Targeting CDK7 function in the RNA Polymerase II transcription cycle in inflammatory arthritis [ChIP-seq]

Macrophages are main drivers of inflammation and tissue damage in autoimmune diseases including rheumatoid arthritis. The rate-limiting step for transcription of >70% of inducible genes in macrophages is RNA Polymerase II (Pol II) promoter-proximal pause release, yet, the specific role of Pol II pausing in inflammation or whether it can be modulated therapeutically is unknown. Genetic ablation of a pause-stabilizing negative elongation factor (NELF) in macrophages enhanced the transcriptional response of paused anti-inflammatory genes to LPS, followed by secondary attenuation of inflammatory signaling, and reduced severity of K/BxN-serum transfer (ST) arthritis in mice. To disrupt Pol II pause establishment pharmacologically, we employed covalent inhibitors of the TFIIH-associated cyclin-dependent kinase (CDK) 7, THZ1 and YKL-5-124. Both dramatically reduced Pol II pausing in murine and human macrophages, broadly suppressed induction of pro- but not anti-inflammatory genes, and rapidly reversed pre-established inflammatory macrophage polarization by TNF+IFN?. In vivo, CDK7i ameliorated the acute K/BxN-ST and chronic progressive hTNF-transgenic arthritis in mice. Finally, CDK7i downregulated a pathogenic gene expression signature in synovial explants from arthritis patients. We propose that interfering with Pol II pausing by targeting CDK7 represents a novel therapeutic opportunity for inflammatory diseases. Overall design: Pol II chipSeq in WT and NELF-cKO LPS-treated macrophages Pol II and Ser5-P PolII ChIPseq in TNF-IFNg polarized YKL-treated macrophages NELF-E ChIPseq in YKL treated mouse macrophages NELF-E ChIPseq in YKL treated human PBMC-derived macrophages Pol2 chipseq in mouse macrophages treated with LPS, YKS or both