Study-Aware Meta-Analysis Reveals a Recurrent Proteostasis Program and Context-Dependent Gene-Level Responses in Bovine Heat-Stress Transcriptomes.

Background/

Objectives

Bovine heat-stress RNA-seq studies differ in tissue, age, physiological state, and exposure design. We asked which responses recur across these contexts and which depend on the evidence base.

Methods

We reprocessed 107 libraries from five in vivo Bos taurus studies and synthesized within-study heat-minus-control log2 fold changes using restricted maximum-likelihood random-effects models with modified Knapp-Hartung inference. Eight tissue- and age-aware scenarios tested the cross-context estimate. A six-component heat-stress transcriptomic stability index (HSTSI) was benchmarked against five simpler rankings, and an independent mammary single-nucleus dataset provided cell-resolved comparison.

Results

Of 266 FDR-significant pathways, 259 retained direction across all five study deletions and 21 remained significant in every deletion. Translation, ribosome, protein folding, endoplasmic-reticulum processing, proteasome, and heat-response programs formed the most recurrent axis. Four principal sensitivity scenarios retained 0.920-0.932 gene-direction agreement and 0.957-0.981 effect-rank correlation with the five-study analysis. In the single-nucleus dataset, leading-edge genes from the principal proteostasis programs showed 89.4-100% pooled-nucleus direction agreement and 94.7-100% agreement among published cluster-level differentially expressed genes. HSTSI had the highest mean top-200 held-out direction agreement (0.583 versus 0.516-0.562), with variation among folds. None of 16,756 genes met a modified Knapp-Hartung FDR below 0.10. IL1R2 and SDCBP2 were externally concordant, whereas GZMK and CD8A were context-dependent.

Conclusions

A coordinated proteostasis program was the most transferable heat-stress signal. Energy remodeling, immune-associated bulk signals, and individual genes showed greater context dependence and define priorities for tissue-matched follow-up.