CK1 Delta Is an mRNA Cap-Associated Protein That Drives Translation Initiation and Tumor Growth

Whether translation is differentially regulated across liquid and solid tumors remains poorly understood. Here we report the discovery that Casein Kinase 1 delta (CK1δ) plays a key role in regulating translation initiation in blood cancers, but interestingly, not in solid tumors. In lymphomas, CK1δ is a key positive regulator of 4E-BP1 and p70S6K phosphorylation, assembly of eIF4F, and translation initiation. Furthermore, CK1δ is pulled down by m7GTP-agarose that mimics the mRNA m7G cap, consistent with the regulatory role of CK1δ in translation initiation. Targeting CK1δ using a small molecule inhibitor, namely SR-3029, potently kills lymphoma cell lines and primary lymphoma cells across histology subtypes. While SR-3029 shares with mTORC1 inhibitors the overlapping mechanism of repressing 4E-BP1 and p70S6K/RPS6 phosphorylation, the kinetics of repression is slow with SR-3029 and fast with mTORC1 inhibitors such as Torin-1. Remarkably, it is slower-acting SR-3029, but not fast-acting Torin-1, that kills lymphoma cells consistently across multiple histology subtypes. Proteomics and RNA sequencing studies show that SR-3029 represses the expression of many genes preferentially at the translation step, such as genes in the Reactome translation initiation pathway. SR-3029 markedly represses the protein level of the C-MYC oncogene without decreasing its mRNA level. In contrast, Torin-1 fails to reduce the protein level of C-MYC in the same lymphoma cells. While SR-3029 also demonstrates potent activity in select solid tumors, its mechanism of action in solid tumors is different. In breast cancer cells SR-3029 inhibits nuclear localization of β-catenin but at the same concentrations does not inhibit 4E-BP1 and p70S6K phosphorylation or global protein synthesis. Likewise, SR-3029 does not inhibit nuclear localization of β-catenin in lymphoma cells. Our results indicate that CK1δ is an mRNA cap-associated protein and an upstream kinase required for 4E-BP1 and p70S6K phosphorylation. CK1δ stimulates assembly of eIF4F and translation initiation and is a critical driver for tumor growth in blood cancers across multiple histology types. CK1δ invokes the alternative mechanism of regulating β-catenin in select solid tumors. Our results indicate that CK1δ inhibition is a promising therapeutic strategy in both liquid and solid tumors, and the distinct roles of CK1δ in these malignancies may serve as biomarkers to enable precision cancer treatment.