CDK12-mediated transcriptional regulation of noncanonical NF-κB components is essential for signaling

Members of the family of nuclear factor kappa B (NF-kappa B) transcription factors are critical for multiple cellular processes, including regulating innate and adaptive immune responses, cell proliferation, and cell survival. Canonical NF-kappa B complexes are retained in the cytoplasm by the inhibitory protein I kappa B alpha, whereas noncanonical NF-kappa B complexes are retained by p100. Although activation of canonical NF-kappa B signaling through the I kappa B alpha kinase complex is well studied, few regulators of the NF-kappa B-inducing kinase (NIK)-dependent processing of noncanonical p100 to p52 and the subsequent nuclear translocation of p52 have been identified. We discovered a role for cyclin-dependent kinase 12 (CDK12) in transcriptionally regulating the noncanonical NF-kappa B pathway. High-content phenotypic screening identified the compound 919278 as a specific inhibitor of the lymphotoxin beta receptor (LT beta R), and tumor necrosis factor (TNF) receptor superfamily member 12A (FN14)-dependent nuclear translocation of p52, but not of the TNF-alpha receptor-mediated nuclear translocation of p65. Chemoproteomics identified CDK12 as the target of 919278. CDK12 inhibition by 919278, the CDK inhibitor THZ1, or siRNA-mediated knockdown resulted in similar global transcriptional changes and prevented the LT beta R-and FN14-dependent expression of MAP3K14 (which encodes NIK) as well as NIK accumulation by reducing phosphorylation of the carboxyl-terminal domain of RNApolymerase II. By coupling a phenotypic screen with chemoproteomics, we identified a pathway for the activation of the noncanonical NF-kappa B pathway that could serve as a therapeutic target in autoimmunity and cancer.