Kinase Switch Research Articles

Large-scale analysis of the N-terminal regulatory elements of the kinase domain in plant Receptor-like kinase family

BackgroundThe N-terminal regulatory element (NRE) of Receptor-like kinases (RLKs), consisting of the juxtamembrane segment in receptor kinases (RKs) and the N-terminal extension segment in RLCKs, is a crucial component that regulates the activities of these proteins. However, the features and functions of the NRE have remained largely unexplored. Herein, we comprehensively analyze 510,233 NRE sequences in RLKs from 528 plant species, using information theory and data mining techniques to unravel their common characteristics and diversity. We also use recombinant RKs to investigate the function of the NRE in vitro.ResultsOur findings indicate that the majority of NRE segments are around 40–80 amino acids in length and feature a serine-rich region and a 14-amino-acid consensus sequence, ‘FSYEELEKAT[D/N]NF[S/D]’, which contains a characteristic α-helix and ST motif that connects to the core kinase domain. This conserved signature sequence is capable of suppressing FERONIA’s kinase activity. A motif discovery algorithm identifies 29 motifs with highly conserved phosphorylation sites in RK and RLCK classes, especially the motif ‘VGPWKpTGLpSGQLQKAFVTGVP’ in LRR-VI-2 class. Phosphorylation of an NRE motif in an LRR-VI-2 member, MDIS1, modulates the auto-phosphorylation of its co-receptor, MIK1, indicating the potential role of NRE as a ‘kinase switch’ in RLK activation. Furthermore, the characterization of phosphorylatable NRE motifs improves the accuracy of predicting phosphorylatable sites.ConclusionsOur study provides a comprehensive dataset to investigate NRE segments from individual RLKs and enhances our understanding of the underlying mechanisms of RLK signal transduction and kinase activation processes in plant adaptation.

Phosphatase to kinase switch of a critical enzyme contributes to timing of cell differentiation.

The process of cell differentiation is highly regulated in both prokaryotic and eukaryotic organisms. The aquatic bacterium, Caulobacter crescentus, undergoes programmed cell differentiation from a motile swarmer cell to a stationary stalked cell with each cell cycle. This critical event is regulated at multiple levels. Kinase activity of the bifunctional enzyme, PleC, is limited to a brief period when it initiates the molecular signaling cascade that results in cell differentiation. Conversely, PleC phosphatase activity is required for pili formation and flagellar rotation. We show that PleC is localized to the flagellar pole by the scaffold protein, PodJ, which is known to suppress PleC kinase activity in vitro. PleC mutants that are unable to bind PodJ have increased kinase activity in vivo, resulting in premature differentiation. We propose a model in which PodJ regulation of PleC's enzymatic activity contributes to the robust timing of cell differentiation during the Caulobacter cell cycle.

Phosphatase to kinase switch of a critical enzyme contributes to timing of cell differentiation

Phosphatase to kinase switch of a critical enzyme contributes to timing of cell differentiation

Abstract C077: Updated results of phase 1 study of ripretinib (DCC-2618), a broad-spectrum KIT and PDGFRA inhibitor, in patients with gastrointestinal stromal tumor (GIST) by line of therapy (NCT02571036)

Abstract Objective: Ripretinib (DCC-2618) is a kinase switch control inhibitor designed to broadly inhibit KIT and PDGFRA mutations. Based on clinical activity observed in heavily pretreated patients (pts) with GIST in a Phase 1 study (NCT02571036), ripretinib is under evaluation in two Phase 3 studies: INVICTUS (NCT03353753) in ≥4th-line pts and INTRIGUE (NCT03673501) in 2nd-line pts, each at the recommended dose of 150 mg once daily (QD). This abstract reports updated results from the escalation and expansion phases of the Phase 1 study for pts treated with ≥100 mg daily dose. Methods: The Phase 1 study includes a dose-escalation phase that tested oral ripretinib QD or twice daily (BID) in 28-day cycles, followed by an expansion phase with the recommended Phase 2 dose (RP2D) of 150 mg QD in 6 cohorts, including cohorts for pts with GIST based on prior regimens (2nd/ 3rd, 4th, and >4th-line). Local Response Evaluation Criteria in Solid Tumors (RECIST) response assessments were performed every 2 cycles and pts who progressed per RECIST in the expansion cohorts were allowed to dose escalate to 150 mg BID. Results: At a cut-off date of March 01, 2019, 179 pts with GIST in the escalation and expansion phases (median follow-up of 10.4 months; range, 0.1–32.3) were enrolled at dose levels of ≥100 mg daily with KIT-driven (169 pts), PDGFRA-driven (9 pts), or wild-type-driven GIST (1 pt). Of 178 pts with GIST treated at the ≥100 mg daily dose (1 pt was not included in the intent-to-treat population as the pt only participated in the food effect portion of the study), there were 37 2nd-line pts, 31 3rd-line pts, 60 4th-line pts, and 50 >4th-line pts. The objective response rate (ORR) by best response was 30% in 2nd-line pts (n=11; includes 3 unconfirmed responses), 23% in 3rd-line pts (n=7; includes 3 unconfirmed responses), and 11% in ≥4th-line pts (n=12; includes 4 unconfirmed responses); responses ≥4th-line include 15% in 4th-line pts (n=9; includes 4 unconfirmed responses) and 6% in >4th-line pts (n=3; includes no unconfirmed responses). In 2nd-line pts, the disease control rate (DCR) was 31% (n=9) at 52 weeks. The median progression-free survival (mPFS) was 42 weeks in 2nd-line pts, 40 weeks in 3rd-line pts, and 24 weeks in ≥4th-line pts (includes 30 weeks in 4th-line pts and 16 weeks in >4th-line pts). In 2nd-line pts, the median duration of response was 80 weeks and the median duration of treatment was 44 weeks. For any line, 13% of pts (n=24) experienced treatment-emergent adverse events (TEAEs) leading to study treatment discontinuation, 17% of pts (n=31) experienced TEAEs leading to dose reduction and 49% (n=88) had TEAEs leading to study drug interruption. Grade 3 or 4 TEAEs in >5% of pts were lipase increased (18%; n=33), anemia (11%; n=20), hypertension (7%; n=13), and abdominal pain (6%; n=11). Conclusion: In this Phase 1 study, ripretinib demonstrated encouraging clinical benefit (as measured by mPFS, ORR [best response] and DCR) and was generally well-tolerated in pts with GIST treated in the 2nd-line or later. Preliminary data from this Phase 1 study further supports testing in the ongoing Phase 3 study in 2nd-line GIST. Citation Format: Ping Chi, Filip Janku, Michael Heinrich, Kristen Ganjoo, Hans Gelderblom, Michael Gordon, Robin Jones, Albiruni Razak, Jonathan Trent, Margaret von Mehren, Simin Hu, Ying Su, Rodrigo Ruiz-Soto, Suzanne George. Updated results of phase 1 study of ripretinib (DCC-2618), a broad-spectrum KIT and PDGFRA inhibitor, in patients with gastrointestinal stromal tumor (GIST) by line of therapy (NCT02571036) [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C077. doi:10.1158/1535-7163.TARG-19-C077

LBA87 - INVICTUS: A phase III, interventional, double-blind, placebo-controlled study to assess the safety and efficacy of ripretinib as ≥ 4th-line therapy in patients with advanced gastrointestinal stromal tumors (GIST) who have received treatment with prior anticancer therapies (NCT03353753)

LBA87 - INVICTUS: A phase III, interventional, double-blind, placebo-controlled study to assess the safety and efficacy of ripretinib as ≥ 4th-line therapy in patients with advanced gastrointestinal stromal tumors (GIST) who have received treatment with prior anticancer therapies (NCT03353753)

The dynamic switch mechanism that leads to activation of LRRK2 is embedded in the DFGψ motif in the kinase domain

Leucine-rich repeat kinase 2 (LRRK2) is a large multidomain protein, and LRRK2 mutants are recognized risk factors for Parkinson's disease (PD). Although the precise mechanisms that control LRRK2 regulation and function are unclear, the importance of the kinase domain is strongly implicated, since 2 of the 5 most common familial LRRK2 mutations (G2019S and I2020T) are localized to the conserved DFGψ motif in the kinase core, and kinase inhibitors are under development. Combining the concept of regulatory (R) and catalytic (C) spines with kinetic and cell-based assays, we discovered a major regulatory mechanism embedded within the kinase domain and show that the DFG motif serves as a conformational switch that drives LRRK2 activation. LRRK2 is quite unusual in that the highly conserved Phe in the DFGψ motif, which is 1 of the 4 R-spine residues, is replaced with tyrosine (DY2018GI). A Y2018F mutation creates a hyperactive phenotype similar to the familial mutation G2019S. The hydroxyl moiety of Y2018 thus serves as a "brake" that stabilizes an inactive conformation; simply removing it destroys a key hydrogen-bonding node. Y2018F, like the pathogenic mutant I2020T, spontaneously forms LRRK2-decorated microtubules in cells, while the wild type and G2019S require kinase inhibitors to form filaments. We also explored 3 different mechanisms that create kinase-dead pseudokinases, including D2017A, which further emphasizes the highly synergistic role of key hydrophobic and hydrophilic/charged residues in the assembly of active LRRK2. We thus hypothesize that LRRK2 harbors a classical protein kinase switch mechanism that drives the dynamic activation of full-length LRRK2.

Abstract CT058: Ripretinib (DCC-2618) pharmacokinetics (PK) in a Phase I study in patients with gastrointestinal stromal tumors (GIST) and other advanced malignancies: A retrospective evaluation of the PK effects of proton pump inhibitors (PPIs)

Abstract Objectives: Ripretinib is a novel, oral kinase switch control inhibitor of KIT and PDGFRα. Encouraging clinical benefit from the phase 1 dose escalation and expansion study as measured by ORR, DCR and PFS in 2nd, 3rd, and >4th line GIST patients with a favorable tolerability profile at doses >100 mg/day has been previously reported (ESMO 2018, abstract #1603O). It has been reported that more than 40% of GIST patients use acid-reducing agents. PPIs are the most potent acid-reducing agents that may impair the absorption of kinase inhibitors 1,2. This retrospective analysis aims to explore whether ripretinib can be used regardless of concomitant PPI use. Methods: The analysis assessed the impact of PPIs on the plasma concentration of ripretinib using PK data from the expansion cohort at the recommended Phase 2 dose of 150 mg QD. Plasma concentrations of ripretinib and its active metabolite DP-5439 obtained from patients who used or did not use PPIs were compared on Cycle 1 Day 1 (C1D1, n=106) and Day 15 (C1D15, n=102). Patients using PPIs were defined as those who continuously took PPIs for at least 4 days prior to C1D1 or C1D15. Patients who did not use PPIs were defined as those who did not take PPIs or any other acid-reducing agents during the study. Results: PK profiles were consistent between patients using and not using PPIs (Table 1), indicating a low likelihood of a clinically significant drug interaction between PPIs and ripretinib. Conclusions: This retrospective PK analysis provides supporting evidence that restriction of co-administration of PPIs with ripretinib may not be necessary. A dedicated drug interaction study is planned to provide a definitive assessment.

The TGF\u03b2-miR-499a-SHKBP1 pathway induces resistance to EGFR inhibitors in osteosarcoma cancer stem cell-like cells

Background/aimsA novel paradigm in tumor biology suggests that osteosarcoma (OS) chemo-resistance is driven by osteosarcoma stem cell-like cells (OSCs). As the sensitivity of only a few tumors to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) can be explained by the presence of EGFR tyrosine kinase (TK) domain mutations, there is a need to elucidate mechanisms of resistance to EGFR-targeted therapies in OS that do not harbor TK sensitizing mutations to develop new strategies to circumvent resistance to EGFR inhibitors.MethodsAs a measure of the characters of OSCs, serum-free cultivation, cell viability test with erlotinib, and serial transplantation in vivo was used. Western blot assays were used to detect the association between erlotinib resistance and transforming growth factor beta (TGFβ)-induced epithelial-to-mesenchymal transition (EMT) progression. By using TaqMan qPCR miRNA array, online prediction software, luciferase reporter assays and western blot analysis, we further elucidated the mechanisms.ResultsHere, CD166+ cells are found in 10 out of 10 tumor samples. We characterize that CD166+ cells from primary OS tissues bear hallmarks of OSCs and erlotinib-resistance. TGFβ-induced EMT-associated kinase switch is demonstrated to promote erlotinib-resistance of CD166+ OSCs. Further mechanisms study show that TGFβ-induced EMT decreases miR-499a expression through the direct binding of Snail1/Zeb1 to miR-499a promoter. Overexpression of miR-499a in CD166+ OSCs inhibits TGFβ-induced erlotinib-resistance in vitro and in vivo. SHKBP1, the direct target of miR-499a, regulates EGFR activity reduction occurring concomitantly with a TGFβ-induced EMT-associated kinase switch to an AKT-activated EGFR-independent state. TGFβ-induced activation of AKT co-opts an increased SHKBP1 expression, which further regulates EGFR activity. In clinic, the ratio of the expression levels of SHKBP1 and miR-499a is highly correlated with EMT and resistance to erlotinib.ConclusionTGFβ–miR-499a–SHKBP1 network orchestrates the EMT-associated kinase switch that induces resistance to EGFR inhibitors in CD166+ OSCs, implies that inhibition of TGFβ induced EMT-associated kinase switch may reverse the chemo-resistance of OSCs to EGFR inhibitors. We also suggest that an elevated SHKBP1/miR-499a ratio is a molecular signature that characterizes the erlotinib-resistant OS, which may have clinical value as a predictive biomarker.

An open label, multicenter, phase 1b/2 study of rebastinib (DCC-2036) in combination with carboplatin to assess safety, tolerability, and pharmacokinetics in patients with advanced or metastatic solid tumors.

TPS2666 Background: Rebastinib is a potent, orally administered, kinase switch control inhibitor selectively targeting the tunica interna endothelial cell kinase (TIE2). TIE2 is primarily expressed in endothelial cells and has critical roles in angiogenesis. In addition, TIE2 is highly expressed in a subset of macrophages, TIE2-expressing macrophages (TEMs), which are known to have proangiogenic, pro-metastatic, and immunosuppressive properties. Accumulating evidence suggests that chemotherapies, such as carboplatin, increase the recruitment and activity of pro-tumoral TEMs, leading to chemotherapy resistance. Taken together, investigation of rebastinib in combination with a chemotherapy such as carboplatin, one of the most commonly used agents across different tumor types, is warranted in advanced solid tumors. Methods: This study is an open-label, Phase 1b/2, multicenter study in patients with advanced or metastatic solid tumors. The study has two parts: the first part is the 3+3 dose escalation phase designed to evaluate the safety, tolerability and pharmacokinetics of 50 mg and 100 mg rebastinib twice daily in combination with carboplatin of AUC 5 or 6 administered once every three weeks to determine the recommended phase 2 dose (RP2D). Patients who have exhausted all therapies and for whom carboplatin is considered appropriate treatment will be enrolled. The second part is the dose expansion phase with three cohorts: previously treated breast cancer, recurrent, platinum-sensitive ovarian cancer, and malignant mesothelioma to evaluate the safety, tolerability, and efficacy of the RP2D. A Simon’s two-stage design will be used in the second part and initially up to 18 patients will be enrolled into each cohort. If more than 4 responses are observed, then the cohort will be expanded up to 33 patients. This trial is expected to enroll up to 117 patients in total, with approximately 18 patients in the first part and up to 99 patients in the second part. The study is currently open only in the US. Clinical trial information: NCT03717415.

Targeting of FGF-Signaling Re-Sensitizes Gastrointestinal Stromal Tumors (GIST) to Imatinib In Vitro and In Vivo.

Dysregulation of the fibroblast growth factor (FGF)/fibroblast growth factor receptor (FGFR) signaling pathway is frequently observed in multiple human malignancies, and thus, therapeutic strategies targeting FGFs and FGFRs in human cancer are being extensively explored. We observed the activation of the FGF/FGFR-signaling pathway in imatinib (IM)-resistant gastrointestinal stromal tumor (GIST) cells. Furthermore, we found that the activation of FGFR signaling has a significant impact on IM resistance in GISTs in vitro. Next, we tested the efficacy of BGJ398, a potent and selective FGFR1–3 inhibitor, in xenograft models of GISTs exhibiting secondary IM resistance due to receptor-tyrosine kinase (RTK) switch (loss of c-KIT/gain of FGFR2a). Five to eight-week-old female nu/nu mice were subcutaneously inoculated into the flank areas with GIST T-1R cells. Mice were randomized as control (untreated), IM, BGJ398, or a combination and treated orally for 12 days. IM had a moderate effect on tumor size, thus revealing GIST resistance to IM. Similarly, a minor regression in tumor size was observed in BGJ398-treated mice. Strikingly, a 90% decrease in tumor size was observed in mice treated with a combination of IM and BGJ398. Treatment with BGJ398 and IM also induced major histopathologic changes according to a previously defined histopathologic response score and resulted in massive myxoid degeneration. This was associated with increased intratumoral apoptosis as detected by immunohistochemical staining for cleaved caspase-3 on day 5 of the treatment. Furthermore, treatment with BGJ398 and IM significantly reduced the proliferative activity of tumor cells as measured by positivity for Ki-67 staining. In conclusion, inhibition of FGFR signaling substantially inhibited the growth of IM-resistant GISTs in vitro and showed potent antitumor activity in an IM-resistant GIST model via the inhibition of proliferation, tumor growth, and the induction of apoptosis, thereby suggesting that patients with advanced and metastatic GISTs exhibiting IM resistance might benefit from therapeutic inhibition of FGFR signaling.

Inhibition of fibroblast growth factor receptor-signaling sensitizes imatinib-resistant gastrointestinal stromal tumors to low doses of topoisomerase II inhibitors.

The acquired resistance of gastrointestinal stromal tumors (GISTs) to the targeted-based therapy remains the driving force to identify the novel approaches that are capable of increasing the sensitivity of GISTs to the current therapeutic regimens. Our present data show that BGJ398, a selective fibroblast growth factor receptor (FGFR) inhibitor, sensitizes imatinib (IM)-resistant GIST cells with receptor tyrosine kinase (RTK) switch (loss of c-KIT/gain of pFGFR2a) to the low doses of topoisomerase II inhibitors - doxorubicin (Dox) and etoposide (Eto). Mechanistically, pretreatment of IM-resistant GIST cells with BGJ398 for 12 h markedly enhanced proapoptotic and growth-suppressive effects of Dox (or Eto). Indeed, a significant cleavage of PARP and caspase-3 was observed in GIST cells treated with a combination of FGFR and topoisomerase II inhibitor. In contrast, no signs of apoptosis were detected in IM-resistant GIST cells treated with BGJ398, whereas the low doses of Dox (Eto) exerted the minor proapoptotic effects on GISTs. The mechanism of BGJ398-induced sensitization of GIST to topoisomerase II inhibitors might be because of attenuation of DNA damage signaling and repair. Indeed, we observed a marked decrease in Rad51 expression in GIST cells treated with BGJ398 together with Dox. Similar results were obtained when an overexpressed pFGFR2a was knocked down by corresponding siRNA before Dox (Eto) exposure. Moreover, FGFR inhibition/depletion caused a loss of Rad51 foci in Dox-treated GIST cells, suggesting that FGFR-signaling plays an important regulatory role in homology-mediated DNA repair. Our data show that combined therapy (RTKs inhibitors supplemented with low doses of topoisomerase II inhibitors) might be effective for unresectable and metastatic forms of GISTs. In case of resistance to IM because of RTKs switch indicated above, FGFR inhibitors (e.g. BGJ398) might be potentially useful because of their ability to sensitize tumor cells to topoisomerase II inhibitors and induce tumor cell apoptosis by targeting DNA double-strand breaks repair.

Abstract CT029: Pharmacokinetic (PK), safety, and tolerability profile of DCC-2618 in a phase I trial supports 150mg QD selected for a pivotal phase III trial in gastrointestinal stromal tumor (GIST)

Abstract Background: DCC-2618, a pan-KIT and PDGFRα kinase switch control inhibitor, is being studied in a pivotal, randomized phase 3 trial, INVICTUS (NCT03353753), based on encouraging disease control observed in a phase 1 trial (NCT02571036) in heavily pretreated GIST patients (pts). In the phase 1 trial, escalating doses of DCC-2618 up to 400 mg per day did not result in a DLT or MTD dose level. The RP2D of 150 mg QD was selected based on PK, efficacy and safety observed across the dose escalation cohorts before enrolling pts into expansion cohorts. Methods: Dose escalation in the phase 1 study is complete, and this study is now enrolling pts into 6 expansion cohorts, including 3 GIST cohorts. DCC-2618 was administered in 28-day cycles at daily oral doses of 20 to 200 mg BID or 100 to 250 mg QD in pts with advanced solid tumors, including GIST. The safety and tolerability of DCC-2618 will be reviewed as a function of exposure to study drug. We report PK results from all dose-escalation cohorts and the expansion phase. The impact of dose modifications including intra-patient dose escalation was assessed based on PK. Results: As of Jan 18, 2018, a total of 168 patients had been treated including 141 GIST patients. The most common treatment-emergent adverse effects (TEAE; all grades, ≥10% of patients) for the overall population across all dose levels included fatigue, myalgia, lipase increase (↑), alopecia, constipation, decreased appetite, nausea, hand-foot-syndrome, anaemia, diarrhea, dyspnea, abdominal pain, weight decrease, arthralgia, and hypertension (HTN). The most common TEAEs for the RP2D of 150 mg QD, based on 106 pts, included fatigue, myalgia, lipase ↑, alopecia, constipation and hand-foot-syndrome. G3 or G4 TEAE, regardless of attribution, occurring in ≥2% pts across all dose levels included included lipase ↑, anemia and HTN. 7.2% of patients underwent dose reductions. All patients who could have received at least 1 cycle prior to Dec 1, 2017 were included for further analysis (127 total, 114 GIST). Among these 114 GIST patients, 83 (73%) remain active on treatment, and 27, 14, 9 and 6 patients have been on DCC-2618 for more than 6, 9, 12, or 15 mo, respectively (15 pts were treated beyond progression per RECIST; a total of 21 were allowed to dose escalate while on study). The median follow up is 3.7 months with a range from 1 to 20 months. Population PK modeling using data from 67 patients demonstrated that combined exposures of DCC-2618 and its active metabolite, DP-5439, increase dose-proportionally. Dosing with a high fat meal increased exposure only slightly. The impact of dose escalation on plasma exposure will be shown. Conclusions: The PK, safety and tolerability data presented together with efficacy data from the phase 1 trial demonstrate a favorable profile and broad therapeutic window for DCC-2618 and support the selection of 150 mg QD as the RP2D for the ongoing pivotal phase 3 INVICTUS study of DCC-2618 in pts with >4th-line GIST. Citation Format: Filip Janku, Michael Heinrich, Albiruni Razak, Michael Gordon, Ping Chi, Kristen Ganjoo, Margaret von Mehren, Neeta Somaiah, Jongtae Lee, Keisuke Kuida, Rodrigo Ruiz Soto, Oliver Rosen, Suzanne George. Pharmacokinetic (PK), safety, and tolerability profile of DCC-2618 in a phase I trial supports 150mg QD selected for a pivotal phase III trial in gastrointestinal stromal tumor (GIST) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr CT029.

Abstract 3925: Inhibition of oncogenic and drug-resistant PDGFRA and KIT alterations by DCC-2618

Abstract Introduction: Activating mutations and other genetic alterations in KIT and PDGFRA receptor tyrosine kinases have been identified in certain cancers and proliferative diseases, including most cases of gastrointestinal stromal tumors (GIST) and systemic mastocytosis, and small percentages of gliomas, lung cancer, and leukemias. The treatment of metastatic GIST has been transformed with KIT inhibitors, but heterogeneous drug-resistant mutations arise during therapy, with individual patients often having multiple KIT mutations in different tumor sites. PDGFRA variants in GIST and other cancers also have a significant unmet medical need. DCC-2618 is a kinase switch control inhibitor that potently inhibits the spectrum of exon 9, 11, 13, 14, 17 and 18 mutations in KIT and exons 12, 14 and 18 mutations in PDGFRA. DCC-2618 has been designed to bind as a type II kinase inhibitor that forces the mutant kinases, including strongly activated mutants such as D816V KIT and D842V PDGFRA, into inactive conformations. DCC-2618 has been observed to be potent in enzyme and cell-based assays, and has demonstrated consistent efficacy in xenograft models driven by PDGFRA and KIT alterations. Methods: DCC-2618, and an active human metabolite, DP-5439, were tested for inhibition of PDGFRA and KIT mutants using standard enzyme and binding assays, and a variety of cell-based assays. Levels of phosphorylated PDGFRA and KIT were determined by Western blot or ELISA. Proliferation was measured using the fluorescent dye resazurin. An x-ray crystal structure of an analog of DCC-2618 was determined at Emerald Biostructures. The H1703 PDGFRA-amplified lung cancer and GIST T1 mutant KIT xenograft models were performed at MI Bioresearch. A GIST PDX exon 17 mutant KIT xenograft model was run at Molecular Response. Results: DCC-2618 and the metabolite DP-5439 inhibited KIT and PDGFRA variants with nanomolar potency. In CHO cells transfected with KIT or PDGFRA variants, DCC-2618 was shown to inhibit the full spectrum of the clinically relevant primary and refractory drug-resistant mutations tested. DCC-2618 also inhibited phosphorylation of KIT or PDGFRA in cell lines with various drug-resistant KIT mutations or PDGFRA alterations. DCC-2618 was compared to the FDA-approved KIT inhibitors imatinib, sunitinib, regorafenib, and midostaurin, as well as other KIT and PDGFRA inhibitors. In vivo, treatment with DCC-2618 led to tumor regressions in KIT- and PDGFRA-driven xenograft models. Conclusions: DCC-2618 has been observed to be a potent inhibitor of KIT and PDGFRA alterations, including mutants, fusions, and amplifications. Based on this profile, DCC-2618 may have utility in the treatment of KIT and PDGFRA-driven cancers including GIST, systemic mastocytosis, and a subset of lung cancers, gliomas, and leukemias. DCC-2618 is currently in a Phase 1 clinical trial in KIT and PDGFRA driven cancers (ClinicalTrials.gov Identifier: NCT02571036). Citation Format: Bryan D. Smith, Michael D. Kaufman, Anu Gupta, Cynthia B. Leary, Wei-ping Lu, Stacie L. Bulfer, Gada Al-Ani, Jarnail Singh, Subha Vogeti, Michael C. Heinrich, Daniel L. Flynn. Inhibition of oncogenic and drug-resistant PDGFRA and KIT alterations by DCC-2618 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3925.

An Allosteric Region of Src Tyrosine Kinase Allows for Stabilization of Its Active-Like Conformation

Protein kinases play an essential role as signaling enzymes and their sensitive action in the needs of the cell requires their tight regulation. Their active conformations are exquisitely regulated and their populations controlled by various post-translational modifications. The inactive conformation of Src tyrosine kinase is characterized by its non-phosphorylated activation loop and the rolled-out αC helix in the N-lobe. The inactive conformation has the regulatory kinase spine disassembled as the RS3 residue from the αC helix is displaced. Our umbrella sampling methods to map the energy landscape of these conformations has allowed for defining four states; the inactive, active conformations and two intermediate states. In the present study we extend our umbrella sampling technique to understand the activation allostery in Src tyrosine kinase in three different mutants. The first mutant is the L297F that occupies an allosteric region in the N-terminal of the αC helix and allows for activation of Src tyrosine kinase analogous to RAFs. The second mutant is the V281F mutation in the catalytic spine that allows for the closing of the two kinase lobes in the absence of nucleotide. A double mutant of Src tyrosine kinase V281F/L297F allows for stabilization of a unique catalytically dead kinase conformation in the active-like state. This unique conformation allows for understanding of kinase switching function independent of its catalytic role. A third M314V mutation in the regulatory spine allows us to explore the maneuvering of hydrophobicity in the Src tyrosine kinase core. These studies provide a fresh perspective to understanding conformational switching in Src family of tyrosine kinases and the dynamic allostery that underlies this molecular communication. Our community map analysis of residue networks provides an additional layer of understanding to these observations.

The Selective Tie2 Inhibitor Rebastinib Blocks Recruitment and Function of Tie2Hi Macrophages in Breast Cancer and Pancreatic Neuroendocrine Tumors.

Tumor-infiltrating myeloid cells promote tumor progression by mediating angiogenesis, tumor cell intravasation, and metastasis, which can offset the effects of chemotherapy, radiation, and antiangiogenic therapy. Here, we show that the kinase switch control inhibitor rebastinib inhibits Tie2, a tyrosine kinase receptor expressed on endothelial cells and protumoral Tie2-expressing macrophages in mouse models of metastatic cancer. Rebastinib reduces tumor growth and metastasis in an orthotopic mouse model of metastatic mammary carcinoma through reduction of Tie2+ myeloid cell infiltration, antiangiogenic effects, and blockade of tumor cell intravasation mediated by perivascular Tie2Hi/Vegf-AHi macrophages in the tumor microenvironment of metastasis (TMEM). The antitumor effects of rebastinib enhance the efficacy of microtubule inhibiting chemotherapeutic agents, either eribulin or paclitaxel, by reducing tumor volume, metastasis, and improving overall survival. Rebastinib inhibition of angiopoietin/Tie2 signaling impairs multiple pathways in tumor progression mediated by protumoral Tie2+ macrophages, including TMEM-dependent dissemination and angiopoietin/Tie2-dependent angiogenesis. Rebastinib is a promising therapy for achieving Tie2 inhibition in cancer patients. Mol Cancer Ther; 16(11); 2486-501. ©2017 AACR.

Coexpression of receptor tyrosine kinase AXL and EGFR in human primary lung adenocarcinomas

AXL has been identified as a tyrosine kinase switch that causes resistance to inhibitors targeting epidermal growth factor receptor (EGFR) signaling in non-small cell lung cancer (NSCLC). However, the relationship between 2 receptor tyrosine kinases, AXL and EGFR, and the relevance of AXL expression with EGFR mutation status in treatment-naive human NSCLCs remain uncertain. In this study, we evaluated the coexpression pattern of AXL, EGFR, and pEGFR(1068) in 109 lung adenocarcinoma patients with or without an EGFR mutation. There were 68 (62.4%) patients with tumors harboring EGFR mutations such as 19 del and/or L858R; 2 patients were T790M positive. The expression of AXL, EGFR, and pEGFR(1068) was detected in 60 (55%), 68 (62.4%), and 57 (52.3%) of 109 patients, respectively. The positive rates of EGFR and pEGFR(1068) were associated with the L858R mutation alone or with the 19 del and L858R mutation status. Further analysis indicated that the percentage of AXL(+)/EGFR(+)/pEGFR(1068) coexpression in 68 EGFR-activating mutations patients was significantly higher than that in 39 EGFR wild-type patients (30.9% versus 10.3%, P=.015). Furthermore, in the subgroup of AXL(+) patients (35 mutation(+) and 23 wild-type patients), the coexpression rates of AXL(+)/pEGFR(1068+) and AXL(+)/EGFR(+)/pEGFR(1068+) in patients with EGFR mutations were significantly higher compared with those in wild-type patients (both P<.05). Our study emphasized that the AXL and EGFR receptor tyrosine kinases were coexpressed in a subgroup of treatment-naive lung adenocarcinomas with or without EGFR mutations. Anti-AXL therapeutics delivered up front in combination with an EGFR inhibitor might prevent or delay resistance in patients with AXL-positive, EGFR-mutant, or wild-type NSCLC.

Reduced expression of EI24 confers resistance to gefitinib through IGF-1R signaling in PC9 NSCLC cells.

Lung cancer is the commonly diagnosed cancer and is the leading cause of cancer-related mortality worldwide. The most prevalent form of lung cancer is NSCLC, comprising 80% of all lung cancer cases, and epidermal growth factor receptor (EGFR) is frequently mutated in NSCLC. EI24 is a p53-responsive gene and plays an important role in tumor suppression. In the current study, we found that reduced expression of EI24 conferred resistance to EGFR-tyrosine-kinase inhibitor (TKI) in NSCLC cells. The correlation between EI24 expression and EGFR-TKI drug resistance in EGFR-driven tumors were determined from microarray datasets. The phospho-protein expression profiles of receptor tyrosine kinases and protein kinases were examined using antibody arrays method in PC9 cells expressing shRNAs targeting EI24 and gefitinib-resistant PC9-GR cells expressing exogenous EI24. The EGFR-TKI resistant clones had reduced expression of EI24 mRNA compared to the sensitive clones, and EI24 knockdown rendered sensitive cells resistant to EGFR-TKI. Receptor tyrosine kinase screening revealed the involvement of a kinase switch in EI24-mediated regulation of drug sensitivity. We found that EI24 modulates the insulin growth factor-1 receptor (IGF-1R) pathway through the induction of IGF-1. Combination treatment with EGFR and IGF-1R inhibitors significantly reduced the viability of EI24 knockdown-induced resistant cell lines compared to single-agent treatments. We also showed that low EI24 and high IGF-1R expressions in lung cancer patients were correlated with reduced overall survival. Taken together, these results suggest a potential role for EI24 as a biomarker of drug resistance, and indicate that combination therapy with EGFR and IGF-1R inhibitors would be effective in NSCLC patients with low EI24 expression.

Abstract LB-059: Opposing roles for protein tyrosine kinase 6 (PTK6) in colon cancer

Abstract Background: Protein Tyrosine Kinase 6 (PTK6, also called BRK) is a non-receptor tyrosine kinase expressed in differentiated epithelial cells of the skin, gastrointestinal tract, and prostate. Disruption of the Ptk6 gene led to impaired intestinal differentiation and increased intestinal proliferation in mice. However, PTK6 also has a tumor-promoting role in the colon, as disruption of the Ptk6 gene impaired carcinogen-induced STAT3 activation and tumorigenesis in mice. PTK6 also promotes survival of human colon cancer cell lines following DNA damaging treatments including γ-irradiation and chemotherapeutic drugs via STAT3 activation. Results: We examined and manipulated colon cancer cell lines to understand these two seemingly contradictory roles for PTK6 in the colon. The human colon adenocarcinoma cell lines SW480 and SW620 represent a primary colon tumor and a metastasis from the same patient, respectively. PTK6 is highly expressed in SW480 cells and significantly reduced in SW620 cells. Active PTK6, phosphorylated on tyrosine residue 342, is not detectable in either cell line. Stable knockdown of PTK6 in SW480 cells results in an epithelial-to-mesenchymal transition (EMT), evidenced by decreased E-cadherin expression and increased ZEB-1 and Vimentin; as well as increased migration, wound-healing, and anchorage-independent growth of cells in culture. Additionally, knockdown of PTK6 led to increased in vivo tumorigenesis of xenograft cells in nude mice. Ectopic expression of wild-type PTK6 in SW620 cells drives the reverse process (MET), demonstrating a rescue of the EMT phenotype. When a constitutively active PTK6 construct is expressed in SW620 cells, it promotes activation of cytoplasmic oncogenic targets and downstream effectors, STAT3, FAK, BCAR1 and ERK5. Analysis of patient tissues demonstrates a downregulation of mRNA and protein levels, as well as a change in protein localization in tumor versus normal tissues; while PTK6 is detectable in the nuclei of differentiating normal cells it is excluded from nuclei in colon tumors. Conclusions: Our studies indicate that PTK6 promotes the epithelial phenotype to antagonize the EMT in a kinase-independent manner and a kinase switch activates PTK6 to promote oncogenic signaling. PTK6 protein localization may function to regulate its specific role. Further examination of the complex role of this kinase could allow for a more nuanced understanding of colon cancer initiation and progression for the development of novel treatments. Citation Format: Priya S. Mathur, Jessica J. Gierut, Rosa M. Xicola, Xavier Llor, Angela L. Tyner. Opposing roles for protein tyrosine kinase 6 (PTK6) in colon cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-059. doi:10.1158/1538-7445.AM2015-LB-059

Acidosis Mediates the Switching of Gs-PKA and Gi-PKCε Dependence in Prolonged Hyperalgesia Induced by Inflammation.

Chronic inflammatory pain, when not effectively treated, is a costly health problem and has a harmful effect on all aspects of health-related quality of life. Previous studies suggested that in male Sprague Dawley rats, prostaglandin E2 (PGE2)-induced short-term hyperalgesia depends on protein kinase A (PKA) activity, whereas long-lasting hyperalgesia induced by PGE2 with carrageenan pre-injection, requires protein kinase Cε (PKCε). However, the mechanism underlying the kinase switch with short- to long-term hyperalgesia remains unclear. In this study, we used the inflammatory agents carrageenan or complete Freund’s adjuvant (CFA) to induce long-term hyperalgesia, and examined PKA and PKCε dependence and switching time. Hyperalgesia induced by both agents depended on PKA/PKCε and Gs/Gi-proteins, and the switching time from PKA to PKCε and from Gs to Gi was about 3 to 4 h after inflammation induction. Among the single inflammatory mediators tested, PGE2 and 5-HT induced transient hyperalgesia, which depended on PKA and PKCε, respectively. Only acidic solution-induced hyperalgesia required Gs-PKA and Gi-PKCε, and the switch time for kinase dependency matched inflammatory hyperalgesia, in approximately 2 to 4 h. Thus, acidosis in inflamed tissues may be a decisive factor to regulate switching of PKA and PKCε dependence via proton-sensing G-protein–coupled receptors.

Abstract 5322: Collections of simultaneously altered genes as highly predictive markers of cancer cell drug response

Abstract Introduction: Many genetic markers of drug response have been reported in cancer pharmacogenomics studies. However, most of these markers fail to achieve clinical utility because they capture response in only a small fraction of the patient population; this shortcoming might result from a reliance on single-gene markers in contemporary personalized medicine. While there is growing evidence that therapeutic response can be modulated by the concerted impact of multiple genetic alterations, the combinatorics associated with many-body interactions has mostly prohibited the discovery of multi-gene biomarkers, even using computational methods. We developed a computational approach, MOCA (Multivariate Organization of Combinatorial Alterations), to partially address these challenges. Extending our method that accounts for pairwise interactions, MOCA combines many genomic alterations into biomarkers of drug response, using Boolean set operations coupled with optimization; in this framework the union, intersection, and difference Boolean set operations are proxies of molecular redundancy, synergy, and interference. The algorithm is fast, broadly applicable to genomics data, of immediate utility for prioritizing cancer pharmacogenomics experiments, and recovers known clinical findings without bias. Furthermore, results from this work connect many important, previously isolated observations. Major Findings: When applied to 416 pharmacogenomically characterized cancer cell lines from the Cancer Cell Line Encyclopedia, MOCA identified many known and potential markers of drug response. For example, correlation of ERBB inhibitor response drastically increased when considering EGFR (ERBB1), ERBB2, ERBB3, ERBB4, and KRAS alterations in a single marker. Similarly, a marker combining IGF1, IGF1R, and RAD51 alterations drastically increased correlation with IGF1R inhibitor response, relative to any of these three genetic markers considered in isolation. This approach is also powerful for determining subsets of gene-specific mutations that increase correlation with drug response. For instance, MOCA accurately captures the differential EGFR inhibitor response conferred by known activating EGFR mutations. Similarly, we find specific HDAC1 mutations cooperate with HDAC5 overexpression to potentiate cells to the HDAC inhibitor panobinostat. Additionally, considering all pairwise gene-drug interactions, MOCA recovers known and compelling correlations, including: RTK inhibitor resistance via c-MET, EGFR, ERBB2, and PDGFRB kinase switching; mutual exclusivity of TP53 mutation and response to the MDM2 inhibitor nutlin-3; greater nutlin-3 potentiation via MDM4, rather than MDM2, overexpression; MEK and RAF inhibitor response in BRAF mutated cell lines; and MEK inhibitor potentiating NRAS mutations. Masica, David L., &amp; Rachel Karchin. Cancer Research 73 (2013): 1699-1708. Citation Format: David L. Masica, Rachel Karchin. Collections of simultaneously altered genes as highly predictive markers of cancer cell drug response. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5322. doi:10.1158/1538-7445.AM2014-5322