(H) A crystal violet staining image of MDA-MB-468-KRAB-dCas9 cells transduced with doxycycline-inducible sgRNA constructs after treatment with or without doxycycline (100 ng/mL) for 9 days with an initial seeding of 10,000 cells in a 12-well plate

(H) A crystal violet staining image of MDA-MB-468-KRAB-dCas9 cells transduced with doxycycline-inducible sgRNA constructs after treatment with or without doxycycline (100 ng/mL) for 9 days with an initial seeding of 10,000 cells in a 12-well plate. (BBC). In common culture conditions, we found that small molecule inhibition, genetic deletion, or acute depletion of MELK did not significantly affect cellular growth. This discrepancy to previous findings illuminated selectivity issues of the widely used MELK inhibitor OTSSP167, and potential off-target effects of MELK-targeting short hairpins. The different genetic and Busulfan (Myleran, Busulfex) chemical tools developed here allow for the identification and validation of any causal roles MELK may play in cancer biology, which will be required to guide future MELK drug discovery efforts. Furthermore, our study provides a general framework for preclinical target validation. TREEanalysis of MELK inhibitors.(A) Kinase profile of JW-7-25-1 at 10 M (KINOMEand the actual sequences of the PCR amplicons from three clones isolated from MDA-MB-468 cells transfected with Cas9/sgMELK-3, including clone (A) E9, (B) C7 and (C) C9. dTAG-mediated loss of MELK does not impair growth of MDA-MB-468 cells As the process for deriving and isolating clonal lines of MELK?/? MDA-MB-468 cells requires an extended period of time, we were concerned that these clonal lines would be able to compensate for loss of MELK during this process. Thus, to understand the immediate effect Busulfan (Myleran, Busulfex) of MELK loss, we employed a novel chemical genetic system (the dTAG system) whereby tagged proteins are targeted for degradation by the E3 ubiquitin ligase cereblon (CRL4CRBN) (Erb et al., 2017). In this system, mutant FKBP12 (FKBP12F36V) serves as a degradation tag (dTAG) and is fused to a protein of interest. The F36V mutation introduces a hole in the FKBP12 binding site that accommodates a bump on the FKBP12F36V-binding ligand, Busulfan (Myleran, Busulfex) which does not effectively bind to wild-type FKBP12 (Clackson et al., 1998). We synthesized heterobifunctional molecules (dTAG molecules) by conjugating FKBP12F36V binders to thalidomide, which is a potent ligand for CRL4CRBN. These molecules bring the FKBP12F36V-fusion protein and CRL4CRBN into close proximity, thus inducing rapid ubiquitination and subsequent proteasomal degradation of the tagged protein while sparing endogenous FKBP12 (Erb et al., 2017; Winter et al., 2015). To maintain continuous expression of MELK, we first expressed N-terminally tagged MELK (FKBP12F36V-MELK) in MDA-MB-468 cells, and then deleted endogenous MELK using CRISPR/Cas9. A single point mutation in the protospacer adjacent motif targeted by sgMELK-3 (termed sg3R) prevented CRISPR editing of the transgene encoding FKBP12F36V-MELK(sg3R). We isolated 24 clones with varying levels of FKBP12F36V-MELK(sg3R) expression and varying endogenous MELK status (Figure 4figure supplement 1). Two validated MELK?/? clones expressing high levels of FKBP12F36V-MELK(sg3R) were chosen for further studies. Importantly, the exogenous MELK fusion protein was still sensitive to MRT199665-induced degradation, and was stabilized and hyperphosphorylated during mitosis, suggesting that FKBP12F36V-MELK(sg3R) is DRTF1 similarly regulated as endogenous MELK (Figure 4figure supplement 2). Four dTAG molecules (7, 13, 36 and 47) that vary in linker length and chemical structure were tested for their efficiency at depleting FKBP12F36V-MELK(sg3R) (Figure 4A, Figure 4figure supplement 3). All four degraders efficiently depleted FKBP12F36V-MELK(sg3R) within 4 hours (Figure 4B); in particular, dTAG-13, 36, and 47 demonstrated sustained degradation of FKBP12F36V-MELK(sg3R) for up to 72 hours (Figure 4C). A multiplexed quantitative mass spectrometry-based proteomics experiment demonstrated that only FKBP12F36V-MELK was significantly degraded, confirming the selectivity of the system (Figure 4D) (McAlister et al., 2012). In a 9-day proliferation assay, neither of the FKBP12F36V-MELK(sg3R) MELK?/? clones exhibited growth impairment when treated by dTAG-47 (Figure 4E), confirming that MDA-MB-468 cells are not sensitive to acute and.