Precise DCLK1 Protein Degradation via PROTAC Delays Cyst Growth in ADPKD

Background: Doublecortin-like kinase 1 (DCLK1) is a cyclic AMP-dependent serine/threonine kinase, which is recognized as a prooncogenic factor in various cancers. However, little is known about the role of DCLK1 as a therapeutic target in ADPKD. A type of proteolysis-targeting chimera (PROTAC) is a protein depletion approach that bridges a protein of interest with the E3 ubiquitin ligase complex for subsequent proteasomal degradation. We hypothesize that targeting DCLK1 with cereblon (CRBN)-based PROTAC may be a promising approach for attenuation of ADPKD. Methods: To define the role of DCLK1 and test the effect of DCLK1 PROTACs in ADPKD, we treated two Pkd1 mutant mouse models with DCLK1 PROTACs and analyzed the kidneys with H&E, immunofluorescence, immunohistochemistry staining and TUNEL assay. The changes of the key PKD associated factors were analyzed by Western blot and qRT-PCR analysis. We identified the DCLK1 interaction protein by mass spectrometry analysis. Results: We found that DCLK1 was upregulated in Pkd1 mutant renal epithelial cells in kidneys. Treatment with Forskolin, which activates adenylate cyclase to increase in intracellular concentration of cAMP, also increases the expression of DCLK1 in mouse IMCD cells. Targeting DCLK1 with newly generated PROTACs, that were generated by adding an alkynyl group at the secondary amino position of DCLK1 inhibitor and conjugating them to E3 ubiquitin ligase ligand targeting CRBN through aliphatic linkers, decreased cyst growth as seen by the decrease of cystic index, kidney weight/body weight (KW/BW) ratios, and blood urea nitrogen (BUN) levels in Pkd1mutant mouse kidneys. Furthermore, treatment with DCLK1 PROTACs decreased cyst lining epithelial cell proliferation through a decrease of activation of ERK, AKT, S6, STAT3, and mitigated renal inflammation through deactivation of nuclear factor-κB. Notably, DCLK1 binds directly with the inhibitor of κB kinase β and induces IKKβ phosphorylation on Ser177/181 to initiate NF-κB pathway. In addition, treatment with DCLK1 PROTAC induced cystic renal epithelial cell death in Pkd1 mutant kidneys. Conclusion: Our study highlights 1) a novel cAMP-DCLK1 signaling in promoting ADPKD progression and 2) an application of PROTAC technology in ADPKD treatment. This study suggests that in contrast to traditional drug approach, targeting DCLK1 with PROTACs is a novel therapeutic strategy for ADPKD. Funding: NIDDK Support