Pathway-Level Synthesis Reveals Contrast-Dependent Rat Brain Transcriptomic Responses to Alcohol

Public rat brain transcriptomic studies differ in sampled region and alcohol paradigm, which complicates assessment of reproducible molecular responses. We assembled 12 datasets, including four primary region-resolved datasets (64 samples) from the hippocampus, ventral tegmental area, amygdala, and nucleus accumbens. Each dataset was analyzed separately and projected onto predefined addiction-related, exercise-related, and stress-related pathway axes; only aligned contrast-level effects were synthesized across datasets. In the closest available two-dataset comparison, both studies used adult male Sprague–Dawley rats, chronic liquid-diet exposure, and 24 h withdrawal. Withdrawal versus control showed directional agreement for all three original axes and their three deterministic derived indices, whereas chronic ethanol versus control agreed for only one of these six summaries. The derived indices do not constitute independent replication, and this two-study result is interpreted as contrast-specific directional concordance under similar protocols without identifying brain region as its cause. Across the broader alcohol-domain resource, effects occupied both directions and showed substantial between-contrast dispersion, defining a boundary to generalization rather than a universal alcohol response. The central interpretation was materially unchanged by alternative scoring algorithms, pathway catalogs, or cluster-balanced reanalysis of overlapping pathways; at a pathway-overlap (Jaccard similarity) threshold of 0.5, the latter preserved sample-level rankings (median Spearman ρ=0.983) and 76 of 78 pairwise effect directions. These results provide a reproducible framework for distinguishing local convergence from broader context dependence in rat alcohol transcriptomics. Candidate biomarkers should therefore be evaluated in harmonized exposure, withdrawal, region, sex, and species settings before translational interpretation.