Genome-Wide Classification of Type I, Type II and Type III Interferon-Stimulated Genes in Chicken Fibroblasts

Abstract

Interferons (IFNs) play central roles in establishing innate immunity and mediating 12 adaptive immunity against multiple pathogens. Three known types of IFNs identify their cognate 13 receptors, initiate cascades of signalling events and eventually result in the induction of myriad of 14 IFN-stimulated genes (ISGs). These ISGs perform multitude of functions and cumulatively 15 corroborate a bespoke antiviral state to safeguard hosts against invading viruses. Owing to unique 16 nature of chicken's immune system and lack of foundational profiling information on the nature and 17 dynamic expression of IFN-specific ISGs at the genome scale, we performed a systematic and 18 extensive analysis of type I, II and III IFN-induced genes in chicken. Employing pan-IFN responsive 19 chicken fibroblasts coupled with transcriptomics we observed an overwhelming over-representation 20 of up-regulated ISGs by all types of IFNs. Intriguingly, prediction of IFN-stimulated response element 21(ISRE) and gamma-IFN activation sequence (GAS) revealed a substantial number of GAS motifs in 22 selective significantly induced ISGs in chicken. Extensive comparative, genome-wide and differential 23 expression analysis of ISGs under equivalent signalling input catalogue a set of genes that were 24 either IFN-specific or independent of types of IFNs used to prime fibroblasts. These comprehensive 25 datasets, first of their kinds in chicken, will establish foundations to elucidate the mechanisms of 26 actions and breadth of antiviral action of ISGs which may propose alternative avenues for the 27 targeted antiviral therapy against viruses of poultry and public health importance.28 29 30 31 32 33 34 35 36 37 65 and Janus Kinase 1 (JAK1). However, type II IFN triggers this pathway via the activation of STAT1 66 homodimers mediated by JAK1 and JAK2 kinases [4]. 68Mammalian type I and type III IFNs signal through the JAK-STAT pathway to activate the 69 heterotrimeric interferon-stimulated gene factor 3 (ISGF3) complex, comprised of phosphorylated 70 STAT1 and STAT2, and interferon regulatory factor 9 (IRF9) [7,8] (yet to be identified in chickens). In 71 contrast, type II IFNs initiate the formation of a STAT1-STAT1 homodimer to assemble GAF, without 72 the need of IRF9. Upon nuclear translocation, ISGF3 and gamma-interferon activation factor (GAF) 73 bind to IFN-stimulated response elements (ISREs) [6] or gamma-IFN activation sequence (GAS) 74 motifs, respectively 7 leading to the transcriptional activation of hundreds of ISGs which encode 75 proteins that act via a variety of mechanisms to restrict viral infection [9-11]. 77It has been demonstrated that JAK-STAT pathway initiates transcriptional regulation of a string of 78 cytokines, chemokine, antimicrobial products and regulators of apoptotic pathways [2,7]. In 79 mammals, a range of genome scale transcriptomics screening approaches has been applied to map 80 the diversity, kinetics and expression patterns of these antiviral factors. Based on these data, recent 81 studies have applied large-sc...

Comparative Study of Protection against Newcastle Disease in Young Broilers Administered Natural Chicken Alpha Interferon via Oral and Intramuscular Routes

“…Three subtypes of chicken type I IFNs are chIFN-α, chIFN-β, and chIFN-κ ( 14 , 15 ). Although the three members of the chicken type I IFN family are structurally diverse, they nevertheless bind to the same complex of heterodimer receptors composed of IFNAR1 and IFNAR2 chains ( 14 , 16 ). Binding of type I IFNs to their corresponding receptor complex initiates a cascade of intracellular events, which ultimately results in the activation of several hundred IFN-stimulated genes (ISGs) via the JAK-STAT pathway ( 16 , 17 ).…”

“…Although the three members of the chicken type I IFN family are structurally diverse, they nevertheless bind to the same complex of heterodimer receptors composed of IFNAR1 and IFNAR2 chains ( 14 , 16 ). Binding of type I IFNs to their corresponding receptor complex initiates a cascade of intracellular events, which ultimately results in the activation of several hundred IFN-stimulated genes (ISGs) via the JAK-STAT pathway ( 16 , 17 ). Several studies have suggested the antiviral activity of recombinant chIFN-α against avian influenza virus (AIV), Newcastle disease virus (NDV), infectious bursal disease virus (IBDV), and infectious bronchitis virus (IBV) ( 18 – 20 ).…”

Systematic identification of chicken type I, II and III interferon-stimulated genes

“…IFN-α-induced ISGs have been identified in different cell types of chicken, according to our and other studies [24,25]. Recently, chicken ISGs induced by type I, II and III IFN were also identified in fibroblasts model at 24 h post IFN treatment [26]. Although hundreds of ISGs have been identified in humans, several more ISGs are expected to be still discovered [12].…”