ABSTRACT
IFNβ typically induces an antiviral and immunoregulatory transcriptional program through the activation of ISGF3 (STAT1, STAT2 and IRF9) transcriptional complexes. The response to IFNβ is context-dependent and is prone to crosstalk with other cytokines, such as TNFα. IFNβ and TNFα synergize to drive a specific delayed transcriptional program. Previous observation led to the hypothesis that an alternative STAT1-independent pathway involving STAT2 and IRF9 might be involved in gene induction by the combination of IFNβ and TNFα. Using genome wide transcriptional profiling by RNASeq, we found that the costimulation with IFNβ and TNFα induces a broad antiviral and immunoregulatory transcriptional program independently of STAT1. Additionally, STAT2 and IRF9 are involved in the regulation of only a subset of these STAT1-independent genes. Consistent with the growing literature, STAT2 and IRF9 act in concert to regulate a subgroup of these genes. Unexpectedly, STAT2 and IRF9 were also engaged in specific independent pathways to regulate distinct sets of IFNβ and TNFα-induced genes. Altogether these observations highlight the existence of distinct previously unrecognized non-canonical STAT1-independent, but STAT2 and/or IRF9-dependent pathways in the establishment of a delayed antiviral and immunoregulatory transcriptional program in conditions where elevated levels of both IFNβ and TNFα are present.
Significance IFNβ exhibit potent anti-proliferative, antiviral and immunoregulatory functions. The response to IFNβ is context-dependent and is prone to crosstalk with other cytokines, including TNFα. Elevated levels of both IFNβ and TNFα are notably observed during infections or chronic autoimmune and inflammatory diseases. A synergistic action of IFNβ and TNFα has previously been described, but the underlying mechanism remained elusive. Formation of ISGF3 (STAT1/STAT2/IRF9) is considered a hallmark of the type I IFN response, and the requirement of STAT1 in a specific setting has become a marker of the engagement of type I IFN signaling. The finding that in the presence of TNFα STAT1 is not required to drive a delayed antiviral and immunoregulatory transcriptional program challenges this paradigm. Similarly, the observation that STAT2 and IRF9 act independently to regulate a distinct subset of genes unveil the existence of previously unrecognized pathways that mediate the synergistic action of IFNβ and TNFα.