Combined transcriptomic and proteomic analyses define conserved host signatures during innate immune perturbations in DF-1 chicken fibroblasts

The interferon system, first discovered in chicken embryonated eggs, plays a pivotal role in defending vertebrates against pathogens, yet comprehensive multi-omics analyses of immune responses in avian species remain scarce. In this study, we employed an integrative approach combining RNA-Seq transcriptomics with SILAC-based quantitative proteomics to characterize global changes in gene and protein expression following immune stimulation in DF-1 chicken fibroblasts. Cells were treated with three distinct immune stimuli: chicken type I interferon, the synthetic double-stranded RNA (dsRNA) analog poly(I:C), and Infectious Bursal Disease Virus (IBDV), a birnavirus with a bi-segmented dsRNA genome. Our analysis revealed a core set of over 110 genes consistently upregulated across all conditions, representing conserved components of the antiviral response. Each stimulus also triggered distinct transcriptional programs, with poly(I:C) eliciting the most robust cytokine induction. At the proteomic level, we quantified more than 2,400 proteins, uncovering asymmetric regulatory patterns in which upregulated proteins exhibited greater fold changes than those that were downregulated. Notably, analysis of transcription-translation coupling revealed a moderate overall correlation between mRNA and protein abundance, which was significantly attenuated following poly(I:C) stimulation, likely reflecting PKR-mediated translational arrest. Ontological analysis corroborated the upregulation of interferon-stimulated genes and proteins involved in inhibiting viral genome replication, as expected. Intriguingly, proteins associated with mitochondrial metabolism and protein synthesis were consistently downregulated, suggesting a coordinated suppression of cellular bioenergetic and translational functions during the antiviral response. These findings underscore the critical role of post-transcriptional regulation in shaping the innate immune landscape, as numerous proteins exhibited altered expression without corresponding mRNA changes. Collectively, this study provides a comprehensive resource for dissecting cellular avian immune signaling and demonstrates the power of integrative multi-omics approaches in uncovering the complex regulatory networks governing host defense.