RNASeq analysis identifies non-canonical role of STAT2 and IRF9 in the regulation of a STAT1-independent antiviral and immunoregulatory transcriptional program induced by IFNβ and TNFα

IFNβ plays a critical role in the host defense against pathogens through the induction of hundreds of antiviral and immunoregulatory genes. Response to IFNβ is context-dependent and is prone to crosstalk with other cytokines. Costimulation with IFNβ and TNFα drives a specific delayed transcriptional program composed of genes that are either not responsive to IFNβ or TNFα separately or are only responsive to either one of the cytokine. The signaling mechanisms engaged downstream of the costimulation with IFNβ and TNFα remained elusive. In the present study, we took advantage of STAT1-deficient cells coupled to RNASeq analysis to characterize the genome wide transcriptional profile induced in response to IFNβ and TNFα. We found that costimulation with IFNβ and TNFα induces a broad antiviral and immunoregulatory transcriptional program independently of STAT1. Additional sequencing performed following silencing of STAT2 or IRF9 allowed us to unveil specific independent roles of STAT2 and IRF9 in the regulation of distinct sets of IFNβ and TNFα-induced genes. Consistent with the growing literature, IFNβ and TNFα synergistic action is in part mediated by the concerted action of STAT2 and IRF9, most likely present in a non-canonical complex. Finally, our study reveals previously unrecognized independent roles of STAT2 and IRF9 in the regulation of distinct sets of IFNβ and TNFα-induced genes. Altogether these observations highlight novel STAT1-independent pathways involved in the establishment of a delayed antiviral and immunoregulatory transcriptional program in conditions where elevated levels of both IFNβ and TNFα are present.