The Kinetic Landscape of Plant Ionizing-Radiation Response

Overview

Radiation response as a dynamic trajectory, not a single snapshot.

Most plant radiation transcriptomics treats exposure as a binary condition at one timepoint. This pipeline instead aggregates 299 samples spanning gamma, HZE-Fe, GCR, UV-B and spaceflight-LEO exposures, deconvolves bulk transcriptomes into pseudo-cell-type profiles, and trains a Gaussian-Process autoencoder with continuous dose, time and linear-energy-transfer (LET) covariates. Inter-tissue signaling is reconstructed with PlantCellChat, co-expression structure with kinetic WGCNA, and tissue stability with a composite Radiation Resilience Index (RRI).

3-phase

Kinetic architecture

Recognition (0–2 h) → crisis nadir (2–6 h) → partial recovery (6–24 h).

0.79→0.68

RRI at the nadir

Tissue resilience drops at 2–6 h, driven by housekeeping-network disruption, then recovers.

2.8×10⁻¹²

Independent validation

Held-out OSD-782 response genes recover the early-response module (2.3× enrichment).

01The resilience trajectory

A single dynamic metric tracks stability degradation and recovery over time.

Radiation Resilience Index over time, showing a nadir at 2–6 hours — The Radiation Resilience Index (RRI) across five timepoint bins. The nadir at 2–6 h (RRI = 0.68) is driven by disruption of housekeeping co-expression networks before partial recovery by 12–30 h.

02Temporally-phased pathways

DNA repair, hormonal signaling and oxidative stress activate in sequence.

Eight radiation-response pathways plotted over five timepoint bins — Pathway activation kinetics: DNA repair peaks at 0.5–2 h, auxin signaling earliest (0–0.5 h), salicylic-acid signaling latest (12–30 h), while jasmonate signaling is consistently suppressed — an abiotic-stress hormonal signature distinct from biotic stress.

03Independent validationheld-out study

The module structure holds on data entirely external to the discovery cohort.

The kinetic modules were projected — without refitting — onto OSD-782 / GLDS-679, a wild-type low-dose gamma time-course (0 / 0.1 / 1 Gy) absent from the training cohort and using a dose regime ~100× below its 100 Gy gamma studies. Radiation-response genes in this held-out study are strongly over-represented in the blue early-response module and depleted in the sustained module, and the projected module scores independently reproduce the crisis-and-recovery trajectory.

Independent validation on held-out study OSD-782 — A. Held-out OSD-782 response genes are enriched in the blue early-response module (41/725, 2.3×, P = 2.8 × 10⁻¹²) and the DDR-core module. B. Projected blue and grey module scores dip through the 1–24 h crisis window and recover by 72 h; the sustained module stays flat.

Cross-pipeline consistency with the earlier DESeq2/WGCNA analysis — Cross-pipeline consistency with the earlier per-contrast DESeq2/WGCNA analysis (preserved under `legacy/`): its radiation DEGs are enriched in the blue module, while the canonical DNA double-strand-break repair genes concentrate in a tight grey DDR-core module.

Data & code

Reproducible, FAIR-aligned, grounded in public NASA data.

Component	Location
Pipeline scripts (01–15)	`code/`
Metadata, expression, model, validation inputs	`data/`
Deconvolution, WGCNA, RRI, CellChat, figures	`results/`
Manuscript draft	`manuscript_chapter.md`
Pipeline reference + data dictionary	`README_pipeline.md`
Earlier per-contrast analysis	`legacy/`

All primary data derive from the NASA Open Science Data Repository (OSDR). The held-out validation study OSD-782 corresponds to GeneLab accession GLDS-679 (the OSD and GLDS numbers differ). The raw OSD-782 count matrix is not versioned in git; it is regenerated from OSDR by code/15_osd782_validation.py.