Protein Homeostasis Screen Identifies CK2 Inhibition as a Driver of CARD9 Depletion

CARD9 is a genetically validated target for autoimmune disease, with human expression quantitative trait loci (eQTLs) linking elevated CARD9 expression to increased disease risk and lower CARD9 expression to protection. Notably, a rare variant leading to a C-terminal truncation of CARD9 (CARD9Δ11) and subsequent loss of function confers protection against inflammatory bowel disease. Despite its therapeutic potential, CARD9 has long been considered "undruggable" as an adaptor protein with complex biology and limited chemical tools. Here, we leverage a protein homeostasis screening strategy to discover that inhibition of casein kinase 2 (CK2/CSNK2) results in the depletion of CARD9, a mechanism conserved across immortalized cell lines and primary cells. Mechanistic studies revealed that CK2 directly binds and phosphorylates CARD9 in its predicted disordered region. CK2 inhibitors prevent this protein-protein interaction, leading to CARD9 destabilization. Furthermore, the interaction between CK2 and CARD9Δ11 is significantly attenuated and resistant to CK2-mediated protein stabilization. Finally, we demonstrate therapeutic proof of concept in vivo using CK2 inhibition to deplete CARD9 in a murine peritonitis model. Our study expands the scope of cellular consequences elicited by kinase inhibition, offers an unconventional approach for engaging a therapeutically intractable target, and identifies a novel mechanism that could contribute to disease protection conferred by the CARD9Δ11 allele.