Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome

Hyperactive interferon (IFN) signaling is a hallmark of Down syndrome (DS), a condition caused by trisomy 21 (T21); strategies that normalize IFN signaling could benefit this population. Mediator-associated kinases CDK8 and CDK19 drive inflammatory responses through incompletely understood mechanisms. Using sibling-matched cell lines with/without T21, we investigated Mediator kinase function in the context of hyperactive IFN in DS. Using both targeted and unbiased, discovery-based approaches, we identified new and diverse mechanisms by which Mediator kinases regulate IFN signaling. Beyond effects on IFN-stimulated transcripts, we discovered that CDK8/CDK19 impact splicing, revealing a novel means by which Mediator kinases control gene expression. Kinase inhibition altered splicing in pathway-specific ways and selectively disrupted IFN-responsive gene splicing in T21 cells. Moreover, Mediator kinase inhibition blocked cytokine responses to IFNγ and severely impacted core metabolic pathways, including up-regulation of anti-inflammatory lipid signaling molecules during IFNγ-stimulation. These lipids included ligands for nuclear receptors and G-protein coupled receptors that can act in an autocrine or paracrine manner, suggesting additional kinase-dependent mechanisms to durably suppress IFNγ responses, beyond initial changes in gene expression. Collectively, our results establish that Mediator kinase inhibition antagonizes IFNγ signaling through transcriptional, metabolic, and cytokine responses, with implications for DS and other chronic inflammatory conditions.