Arabidopsis Spaceflight Omics
LASSO biomarker discovery, single-cell atlas integration, and Ca²⁺-dominated cell–cell communication in the Arabidopsis thaliana spaceflight response.
A multi-track computational meta-analysis of NASA OSDR transcriptomics, a published seed-to-seed single-cell atlas, and plant foundation models. Manuscript prepared for npj Microgravity.
Richard Barker — GeneLab Plant Analysis Working Group, NASA Open Science Data Repository
What this study asks
Individual spaceflight plant experiments are small and confounded by tissue, accession, and flight platform. This project asks whether a stable, cross-study transcriptomic signature of spaceflight can be learned from pooled NASA OSDR data — and whether its biology can be resolved at single-cell and cell–cell-communication resolution.
Three tracks
Track 1 — LASSO biomarker panel
An elastic-net (α = 0.5) model with leave-one-study-out cross-validation across 6 OSDR studies (156 pooled samples, 32,548 genes) yields an 85-gene panel predictive of spaceflight vs. ground (mean CV AUC = 0.734). Four genes are selected at 100% frequency.
Track 2 — scPlantLLM single-cell atlas integration
The scPlantLLM plant foundation model is run zero-shot on 9,998 cells of the Lee et al. (2025) seedling atlas. Poor cross-tissue transfer (loose accuracy ≈28%, ARI 0.033) is reported as an honest negative result on foundation-model domain shift.
Track 3 — Cell–cell communication & spatial mapping
PlantCellChat inference identifies Ca²⁺ signaling as dominant (strength 249.5, 4.6× the next pathway). A CBL9–CIPK23–AKT1 Ca²⁺/K⁺ crosstalk circuit is resolved, with guard cells as the primary signaling hub, and mapped onto plant anatomy with ggPlantmap.
Key results
| Metric | Value |
|---|---|
| LASSO mean cross-study AUC | 0.734 |
| Stable biomarker genes (≥50% selection) | 85 |
| Top genes (100% selection) | AT4G10250, AT3G07365, AT2G14247, AT4G01390 |
| Atlas cells analysed | 9,998 (of 41,314) |
| scPlantLLM zero-shot accuracy (loose) | ≈28% |
| Dominant CCC pathway | Ca²⁺ (strength 249.5, 4.6× next) |
| Ca²⁺/K⁺ circuit | CBL9 → CIPK23 → AKT1 |
Repository contents
track1_lasso_osdr/,track2_scplantllm_atlas/,track3_ccc_ggplantmap/— analysis scripts, data, and figures per trackintegration/— cross-track integration analysismanuscript/— manuscript, 8 main figures (PNG + editable SVG), supplementary figures/tables, andSupplementary_Methods.mdrequirements.txt/environment.R— Python and R dependencies
Data & code availability
- NASA OSDR — biodata API · studies OSD-37, -678, -38, -321, -120, -624
- Seedling atlas — GEO GSE226097 (Lee et al., Nature Plants 2025)
- Methods — scPlantLLM (Cao et al., 2025), PlantCellChat, ggPlantmap (Jo & Kajala, 2024)
- License — MIT · see
LICENSE - Archived release — Zenodo DOI (minted on first GitHub release; add badge here)
Results are discovery-only; no external validation cohort. See the manuscript’s limitations section.