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

Abstract

Members of the family of nuclear factor κB (NF-κB) transcription factors are critical for multiple cellular processes, including regulating innate and adaptive immune responses, cell proliferation, and cell survival. Canonical NF-κB complexes are retained in the cytoplasm by the inhibitory protein IκBα, whereas noncanonical NF-κB complexes are retained by p100. Although activation of canonical NF-κB signaling through the IκBα kinase complex is well studied, few regulators of the NF-κB-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-κB pathway. High-content phenotypic screening identified the compound 919278 as a specific inhibitor of the lymphotoxin β receptor (LTβR), and tumor necrosis factor (TNF) receptor superfamily member 12A (FN14)-dependent nuclear translocation of p52, but not of the TNF-α 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 LTβR- and FN14-dependent expression of (which encodes NIK) as well as NIK accumulation by reducing phosphorylation of the carboxyl-terminal domain of RNA polymerase II. By coupling a phenotypic screen with chemoproteomics, we identified a pathway for the activation of the noncanonical NF-κB pathway that could serve as a therapeutic target in autoimmunity and cancer.

Transcription-Associated Cyclin-Dependent Kinases as Targets and Biomarkers for Cancer Therapy

“…In osteosarcoma, the sensitivity to CDK12 inhibitors may also be explained by MYC levels (140). Targeting CDK12 with compound 919278 also inhibits osteosarcoma cells by transcriptionally regulating components of the noncanonical NFκB signaling pathway (143). Taken together, these data support the notion that in cancers dependent on certain transcription factors (i.e., MYC, EWS-FLI1, NFkB), targeting CDK12 and other transcription-associated CDKs may be a viable strategy.…”

Phosphoproteome profiling uncovers a key role for CDKs in TNF signaling

“…Similarly, less of the cytokine IP10 was released from BMDMs upon addition of CDK inhibitors ( Supplementary Figure 5E ). Consistent with previous studies that investigated the role of CDK9, this indicates that inhibiting transcriptional CDKs 9, 12, and 13 may have an anti-inflammatory effect in disease (Krystof et al, 2012, Henry et al, 2018). The induction of the pro-survival protein FLIP was also strongly inhibited by CDK inhibitors ( Figure 5E-H ).…”

Characterizing CDK8/19 Inhibitors through a NFκB-Dependent Cell-Based Assay

“…In the case of THZ1, one of its targets, CDK7, was shown to regulate NFκB by promoting its nuclear translocation [29]. Another THZ1 target, CDK12, was implicated in NFκB activation [30] but this effect was linked to the non-canonical NFκB activation pathway, which is not analyzed in our assay. Hence, CDK9 and CDK7 are likely to mediate the effects of other CDK inhibitors with NFκB-inhibitory activity.…”