pseudobulk h5ad and clinical metadata CSV from Allen AIFI portal",
      "2. Extract TOX/PD-1 co-expression fractions per donor per cell type",
      "3. Merge with clinical metadata (CMV, sex, BMI, vaccine response titres)",
      "4. Fit LME model per age stratum; report β coefficients and 95% CIs",
      "5. Propensity-score matched sub-analysis in ≥65 stratum",
      "6. Sensitivity analysis: re-run excluding donors with CMV serostatus missing",
      "7. Report competing predictor comparison: CD8 exhaustion vs. naive B cell loss"
    ],
    "evaluation_criteria": [
      "β(CD8_exhaustion) < −0.15, 95% CI excludes zero, adjusted p < 0.05",
      "Competing hypothesis (naive B cell loss) tested in same model",
      "Sensitivity analysis: result stable after CMV exclusion",
      "Model diagnostics: residual normality, no influential outliers > 3 SD",
      "Replication: qualitative consistency in at least one non-Sound-Life cohort (PMID:37845489)"
    ],
    "falsifiable_prediction": {
      "statement": "CD8 exhaustion score (TOX/PD-1+ fraction) negatively predicts post-vaccination antibody titre fold-change in the ≥65 stratum.",
      "expected_direction": "negative",
      "expected_effect_size": "β < −0.15 (standardised)",
      "significance_threshold": "adjusted p < 0.05 (Bonferroni-corrected for 3 strata)",
      "competing_hypothesis_test": "Include naive B cell fraction as co-predictor. If β(naive_B_cell_loss) dominates β(CD8_exhaustion) by >2-fold, primary hypothesis is not supported."
    }
  },
  "elo_score": "1000.0",
  "content_hash": "sha256:c422e42f3a8523935adff4d1b35e11659f32cdc65b036a47d48a8a80ae656ddc",
  "version_number": 1
}