Explainable Machine Learning Reveals 12-Fold Ucp1 Upregulation and Thermogenic Reprogramming in Female Mouse White Adipose Tissue After 37 Days of Microgravity: First AI/ML Analysis of NASA OSD-970

Abstract

Microgravity induces profound metabolic adaptations in mammalian physiology, yet the molecular mechanisms governing thermogenesis in female white adipose tissue (WAT) remain poorly characterized. This paper presents the first machine learning (ML) analysis of NASA Open Science Data Repository (OSDR) dataset OSD-970, derived from the Rodent Research-1 (RR-1) mission. Using RT-qPCR data from 89 adipogenesis and thermogenesis pathway genes in gonadal WAT of 16 female C57BL/6J mice (8 flight, 8 ground control) following 37 days aboard the International Space Station (ISS), we applied differential expression analysis, multiple ML classifiers with Leave-One-Out Cross-Validation (LOO-CV), and Explainable AI via SHapley Additive exPlanations (SHAP). The most striking finding is a dramatic 12.21-fold upregulation of Ucp1 (Delta-Delta-Ct = -3.61, p = 0.0167) in microgravity-exposed WAT, accompanied by significant activation of the thermogenesis pathway (mean pathway fold-change = 3.24). The best-performing model (Random Forest with top-20 features) achieved AUC = 0.922, Accuracy = 0.812, and F1 = 0.824 via LOO-CV. SHAP analysis consistently ranked Ucp1 among the top predictive features, while Angpt2, Irs2, Jun, and Klf-family transcription factors emerged as dominant consensus classifiers. Principal component analysis (PCA) revealed clear separation between flight and ground samples, with PC1 explaining 69.1% of variance. These results suggest rapid thermogenic reprogramming in female WAT as a compensatory response to microgravity. This study demonstrates the power of explainable AI for re-analysis of newly released NASA space biology datasets, with direct implications for female astronaut health on long-duration missions and for Earth-based obesity and metabolic disease research.

Figures (9)

• Figure 1: Analytical pipeline for NASA OSD-970 ML analysis. Raw Ct values from 16 female mice (8 flight, 8 ground) are preprocessed, then subjected to differential expression analysis, multi-classifier LOO-CV, SHAP explainability, and consensus feature ranking with pathway annotation.
• Figure 2: Principal Component Analysis of 89-gene Ct profiles. PC1 (69.1%) and PC2 (11.7%) together explain 80.8% of variance. Flight and ground control samples form distinct clusters along PC1, confirming a strong microgravity-driven transcriptional signal.
• Figure 3: Volcano plot of differential gene expression in gonadal WAT (Flight vs. Ground Control). The $x$-axis shows $\log_2$ fold-change ($\Delta\Delta$Ct) and the $y$-axis shows $-\log_{10}(p\text{-value})$. Ucp1 (red) is the sole significantly upregulated gene (FC $= 12.21$, $p = 0.0167$). Downregulated significant genes are shown in blue. The dashed lines indicate thresholds $|$log$_2$FC$| = 0.585$ and $p = 0.05$.
• Figure 4: UCP1 deep-dive analysis. (A) Individual Ct values by group: flight (mean Ct $= 28.69$) vs. ground (mean Ct $= 32.30$); lower Ct indicates higher expression. (B) Box plot with individual data points. (C) Fold-change visualization ($12.21\times$ upregulation). (D) Distribution density plot showing non-overlapping expression distributions.
• Figure 5: ROC curves for all classifiers under LOO-CV (top-20 gene feature set). The Random Forest and Logistic Regression models achieved the highest AUC of 0.922. All models substantially outperformed random classification (dashed diagonal).