Integrative transcriptomic analysis reveals tissue associated molecular responses to heat stress in chickens

Climate change is intensifying extreme heat events that compromise poultry health, welfare, and productivity. Although RNA-seq has been widely used to investigate heat stress responses, individual studies are constrained by small sample sizes, experimental heterogeneity, and discordant differential expression signatures, limiting the identification of conserved molecular responses across tissues. We conducted an integrative analysis of 11 independent RNA-seq datasets comprising 212 samples (110 liver, 62 breast muscle, and 40 heart) from broiler chickens exposed to heat stress. Differential expression analysis, weighted gene co-expression network analysis (WGCNA), and multi-criteria consensus filtering were combined to identify cross-validated hub genes. We identified conserved hepatic, and breast muscle transcriptional responses that showed distinct tissue associated division of labor model. Liver exhibited metabolic reprogramming involving altered gluconeogenic and fatty acid metabolic pathways, including PCK1 and ACACB, together with changes in insulin-PPAR signaling. Breast muscle showed activation of p53 mediated cell cycle arrest and proteostatic responses involving CDKN1A and DNAJA4. Heart exhibited transcriptional changes in adrenergic-calcium signaling, including CACNA1H and PPP3CA, together with suppression of extracellular matrix remodeling. Transcription factor (TF) activity inference using decoupleR and orthology-mapped DoRothEA regulons suggested tissue associated regulatory patterns involving HSF2, NCOA3, and MEF2A/MEF2C in liver; FOXO4, SOX9, and SP-family TFs in breast muscle; and reduced MEF2A/MEF2C, TEAD1, and JUN activity in heart. This integrative framework identifies high confidence candidate genes and regulatory networks validated by multiple analytical approaches, providing molecular candidates for subsequent genomic and functional studies of climate resilience in poultry.