The type I interferon, interferon-α (IFN-α), regulates host antiviral and immunoregulatory responses. However, deregulated IFN-α production is the cause of several neurological diseases termed “cerebral type I interferonopathies” that include Aicardi-Goutières Syndrome and chronic viral encephalopathies. Importantly, how IFN-α causes these diseases remains unclear. Here, we determined for the first time the effects of IFN-a on global protein phosphorylation in brain cells and tissues.

We first analysed the phosphoproteome of IFN-α-treated primary murine astrocytes and microglia, the main immune responding cells of the of the central nervous system (CNS). Within five minutes of treatment, IFN-α led to altered phosphorylation of more than 1800 peptides. This phosphorylation wave was transient and peaked at 15 minutes before decreasing at 30 minutes. Motif analysis predicted the ERK family and casein kinase II as major regulators of protein phosphorylation. Gene ontology analysis indicated that altered phosphopeptides were associated with the nucleoplasm and biological processes involved in cytoskeleton, transcription and neuron regulation. Further, comparison between astrocytes and microglia revealed cell-type specific changes in the phosphoproteome that reflected the distinct origins of these cells.

We then determined the phosphoproteome in a mouse model for cerebral interferonopathies. Mice with astrocyte-targeted production of IFN-α (termed GIFN mice). recapitulate many key pathological and clinical features of patients with cerebral type I interferonopathies. Chronic IFN-α production in the brains of GIFN mice resulted in phosphorylation changes to 1900 peptides. Motif analysis predicted the ERK family as a major regulator of protein phosphorylation. Further, protein interaction networks indicated the regulated phosphopeptides were involved in cytoskeleton organization, regulation of MAPK signalling, calcium signalling and long term potentiation. The results demonstrate that IFN-α induces extensive and unexpected changes in the phosphoproteome affecting a range of biological processes in brain cells and the CNS of GIFN mice.