Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome
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Curated by eLife
eLife assessment
This is a valuable study providing solid evidence that the Mediator kinase module mediates an elevated inflammatory response, manifested by heightened cytokine levels, associated with Downs syndrome (DS) via transcriptional changes impacting cell signaling and metabolism, which has significance for the treatment of DS and other chronic inflammatory conditions. Particular strengths of the study include the combined experimental approaches of transcriptomics, untargeted metabolomics, cytokine screens, and the use of sibling-matched cell lines (trisomy 21 vs disomy 21) from various donors. Less certain is that the Mediator kinase plays a meaningful role in regulating mRNA splicing. Further evidence that nuclear receptors are activated by changes in lipid levels and that mitochondrial function is substantially reduced on Mediator kinase inhibition would strengthen the work.
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Abstract
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 over a 45min - 24h timeframe. Activation of IFN-response genes was suppressed in cells treated with the CDK8/CDK19 inhibitor cortistatin A (CA), and this occurred through rapid suppression of IFN-responsive transcription factor activity. Moreover, we discovered that CDK8/CDK19 affect splicing, a novel means by which Mediator kinases control gene expression. To further probe Mediator kinase function, we completed cytokine screens and untargeted metabolomics experiments. Cytokines are master regulators of inflammatory responses; by screening 105 different cytokine proteins, we show that Mediator kinases help drive IFN-dependent cytokine responses at least in part through transcriptional regulation of cytokine genes and receptors. Metabolomics revealed that Mediator kinase inhibition altered core metabolic pathways, including broad up-regulation of anti-inflammatory lipid mediators, whose levels were elevated during hyperactive IFN signaling. A subset of these lipid mediators (e.g. oleamide, desmosterol) serve as ligands for nuclear receptors PPAR and LXR, and activation of these receptors occurred specifically during hyperactive IFN signaling in CA-treated cells, revealing a mechanistic link between Mediator kinase activity and nuclear receptor function. Collectively, our results identify new mechanisms by which CDK8/CDK19 regulate gene expression, and establish that Mediator kinase inhibition antagonizes IFN signaling through transcriptional, metabolic, and cytokine responses, with implications for DS and other chronic inflammatory conditions.
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eLife assessment
This is a valuable study providing solid evidence that the Mediator kinase module mediates an elevated inflammatory response, manifested by heightened cytokine levels, associated with Downs syndrome (DS) via transcriptional changes impacting cell signaling and metabolism, which has significance for the treatment of DS and other chronic inflammatory conditions. Particular strengths of the study include the combined experimental approaches of transcriptomics, untargeted metabolomics, cytokine screens, and the use of sibling-matched cell lines (trisomy 21 vs disomy 21) from various donors. Less certain is that the Mediator kinase plays a meaningful role in regulating mRNA splicing. Further evidence that nuclear receptors are activated by changes in lipid levels and that mitochondrial function is substantially reduced on …
eLife assessment
This is a valuable study providing solid evidence that the Mediator kinase module mediates an elevated inflammatory response, manifested by heightened cytokine levels, associated with Downs syndrome (DS) via transcriptional changes impacting cell signaling and metabolism, which has significance for the treatment of DS and other chronic inflammatory conditions. Particular strengths of the study include the combined experimental approaches of transcriptomics, untargeted metabolomics, cytokine screens, and the use of sibling-matched cell lines (trisomy 21 vs disomy 21) from various donors. Less certain is that the Mediator kinase plays a meaningful role in regulating mRNA splicing. Further evidence that nuclear receptors are activated by changes in lipid levels and that mitochondrial function is substantially reduced on Mediator kinase inhibition would strengthen the work.
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Reviewer #1 (Public Review):
Summary:
The main conclusion of this manuscript is that the mediator kinases supporting the IFN response in Downs syndrome cell lines represent an important addition to understanding the pathology of this affliction.
Strengths:
Mediator kinase stimulates cytokine production. Both RNAseq and metabolomics clearly demonstrate a stimulatory role for CDK8/CDK19 in the IFN response. The nature of this role, direct vs. indirect, is inferred by previous studies demonstrating that inflammatory transcription factors are Cdk8/19 substrates. The cytokine and metabolic changes are clear-cut and provide a potential avenue to mitigate these associated pathologies.
Weaknesses:
This study revealed a previously undescribed role for the CKM in splicing. The previous identification of splicing factors as substrates of …
Reviewer #1 (Public Review):
Summary:
The main conclusion of this manuscript is that the mediator kinases supporting the IFN response in Downs syndrome cell lines represent an important addition to understanding the pathology of this affliction.
Strengths:
Mediator kinase stimulates cytokine production. Both RNAseq and metabolomics clearly demonstrate a stimulatory role for CDK8/CDK19 in the IFN response. The nature of this role, direct vs. indirect, is inferred by previous studies demonstrating that inflammatory transcription factors are Cdk8/19 substrates. The cytokine and metabolic changes are clear-cut and provide a potential avenue to mitigate these associated pathologies.
Weaknesses:
This study revealed a previously undescribed role for the CKM in splicing. The previous identification of splicing factors as substrates of CDK8/CDK19 is also intriguing. However, additional studies seem to be necessary in order to attach this new function to the CKM. As the authors point out, the changes in splicing patterns are relatively modest compared to other regulators. In addition, some indication that the proteins encoded by these genes exhibit reduced levels or activities would support their RNAseq findings.
Seahorse analysis is normally calculated with specific units for oxygen consumption, ATP production, etc. It would be of interest to see the actual values of OCR between the D21 and T21 cell lines rather than standardizing the results. This will address the specific question about relative mitochondrial function between these cells. Reduced mitochondrial function has been associated with DS patients. Therefore, it would be important to know whether mitochondrial function is reduced in the T21 cells vs. the D21 control. Importantly for the authors' goal of investigating the use of CDK8/19 inhibitors in DS patients, does CA treatment reduce mitochondrial function to pathological levels?
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Reviewer #2 (Public Review):
Summary:
In this manuscript, Cozzolino et al. demonstrate that inhibition of the Mediator kinase CDK8 and its paralog CDK19 suppresses hyperactive interferon (IFN) signaling in Down syndrome (DS), which results from trisomy of chromosome 21 (T21). Numerous pathologies associated with DS are considered direct consequences of chronic IFN pathway activation, and thus hyperactive IFN signaling lies at the heart of pathophysiology. The collective interrogation of transcriptomics, metabolomics, and cytokine screens in sibling-matched cell lines (T21 vs D21) allows the authors to conclude that Mediator kinase inhibition could mitigate chronic, hyperactive IFN signaling in T21. To probe the functional outcomes of Mediator kinase inhibition, the authors performed cytokine screens, transcriptomic, and untargeted …
Reviewer #2 (Public Review):
Summary:
In this manuscript, Cozzolino et al. demonstrate that inhibition of the Mediator kinase CDK8 and its paralog CDK19 suppresses hyperactive interferon (IFN) signaling in Down syndrome (DS), which results from trisomy of chromosome 21 (T21). Numerous pathologies associated with DS are considered direct consequences of chronic IFN pathway activation, and thus hyperactive IFN signaling lies at the heart of pathophysiology. The collective interrogation of transcriptomics, metabolomics, and cytokine screens in sibling-matched cell lines (T21 vs D21) allows the authors to conclude that Mediator kinase inhibition could mitigate chronic, hyperactive IFN signaling in T21. To probe the functional outcomes of Mediator kinase inhibition, the authors performed cytokine screens, transcriptomic, and untargeted metabolomics. This collective approach revealed that Mediator kinases establish IFN-dependent cytokine responses at least in part through transcriptional regulation of cytokine genes and receptors. Mediator kinase inhibition suppresses cell responses during hyperactive IFN signaling through inhibition of pro-inflammatory transcription factor activity (anti-inflammatory effect) and alteration of core metabolic pathways, including upregulation of anti-inflammatory lipid mediators, which served as ligands for specific nuclear receptors and downstream phenotypic outcomes (e.g., oxygen consumption). These data provided a mechanistic link between Mediator kinase activity and nuclear receptor function. Finally, the authors also disclosed that Mediator kinase inhibition alters splicing outcomes.
Overall, this study reveals a mechanism by which Mediator kinases regulate gene expression and establish that its inhibition antagonizes chronic IFN signaling through collective transcriptional, metabolic, and cytokine responses. The data have implications for DS and other chronic inflammatory conditions, as Mediator kinase inhibition could potentially mitigate pathological immune system hyperactivation.
Strengths:
(1) One major strength of this study is the mechanistic evidence linking Mediator kinases to hyperactive IFN signaling through transcriptional changes impacting cell signaling and metabolism.
(2) Another major strength of this study is the use of sibling-matched cell lines (T21 vs D21) from various donors (not just one sibling pair), and further cross-referencing with data from large cohorts, suggesting that part of the data and conclusions are generalizable.
(3) Another major strength of this study is the combined experimental approach including transcriptomics, untargeted metabolomics, and cytokine screens to define the mechanisms underlying suppression of hyperactive interferon signaling in DS upon Mediator kinase inhibition.
(4) Another major strength of this study is the significance of the work to DS and its potential impact on other chronic inflammatory conditions.
Weakness:
(1) Genetic evidence linking the mentioned nuclear receptors to activation of an anti-inflammatory program upon Mediator kinase inhibition could improve the definition of the mechanism and overall impact of the work.
(2) Page 5 states that "Mediator kinases broadly regulate cholesterol and fatty acid biosynthesis and this was further confirmed by the metabolomics data", but a clear mechanistic explanation was lacking. Likewise, the data suggest but do not prove, that altered lipid metabolites influence the function of nuclear receptors to regulate an anti-inflammatory program in response to Mediator kinase inhibition (p. 6), despite the fact the gene expression changes elicited by Mediator kinase inhibition tracked with downstream metabolic changes.
(3) The figures are outstanding but dense.
(4) Figure 6 (PRO-Seq). The authors refer to pro-inflammatory TFs (e.g. NF-kB/RelA). It is not clear whether the authors have specifically examined TF binding at enhancers or more broadly at every region occupied by the interrogated TFs?
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