A novel, short isoform of the +TIP microtubule (MT) binding protein CLIP170 confers taxane resistance by obstructing the MT pore.

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The taxanes are amongst the most commonly used chemotherapy drugs in clinical oncology, and are a mainstay of treatment in gastric cancer. However, despite their use in both first and second line therapy, patients commonly exhibit intrinsic resistance resulting in marginal benefit. A post hoc analysis of taxane therapy in an international clinical trial (TAX-325) confirmed this observation; we found that GC patients with diffuse histological subtype did not benefit from DTX therapy, suggesting that diffuse GC is may be intrinsically resistant to taxanes. To date, despite the wide use of taxanes in oncology, the molecular underpinnings of clinical taxane resistance remain poorly elucidated. Using preclinical models of GC intrinsic resistance, we identified a novel faster-migrating isoform of the microtubule (MT) plus-end binding protein CLIP-170, hereafter CLIP-170S, which was enriched in GC cell lines with intrinsic taxane resistance. The canonical full-length CLIP-170 protein belongs to the family of MT plus- end-tracking proteins (+TIPs) which accumulate at the distal ends of growing MTs, linking MT ends to various cell structures and regulating MT dynamics. Mass-spec proteomics and 5’RACE revealed that CLIP-170S was missing the first 150 amino acids, including the first Cap-Gly (domain, required for proper +TIP localization. Confocal microscopy experiments showed that CLIP-170S was miss-localized from the MT ends to the MT lattice. Live-cell imaging of native cytoskeletons using fluorescently- labeled paclitaxel (Flutax) revealed significantly faster dissociation rates of Flutax from MTs in the cells expressing CLIP-170S, indicating transient interaction with MTs. Taxane binding to MTs is a two-step process. First, taxanes bind to the MT outer surface by interacting with their low affinity binding site at the MT pore, then, they get internalized to the MT lumen where they bind to their high affinity luminal binding site. Our data using chemical probes specific for the outer and inner surface of the MT pore showed that CLIP-170S expression was associated with decreased binding affinity of taxanes for MTs. Stable knock- down (KD) of CLIP-170S reversed completely taxane resistance (~300-fold)— while KD of the canonical CLIP-170 had no effect on drug activity— thereby, suggesting a cause-effect relationship between CLIP-170S expression and taxane resistance. Together these data led us propose a model where CLIP-170S blocks the MT-pore, impairs taxane binding to the MT outer surface inhibiting taxane access to the high-affinity luminal binding site resulting in drug resistance. We have developed a drug discovery platform, BANDIT (Bayesian Analysis to Identify Drug Interaction Targets), which allows for accurate identification of target proteins for orphan drugs or small molecules. BANDIT identified Imatinib as a drug predicted to be active in taxane-resistant GC cells. Experimental validation showed that Imatinib not only was able to completely reverse taxane resistance, but it did so by inhibiting specifically the expression of CLIP-170S. Our central hypothesis is that CLIP-170S, by lacking the first N-terminus CAP-GLY motif is miss-localized from the +TIP to the MT lattice, obstructing the MT-pore and blocking taxane access to its high affinity luminal drug binding-site. Computational modeling predicted that Imatinib would reverse taxane resistance. Experimental validation of this prediction led us further hypothesize that additional clinically used tyrosine kinase inhibitors (TKIs), may share this mode of action with Imatinib, and synergize with taxanes providing a new targeted therapeutic strategy for GC patients.