134 results on '"Rix, U"'
Search Results
2. Target interaction profiling of midostaurin and its metabolites in neoplastic mast cells predicts distinct effects on activation and growth
- Author
-
Peter, B, Winter, G E, Blatt, K, Bennett, K L, Stefanzl, G, Rix, U, Eisenwort, G, Hadzijusufovic, E, Gridling, M, Dutreix, C, Hoermann, G, Schwaab, J, Radia, D, Roesel, J, Manley, P W, Reiter, A, Superti-Furga, G, and Valent, P
- Published
- 2016
- Full Text
- View/download PDF
3. A chemical biology approach identifies AMPK as a modulator of melanoma oncogene MITF
- Author
-
Borgdorff, V, Rix, U, Winter, G E, Gridling, M, Müller, A C, Breitwieser, F P, Wagner, C, Colinge, J, Bennett, K L, Superti-Furga, G, and Wagner, S N
- Published
- 2014
- Full Text
- View/download PDF
4. A comprehensive target selectivity survey of the BCR-ABL kinase inhibitor INNO-406 by kinase profiling and chemical proteomics in chronic myeloid leukemia cells
- Author
-
Rix, U, Remsing Rix, L L, Terker, A S, Fernbach, N V, Hantschel, O, Planyavsky, M, Breitwieser, F P, Herrmann, H, Colinge, J, Bennett, K L, Augustin, M, Till, J H, Heinrich, M C, Valent, P, and Superti-Furga, G
- Published
- 2010
- Full Text
- View/download PDF
5. Global target profile of the kinase inhibitor bosutinib in primary chronic myeloid leukemia cells
- Author
-
Remsing Rix, L L, Rix, U, Colinge, J, Hantschel, O, Bennett, K L, Stranzl, T, Müller, A, Baumgartner, C, Valent, P, Augustin, M, Till, J H, and Superti-Furga, G
- Published
- 2009
- Full Text
- View/download PDF
6. Dissecting the landscape of CAF-mediated drug resistance mechanisms in ALK-rearranged NSCLC
- Author
-
Hu, Q., primary, Rix, L.L. Remsing, additional, Li, X., additional, Welsh, E.A., additional, Fang, B., additional, Yun, S., additional, Kroeger, J., additional, Lawrence, H.R., additional, Marusyk, A., additional, Koomen, J.M., additional, Haura, E.B., additional, and Rix, U., additional
- Published
- 2020
- Full Text
- View/download PDF
7. B40 IGF-Binding Protein-Mediated Sensitization of EGFR-Mutant NSCLC Cells to Osimertinib by Cancer-Associated Fibroblast
- Author
-
Remsing Rix, L.L., primary, Sumi, N.J., additional, Bryant, A.T., additional, Desai, B., additional, Li, X., additional, Welsh, E.A., additional, Fang, B., additional, Kuenzi, B.M., additional, Antonia, S.J., additional, Lovly, C.M., additional, Koomen, J.M., additional, Marusyk, A., additional, Haura, E.B., additional, and Rix, U., additional
- Published
- 2020
- Full Text
- View/download PDF
8. Immunosuppression and atypical infections in CML patients treated with dasatinib at 140 mg daily
- Author
-
Sillaber, C., Herrmann, H., Bennett, K., Rix, U., Baumgartner, C., Böhm, A., Herndlhofer, S., Tschachler, E., Superti-Furga, G., Jäger, U., and Valent, P.
- Published
- 2009
- Full Text
- View/download PDF
9. Molecular networks, molecular medicine and the mechanism of action of drugs: IL3D-3
- Author
-
Superti-Furga, G., Rix, U., Fernbach, N., Durnberger, G., Brehme, M., Remsing-Rix, L., Burkhard, T., Valent, P., Colinge, J., Bennett, K., and Hantschel, T. B. O.
- Published
- 2008
10. Function of glycosyltransferase genes involved in urdamycin A biosynthesis
- Author
-
Trefzer, A, Hoffmeister, D, Künzel, E, Stockert, S, Weitnauer, G, Westrich, L, Rix, U, Fuchser, J, Bindseil, KU, Rohr, J, and Bechthold, A
- Published
- 2000
- Full Text
- View/download PDF
11. Repurposing Ceritinib Using Systems Polypharmacology
- Author
-
Kuenzi, B., primary, Remsing Rix, L., additional, Stewart, P., additional, Fang, B., additional, Kinose, F., additional, Bryant, A., additional, Boyle, T., additional, Koomen, J., additional, Haura, E., additional, and Rix, U., additional
- Published
- 2017
- Full Text
- View/download PDF
12. Targeting a cell state common to triple‐negative breast cancers
- Author
-
Muellner, M. K., Mair, B., Ibrahim, Y., Kerzendorfer, C., Lechtermann, H., Trefzer, C., Klepsch, F., Muller, A. C., Leitner, E., Macho-Maschler, S., Superti-Furga, G., Bennett, K. L., Baselga, J., Rix, U., Kubicek, S., Colinge, J., Serra, V., Nijman, S. M., CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria, Vall d'Hebron Institute of Oncology [Barcelone] (VHIO), Vall d'Hebron University Hospital [Barcelona], Memorial Sloane Kettering Cancer Center [New York], H. Lee Moffitt Cancer Center and Research Institute, Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), and KARLI, Mélanie
- Subjects
Proteomics ,STAT3 Transcription Factor ,Cell Survival ,Antineoplastic Agents ,Apoptosis ,Triple Negative Breast Neoplasms ,[SDV.CAN]Life Sciences [q-bio]/Cancer ,Mice ,Drug Delivery Systems ,breast cancer ,[SDV.CAN] Life Sciences [q-bio]/Cancer ,small-molecule screen ,Transforming Growth Factor beta ,Cell Line, Tumor ,Animals ,Humans ,Syk Kinase ,Protein Interaction Domains and Motifs ,Molecular Targeted Therapy ,Cell Proliferation ,Sequence Analysis, RNA ,Gene Expression Profiling ,Intracellular Signaling Peptides and Proteins ,Cell Differentiation ,Articles ,Protein-Tyrosine Kinases ,Staurosporine ,Xenograft Model Antitumor Assays ,small‐molecule screen ,Molecular Docking Simulation ,Female ,cell state ,Signal Transduction - Abstract
International audience; Some mutations in cancer cells can be exploited for therapeutic intervention. However, for many cancer subtypes, including triple-negative breast cancer (TNBC), no frequently recurring aberrations could be identified to make such an approach clinically feasible. Characterized by a highly heterogeneous mutational landscape with few common features, many TNBCs cluster together based on their 'basal-like' transcriptional profiles. We therefore hypothesized that targeting TNBC cells on a systems level by exploiting the transcriptional cell state might be a viable strategy to find novel therapies for this highly aggressive disease. We performed a large-scale chemical genetic screen and identified a group of compounds related to the drug PKC412 (midostaurin). PKC412 induced apoptosis in a subset of TNBC cells enriched for the basal-like subtype and inhibited tumor growth in vivo. We employed a multi-omics approach and computational modeling to address the mechanism of action and identified spleen tyrosine kinase (SYK) as a novel and unexpected target in TNBC. Quantitative phosphoproteomics revealed that SYK inhibition abrogates signaling to STAT3, explaining the selectivity for basal-like breast cancer cells. This non-oncogene addiction suggests that chemical SYK inhibition may be beneficial for a specific subset of TNBC patients and demonstrates that targeting cell states could be a viable strategy to discover novel treatment strategies.
- Published
- 2015
- Full Text
- View/download PDF
13. Target interaction profiling of midostaurin and its metabolites in neoplastic mast cells predicts distinct effects on activation and growth
- Author
-
Peter, B, primary, Winter, G E, additional, Blatt, K, additional, Bennett, K L, additional, Stefanzl, G, additional, Rix, U, additional, Eisenwort, G, additional, Hadzijusufovic, E, additional, Gridling, M, additional, Dutreix, C, additional, Hoermann, G, additional, Schwaab, J, additional, Radia, D, additional, Roesel, J, additional, Manley, P W, additional, Reiter, A, additional, Superti-Furga, G, additional, and Valent, P, additional
- Published
- 2015
- Full Text
- View/download PDF
14. Deploying Ibrutinib to Lung Cancer: Another Step in the Quest Towards Drug Repurposing
- Author
-
Haura, E. B., primary and Rix, U., additional
- Published
- 2014
- Full Text
- View/download PDF
15. A chemical biology approach identifies AMPK as a modulator of melanoma oncogene MITF
- Author
-
Borgdorff, V, primary, Rix, U, additional, Winter, G E, additional, Gridling, M, additional, Müller, A C, additional, Breitwieser, F P, additional, Wagner, C, additional, Colinge, J, additional, Bennett, K L, additional, Superti-Furga, G, additional, and Wagner, S N, additional
- Published
- 2013
- Full Text
- View/download PDF
16. A comprehensive target selectivity survey of the BCR-ABL kinase inhibitor INNO-406 by kinase profiling and chemical proteomics in chronic myeloid leukemia cells
- Author
-
Rix, U, primary, Remsing Rix, L L, additional, Terker, A S, additional, Fernbach, N V, additional, Hantschel, O, additional, Planyavsky, M, additional, Breitwieser, F P, additional, Herrmann, H, additional, Colinge, J, additional, Bennett, K L, additional, Augustin, M, additional, Till, J H, additional, Heinrich, M C, additional, Valent, P, additional, and Superti-Furga, G, additional
- Published
- 2009
- Full Text
- View/download PDF
17. Global target profile of the kinase inhibitor bosutinib in primary chronic myeloid leukemia cells
- Author
-
Remsing Rix, L L, primary, Rix, U, additional, Colinge, J, additional, Hantschel, O, additional, Bennett, K L, additional, Stranzl, T, additional, Müller, A, additional, Baumgartner, C, additional, Valent, P, additional, Augustin, M, additional, Till, J H, additional, and Superti-Furga, G, additional
- Published
- 2008
- Full Text
- View/download PDF
18. Synthesis, Pharmacokinetics, Efficacy, and Rat Retinal Toxicity of a Novel Mitomycin C-Triamcinolone Acetonide Conjugate
- Author
-
Macky, T. A., Oelkers, C., Rix, U., Heredia, M. L., Kunzel, E., Wimberly, M., Rohrer, B., Crosson, C. E., and Rohr, J.
- Abstract
A novel conjugate of mitomycin C (MMC) and triamcinolone acetonide (TA) was synthesized using glutaric acid as a linker molecule. To determine the rate of hydrolysis, the conjugate was dissolved in aqueous solution and the rate of appearance of free MMC and TA was determined by high-performance liquid chromatography analysis. Antiproliferative activity of the MMC−TA conjugate and parent compounds was assessed using an NIH 3T3 fibroblast cell line. Cell growth was quantified using the MTT assay. Kinetic analysis of the hydrolysis rate demonstrated that the conjugate had a half-life of 23.6 h in aqueous solutions. The antiproliferative activities of the MMC−TA conjugate and MMC were both concentration dependent, with similar IC
50 values of 2.4 and 1.7 μM, respectively. However, individual responses at concentrations above 3 μM showed that the conjugate was less active than MMC alone. TA alone showed only limited inhibition of cell growth. Studies evaluating intravitreal injection of the conjugate demonstrate that this agent produced no measurable toxicity. Our data provide evidence that the MMC−TA conjugate could be used as a slow-release drug delivery system. This could in turn be used to modulate a posttreatment wound healing process or to treat various proliferative diseases.- Published
- 2002
- Full Text
- View/download PDF
19. PRO-ATHEROGENIC AND ANTI-ANGIOGENIC EFFECTS OF NILOTINIB ON ENDOTHELIAL CELLS: A POTENTIAL MECHANISM TO EXPLAIN VASCULOPATHIES IN CML PATIENTS TREATED WITH NILOTINIB
- Author
-
Hadzijusufovic, E., Albrecht-Schgoer, K., Huber, K., Grebien, F., Eisenwort, G., Schgoer, W., Ghanim, V., Kaun, C., Herndlhofer, S., Theurl, M., Cerny-Reiterer, S., Sadovnik, I., Hoermann, G., Jilma, B., Sperr, W. R., Rix, U., Johann Wojta, Wolf, D., Superti-Furga, G., Kirchmair, R., and Valent, P.
20. Nilotinib exerts proatherogenic and growth-inhibitory effects on endothelial cells: a potential mechanism underlying drug-related vasculopathy in Ph plus CML
- Author
-
Hadzijusufovic, E., Albrecht-Schgoer, K., Huber, K., Grebien, F., Eisenwort, G., Schgoer, W., Ghanim, V., Sadovnik, I., Christoph Kaun, Herndlhofer, S., Theurl, M., Cerny-Reiterer, S., Hoermann, G., Jilma, B., Sperr, W. R., Rix, U., Wojta, J., Wolf, D., Superti-Furga, G., Kirchmair, R., and Valent, P.
21. 174 Poster - Dissecting the landscape of CAF-mediated drug resistance mechanisms in ALK-rearranged NSCLC.
- Author
-
Hu, Q., Rix, L.L. Remsing, Li, X., Welsh, E.A., Fang, B., Yun, S., Kroeger, J., Lawrence, H.R., Marusyk, A., Koomen, J.M., Haura, E.B., and Rix, U.
- Subjects
- *
THERAPEUTIC use of antineoplastic agents , *CANCER , *CELL lines , *CELLULAR signal transduction , *CONFERENCES & conventions , *DRUG resistance in cancer cells , *FIBROBLASTS , *LUNG cancer , *NERVE tissue proteins , *ANAPLASTIC lymphoma kinase - Published
- 2020
- Full Text
- View/download PDF
22. SART1 modulates poly-(ADP-ribose) chain accumulation and PARP1 chromatin localization.
- Author
-
Lodovichi S, Nepomuceno TC, Woods NT, Rix U, Koomen JM, Pellicioli A, Galli A, and Monteiro ANA
- Abstract
PARP1 inhibitors (PARPis) are used for treatment of cancers with mutations in BRCA1 or BRCA2 that are deficient in homologous recombination. The identification of modulators of PARP1 activity is critical to understand and overcome resistance to PARPis. We integrated data from three omics-scale screens to discover new regulators of PARP1 activity. We identified SART1 and show that its silencing leads to an increase in poly-ADP ribosylation and chromatin-bound PARP1. SART1 is recruited to chromatin following DNA damage and limits PARP1 chromatin retention and activity. The SART1 N-terminus is sufficient to regulate the accumulation of PAR chains and PARP1 on chromatin, an activity dependent on the RGG/RG box. Silencing of SART1 leads to an increased sensitivity of cells to DNA damage induced by IR, irrespective of BRCA1 status and to PARPis only in absence of BRCA1 . These results suggest that SART1 could be clinically utilized to improve PARPi efficacy., Competing Interests: The authors state that they have no conflict of interest to disclose., (© 2024 The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
23. Cancer-associated fibroblasts confer ALK inhibitor resistance in EML4-ALK -driven lung cancer via concurrent integrin and MET signaling.
- Author
-
Hu Q, Remsing Rix LL, Desai B, Miroshnychenko D, Li X, Welsh EA, Fang B, Wright GM, Chaudhary N, Kroeger JL, Doebele RC, Koomen JM, Haura EB, Marusyk A, and Rix U
- Abstract
Cancer-associated fibroblasts (CAFs) are associated with tumor progression and modulate drug sensitivity of cancer cells. However, the underlying mechanisms are often incompletely understood and crosstalk between tumor cells and CAFs involves soluble secreted as well as adhesion proteins. Interrogating a panel of non-small cell lung cancer (NSCLC) cell lines driven by EML4-ALK fusions, we observed substantial CAF-mediated drug resistance to clinical ALK tyrosine kinase inhibitors (TKIs). Array-based cytokine profiling of fibroblast-derived conditioned- media identified HGF-MET signaling as a major contributor to CAF-mediated paracrine resistance that can be overcome by MET TKIs. However, 'Cell Type specific labeling using Amino acid Precursors' (CTAP)-based expression and phosphoproteomics in direct coculture also highlighted a critical role for the fibronectin-integrin pathway. Flow cytometry analysis confirmed activation of integrin β1 (ITGB1) in lung cancer cells by CAF coculture. Treatment with pharmacological inhibitors, cancer cell-specific silencing or CRISPR-Cas9-mediated knockout of ITGB1 overcame adhesion protein-mediated resistance. Concurrent targeting of MET and integrin signaling effectively abrogated CAF-mediated resistance of EML4-ALK -driven NSCLC cells to ALK TKIs in vitro . Consistently, combination of the ALK TKI alectinib with the MET TKI capmatinib and/or the integrin inhibitor cilengitide was significantly more efficacious than single agent treatment in suppressing tumor growth using an in vivo EML4-ALK -dependent allograft mouse model of NSCLC. In summary, these findings emphasize the complexity of resistance-associated crosstalk between CAFs and cancer cells, which can involve multiple concurrent signaling pathways, and illustrate how comprehensive elucidation of paracrine and juxtacrine resistance mechanisms can inform on more effective therapeutic approaches.
- Published
- 2024
- Full Text
- View/download PDF
24. Differential network analysis of ROS1 inhibitors reveals lorlatinib polypharmacology through co-targeting PYK2.
- Author
-
Liao Y, Remsing Rix LL, Li X, Fang B, Izumi V, Welsh EA, Monastyrskyi A, Haura EB, Koomen JM, Doebele RC, and Rix U
- Subjects
- Humans, Aminopyridines pharmacology, Anaplastic Lymphoma Kinase genetics, Focal Adhesion Kinase 2 antagonists & inhibitors, Lactams, Macrocyclic, Polypharmacology, Protein Kinase Inhibitors pharmacology, Proto-Oncogene Proteins, Carcinoma, Non-Small-Cell Lung drug therapy, Lactams, Lung Neoplasms drug therapy, Protein-Tyrosine Kinases antagonists & inhibitors, Pyrazoles
- Abstract
Multiple tyrosine kinase inhibitors (TKIs) are often developed for the same indication. However, their relative overall efficacy is frequently incompletely understood and they may harbor unrecognized targets that cooperate with the intended target. We compared several ROS1 TKIs for inhibition of ROS1-fusion-positive lung cancer cell viability, ROS1 autophosphorylation and kinase activity, which indicated disproportionately higher cellular potency of one TKI, lorlatinib. Quantitative chemical and phosphoproteomics across four ROS1 TKIs and differential network analysis revealed that lorlatinib uniquely impacted focal adhesion signaling. Functional validation using pharmacological probes, RNA interference, and CRISPR-Cas9 knockout uncovered a polypharmacology mechanism of lorlatinib by dual targeting ROS1 and PYK2, which form a multiprotein complex with SRC. Rational multi-targeting of this complex by combining lorlatinib with SRC inhibitors exhibited pronounced synergy. Taken together, we show that systems pharmacology-based differential network analysis can dissect mixed canonical/non-canonical polypharmacology mechanisms across multiple TKIs enabling the design of rational drug combinations., Competing Interests: Declaration of interests R.C.D. is an employee and shareholder of Rain Oncology and reports licensing fees from Voronoi, Takeda, Loxo@Lilly, Foundation Medicine, Histocyte, Black Diamond, and ThermoFisher. JMK reports support from Bristol-Myers Squibb on an unrelated project. E.B.H. serves in a consulting or advisory role to Amgen, Ellipses Pharma, Janssen Oncology, Janssen Research & Development and Revolution Medicines; reports research funding (paid to his institution) from AstraZeneca, Genentech, Incyte, Janssen, Novartis, Revolution Medicines and Spectrum Pharmaceuticals; and reports patents, royalties or other intellectual property from ProteinProtein Interactions as Biomarkers Patent., (Copyright © 2023 Elsevier Ltd. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
25. PTEN Lipid Phosphatase Activity Suppresses Melanoma Formation by Opposing an AKT/mTOR/FRA1 Signaling Axis.
- Author
-
Xu X, Bok I, Jasani N, Wang K, Chadourne M, Mecozzi N, Deng O, Welsh EA, Kinose F, Rix U, and Karreth FA
- Subjects
- Animals, Mice, Signal Transduction genetics, PTEN Phosphohydrolase genetics, PTEN Phosphohydrolase metabolism, TOR Serine-Threonine Kinases metabolism, Cell Proliferation, Lipids, Proto-Oncogene Proteins c-akt metabolism, Melanoma genetics, Melanoma metabolism
- Abstract
Inactivating mutations in PTEN are prevalent in melanoma and are thought to support tumor development by hyperactivating the AKT/mTOR pathway. Conversely, activating mutations in AKT are relatively rare in melanoma, and therapies targeting AKT or mTOR have shown disappointing outcomes in preclinical models and clinical trials of melanoma. This has led to the speculation that PTEN suppresses melanoma by opposing AKT-independent pathways, potentially through noncanonical functions beyond its lipid phosphatase activity. In this study, we examined the mechanisms of PTEN-mediated suppression of melanoma formation through the restoration of various PTEN functions in PTEN-deficient cells or mouse models. PTEN lipid phosphatase activity predominantly inhibited melanoma cell proliferation, invasion, and tumor growth, with minimal contribution from its protein phosphatase and scaffold functions. A drug screen underscored the exquisite dependence of PTEN-deficient melanoma cells on the AKT/mTOR pathway. Furthermore, activation of AKT alone was sufficient to counteract several aspects of PTEN-mediated melanoma suppression, particularly invasion and the growth of allograft tumors. Phosphoproteomics analysis of the lipid phosphatase activity of PTEN validated its potent inhibition of AKT and many of its known targets, while also identifying the AP-1 transcription factor FRA1 as a downstream effector. The restoration of PTEN dampened FRA1 translation by inhibiting AKT/mTOR signaling, and FRA1 overexpression negated aspects of PTEN-mediated melanoma suppression akin to AKT. This study supports AKT as the key mediator of PTEN inactivation in melanoma and identifies an AKT/mTOR/FRA1 axis as a driver of melanomagenesis., Significance: PTEN suppresses melanoma predominantly through its lipid phosphatase function, which when lost, elevates FRA1 levels through AKT/mTOR signaling to promote several aspects of melanomagenesis., (©2024 American Association for Cancer Research.)
- Published
- 2024
- Full Text
- View/download PDF
26. Targeting BET Proteins Downregulates miR-33a To Promote Synergy with PIM Inhibitors in CMML.
- Author
-
Letson CT, Balasis ME, Newman H, Binder M, Vedder A, Kinose F, Ball M, Kruer T, Quintana A, Lasho TL, Finke CM, Almada LL, Grants JM, Zhang G, Fernandez-Zapico ME, Gaspar-Maia A, Lancet J, Komrokji R, Haura E, Sallman DA, Reuther GW, Karsan A, Rix U, Patnaik MM, and Padron E
- Subjects
- Humans, Cell Line, Tumor, Proteins, Leukemia, Myelomonocytic, Chronic, MicroRNAs genetics, MicroRNAs metabolism
- Abstract
Purpose: Preclinical studies in myeloid neoplasms have demonstrated efficacy of bromodomain and extra-terminal protein inhibitors (BETi). However, BETi demonstrates poor single-agent activity in clinical trials. Several studies suggest that combination with other anticancer inhibitors may enhance the efficacy of BETi., Experimental Design: To nominate BETi combination therapies for myeloid neoplasms, we used a chemical screen with therapies currently in clinical cancer development and validated this screen using a panel of myeloid cell line, heterotopic cell line models, and patient-derived xenograft models of disease. We used standard protein and RNA assays to determine the mechanism responsible for synergy in our disease models., Results: We identified PIM inhibitors (PIMi) as therapeutically synergistic with BETi in myeloid leukemia models. Mechanistically, we show that PIM kinase is increased after BETi treatment, and that PIM kinase upregulation is sufficient to induce persistence to BETi and sensitize cells to PIMi. Furthermore, we demonstrate that miR-33a downregulation is the underlying mechanism driving PIM1 upregulation. We also show that GM-CSF hypersensitivity, a hallmark of chronic myelomonocytic leukemia (CMML), represents a molecular signature for sensitivity to combination therapy., Conclusions: Inhibition of PIM kinases is a potential novel strategy for overcoming BETi persistence in myeloid neoplasms. Our data support further clinical investigation of this combination., (©2023 American Association for Cancer Research.)
- Published
- 2023
- Full Text
- View/download PDF
27. Differential Chemoproteomics Reveals MARK2/3 as Cell Migration-Relevant Targets of the ALK Inhibitor Brigatinib.
- Author
-
Hu Q, Liao Y, Cao J, Fang B, Yun SY, Kinose F, Haura EB, Lawrence HR, Doebele RC, Koomen JM, and Rix U
- Subjects
- Humans, Anaplastic Lymphoma Kinase therapeutic use, Organophosphorus Compounds pharmacology, Protein Kinase Inhibitors pharmacology, Cell Movement, Protein Serine-Threonine Kinases, Carcinoma, Non-Small-Cell Lung drug therapy, Carcinoma, Non-Small-Cell Lung genetics, Carcinoma, Non-Small-Cell Lung pathology, Lung Neoplasms drug therapy, Lung Neoplasms pathology
- Abstract
Metastasis poses a major challenge in cancer management, including EML4-ALK-rearranged non-small cell lung cancer (NSCLC). As cell migration is a critical step during metastasis, we assessed the anti-migratory activities of several clinical ALK inhibitors in NSCLC cells and observed differential anti-migratory capabilities despite similar ALK inhibition, with brigatinib displaying superior anti-migratory effects over other ALK inhibitors. Applying an unbiased in situ mass spectrometry-based chemoproteomics approach, we determined the proteome-wide target profile of brigatinib in EML4-ALK+ NSCLC cells. Dose-dependent and cross-competitive chemoproteomics suggested MARK2 and MARK3 as relevant brigatinib kinase targets. Functional validation showed that combined pharmacological inhibition or genetic modulation of MARK2/3 inhibited cell migration. Consistently, brigatinib treatment induced inhibitory YAP1 phosphorylation downstream of MARK2/3. Collectively, our data suggest that brigatinib exhibits unusual cross-phenotype polypharmacology as, despite similar efficacy for inhibiting EML4-ALK-dependent cell proliferation as other ALK inhibitors, it more effectively prevented migration of NSCLC cells due to co-targeting of MARK2/3., (© 2023 Wiley-VCH GmbH.)
- Published
- 2023
- Full Text
- View/download PDF
28. Chemical Proteomics with Novel Fully Functionalized Fragments and Stringent Target Prioritization Identifies the Glutathione-Dependent Isomerase GSTZ1 as a Lung Cancer Target.
- Author
-
Liao Y, Chin Chan S, Welsh EA, Fang B, Sun L, Schönbrunn E, Koomen JM, Duckett DR, Haura EB, Monastyrskyi A, and Rix U
- Subjects
- Humans, Proteomics, Proteins, Glutathione, Glutathione Transferase metabolism, Carcinoma, Non-Small-Cell Lung, Lung Neoplasms drug therapy
- Abstract
Photoreactive fragment-like probes have been applied to discover target proteins that constitute novel cellular vulnerabilities and to identify viable chemical hits for drug discovery. Through forming covalent bonds, functionalized probes can achieve stronger target engagement and require less effort for on-target mechanism validation. However, the design of probe libraries, which directly affects the biological target space that is interrogated, and effective target prioritization remain critical challenges of such a chemical proteomic platform. In this study, we designed and synthesized a diverse panel of 20 fragment-based probes containing natural product-based privileged structural motifs for small-molecule lead discovery. These probes were fully functionalized with orthogonal diazirine and alkyne moieties and used for protein crosslinking in live lung cancer cells, target enrichment via "click chemistry," and subsequent target identification through label-free quantitative liquid chromatography-tandem mass spectrometry analysis. Pair-wise comparison with a blunted negative control probe and stringent prioritization via individual cross-comparisons against the entire panel identified glutathione S -transferase zeta 1 (GSTZ1) as a specific and unique target candidate. DepMap database query, RNA interference-based gene silencing, and proteome-wide tyrosine reactivity profiling suggested that GSTZ1 cooperated with different oncogenic alterations by supporting survival signaling in refractory non-small cell lung cancer cells. This finding may form the basis for developing novel GSTZ1 inhibitors to improve the therapeutic efficacy of oncogene-directed targeted drugs. In summary, we designed a novel fragment-based probe panel and developed a target prioritization scheme with improved stringency, which allows for the identification of unique target candidates, such as GSTZ1 in refractory lung cancer.
- Published
- 2023
- Full Text
- View/download PDF
29. Integrated proteomics identifies PARP inhibitor-induced prosurvival signaling changes as potential vulnerabilities in ovarian cancer.
- Author
-
Deng O, Dash S, Nepomuceno TC, Fang B, Yun SY, Welsh EA, Lawrence HR, Marchion D, Koomen JM, Monteiro AN, and Rix U
- Subjects
- Humans, Female, Proteomics, Proto-Oncogene Proteins c-akt, Drug Resistance, Neoplasm, Cell Line, Tumor, BRCA1 Protein genetics, BRCA1 Protein metabolism, Poly(ADP-ribose) Polymerase Inhibitors pharmacology, Ovarian Neoplasms drug therapy, Ovarian Neoplasms genetics, Ovarian Neoplasms pathology
- Abstract
BRCA1/2-deficient ovarian carcinoma (OC) has been shown to be particularly sensitive to poly (ADP-ribose) polymerase inhibitors (PARPis). Furthermore, BRCA1/2 mutation status is currently used as a predictive biomarker for PARPi therapy. Despite providing a major clinical benefit to the majority of patients, a significant proportion of BRCA1/2-deficient OC tumors do not respond to PARPis for reasons that are incompletely understood. Using an integrated chemical, phospho- and ADP-ribosylation proteomics approach, we sought here to develop additional mechanism-based biomarker candidates for PARPi therapy in OC and identify new targets for combination therapy to overcome primary resistance. Using chemical proteomics with PARPi baits in a BRCA1-isogenic OC cell line pair, as well as patient-derived BRCA1-proficient and BRCA1-deficient tumor samples, and subsequent validation by coimmunoprecipitation, we showed differential PARP1 and PARP2 protein complex composition in PARPi-sensitive, BRCA1-deficient UWB1.289 (UWB) cells compared to PARPi-insensitive, BRCA1-reconstituted UWB1.289+BRCA1 (UWB+B) cells. In addition, global phosphoproteomics and ADP-ribosylation proteomics furthermore revealed that the PARPi rucaparib induced the cell cycle pathway and nonhomologous end joining (NHEJ) pathway in UWB cells but downregulated ErbB signaling in UWB+B cells. In addition, we observed AKT PARylation and prosurvival AKT-mTOR signaling in UWB+B cells after PARPi treatment. Consistently, we found the synergy of PARPis with DNAPK or AKT inhibitors was more pronounced in UWB+B cells, highlighting these pathways as actionable vulnerabilities. In conclusion, we demonstrate the combination of chemical proteomics, phosphoproteomics, and ADP-ribosylation proteomics can identify differential PARP1/2 complexes and diverse, but actionable, drug compensatory signaling in OC., Competing Interests: Conflict of interest J. M. K. reports support from Bristol-Myers Squibb on an unrelated project. All other authors declare that they have no conflict of interest with the contents of this article., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
30. IGF-binding proteins secreted by cancer-associated fibroblasts induce context-dependent drug sensitization of lung cancer cells.
- Author
-
Remsing Rix LL, Sumi NJ, Hu Q, Desai B, Bryant AT, Li X, Welsh EA, Fang B, Kinose F, Kuenzi BM, Chen YA, Antonia SJ, Lovly CM, Koomen JM, Haura EB, Marusyk A, and Rix U
- Subjects
- Animals, Cell Line, Tumor, Culture Media, Conditioned pharmacology, ErbB Receptors metabolism, Fibroblasts metabolism, Insulin-Like Growth Factor Binding Proteins metabolism, Insulin-Like Growth Factor Binding Proteins pharmacology, Insulin-Like Growth Factor Binding Proteins therapeutic use, Lung metabolism, Mice, Tumor Microenvironment, Cancer-Associated Fibroblasts metabolism, Lung Neoplasms drug therapy, Lung Neoplasms genetics, Lung Neoplasms pathology
- Abstract
Cancer-associated fibroblasts (CAFs) in the tumor microenvironment are often linked to drug resistance. Here, we found that coculture with CAFs or culture in CAF-conditioned medium unexpectedly induced drug sensitivity in certain lung cancer cell lines. Gene expression and secretome analyses of CAFs and normal lung-associated fibroblasts (NAFs) revealed differential abundance of insulin-like growth factors (IGFs) and IGF-binding proteins (IGFBPs), which promoted or inhibited, respectively, signaling by the receptor IGF1R and the kinase FAK. Similar drug sensitization was seen in gefitinib-resistant, EGFR -mutant PC9GR lung cancer cells treated with recombinant IGFBPs. Conversely, drug sensitivity was decreased by recombinant IGFs or conditioned medium from CAFs in which IGFBP5 or IGFBP6 was silenced. Phosphoproteomics and receptor tyrosine kinase (RTK) array analyses indicated that exposure of PC9GR cells to CAF-conditioned medium also inhibited compensatory IGF1R and FAK signaling induced by the EGFR inhibitor osimertinib. Combined small-molecule inhibition of IGF1R and FAK phenocopied the CAF-mediated effects in culture and increased the antitumor effect of osimertinib in mice. Cells that were osimertinib resistant and had MET amplification or showed epithelial-to-mesenchymal transition also displayed residual sensitivity to IGFBPs. Thus, CAFs promote or reduce drug resistance in a context-dependent manner, and deciphering the relationship between the differential content of CAF secretomes and the signaling dependencies of the tumor may reveal effective combination treatment strategies.
- Published
- 2022
- Full Text
- View/download PDF
31. The non-canonical target PARP16 contributes to polypharmacology of the PARP inhibitor talazoparib and its synergy with WEE1 inhibitors.
- Author
-
Palve V, Knezevic CE, Bejan DS, Luo Y, Li X, Novakova S, Welsh EA, Fang B, Kinose F, Haura EB, Monteiro AN, Koomen JM, Cohen MS, Lawrence HR, and Rix U
- Subjects
- Aged, Antineoplastic Agents chemistry, Cell Cycle drug effects, Cell Cycle Proteins metabolism, Cell Proliferation drug effects, Cell Survival drug effects, DNA Damage, Drug Screening Assays, Antitumor, Female, Humans, Male, Phthalazines chemistry, Poly(ADP-ribose) Polymerase Inhibitors chemistry, Protein-Tyrosine Kinases metabolism, Tumor Cells, Cultured, Antineoplastic Agents pharmacology, Cell Cycle Proteins antagonists & inhibitors, Phthalazines pharmacology, Poly(ADP-ribose) Polymerase Inhibitors pharmacology, Poly(ADP-ribose) Polymerases metabolism, Protein-Tyrosine Kinases antagonists & inhibitors
- Abstract
PARP inhibitors (PARPis) display single-agent anticancer activity in small cell lung cancer (SCLC) and other neuroendocrine tumors independent of BRCA1/2 mutations. Here, we determine the differential efficacy of multiple clinical PARPis in SCLC cells. Compared with the other PARPis rucaparib, olaparib, and niraparib, talazoparib displays the highest potency across SCLC, including SLFN11-negative cells. Chemical proteomics identifies PARP16 as a unique talazoparib target in addition to PARP1. Silencing PARP16 significantly reduces cell survival, particularly in combination with PARP1 inhibition. Drug combination screening reveals talazoparib synergy with the WEE1/PLK1 inhibitor adavosertib. Global phosphoproteomics identifies disparate effects on cell-cycle and DNA damage signaling thereby illustrating underlying mechanisms of synergy, which is more pronounced for talazoparib than olaparib. Notably, silencing PARP16 further reduces cell survival in combination with olaparib and adavosertib. Together, these data suggest that PARP16 contributes to talazoparib's overall mechanism of action and constitutes an actionable target in SCLC., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 Elsevier Ltd. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
32. CDK4/6 inhibition synergizes with inhibition of P21-Activated Kinases (PAKs) in lung cancer cell lines.
- Author
-
Wright GM, Gimbrone NT, Sarcar B, Percy TR, Gordián ER, Kinose F, Sumi NJ, Rix U, and Cress WD
- Subjects
- Aminopyridines pharmacology, Benzimidazoles pharmacology, Cell Line, Tumor, Cell Proliferation drug effects, Cell Survival drug effects, Cyclin-Dependent Kinase 4 metabolism, Cyclin-Dependent Kinase 6 metabolism, Drug Screening Assays, Antitumor, Drug Synergism, Gene Expression Regulation, Neoplastic drug effects, Humans, Lung Neoplasms drug therapy, Piperazines pharmacology, Pyridines pharmacology, Antineoplastic Agents pharmacology, Cyclin-Dependent Kinases antagonists & inhibitors, Lung Neoplasms metabolism, Protein Kinase Inhibitors pharmacology, p21-Activated Kinases antagonists & inhibitors
- Abstract
Theoretically, small molecule CDK4/6 inhibitors (CDK4/6is) represent a logical therapeutic option in non-small cell lung cancers since most of these malignancies have wildtype RB, the key target of CDKs and master regulator of the cell cycle. Unfortunately, CDK4/6is are found to have limited clinical activity as single agents in non-small cell lung cancer. To address this problem and to identify effective CDK4/6i combinations, we screened a library of targeted agents for efficacy in four non-small cell lung cancer lines treated with CDK4/6 inhibitors Palbociclib or Abemaciclib. The pan-PAK (p21-activated kinase) inhibitor PF03758309 emerged as a promising candidate with viability ratios indicating synergy in all 4 cell lines and for both CDK4/6is. It is noteworthy that the PAKs are downstream effectors of small GTPases Rac1 and Cdc42 and are overexpressed in a wide variety of cancers. Individually the compounds primarily induced cell cycle arrest; however, the synergistic combination induced apoptosis, accounting for the synergy. Surprisingly, while the pan-PAK inhibitor PF03758309 synergizes with CDK4/6is, no synergy occurs with group I PAK inhibitors FRAX486 or FRAX597. Cell lines treated only with Ribociclib, FRAX486 or FRAX597 underwent G1/G0 arrest, whereas combination treatment with these compounds predominantly resulted in autophagy. Combining high concentrations of FRAX486, which weakly inhibits PAK4, and Ribociclib, mimics the autophagy and apoptotic effect of PF03758309 combined with Ribociclib. FRAX597, a PAKi that does not inhibit PAK4 did not reduce autophagy in combination with Ribociclib. Our results suggest that a unique combination of PAKs plays a crucial role in the synergy of PAK inhibitors with CDK4/6i. Targeting this unique PAK combination, could greatly improve the efficacy of CDK4/6i and broaden the spectrum of cancer treatment., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2021
- Full Text
- View/download PDF
33. Novel Human-Derived RET Fusion NSCLC Cell Lines Have Heterogeneous Responses to RET Inhibitors and Differential Regulation of Downstream Signaling.
- Author
-
Schubert L, Le AT, Estrada-Bernal A, Doak AE, Yoo M, Ferrara SE, Goodspeed A, Kinose F, Rix U, Tan AC, and Doebele RC
- Subjects
- Animals, Carcinoma, Non-Small-Cell Lung metabolism, Carcinoma, Non-Small-Cell Lung pathology, Cell Cycle drug effects, Cell Line, Tumor, Female, Humans, Lung Neoplasms metabolism, Lung Neoplasms pathology, Mice, Mice, Nude, Proto-Oncogene Proteins c-ret genetics, Recombinant Fusion Proteins drug effects, Recombinant Fusion Proteins genetics, Recombinant Fusion Proteins metabolism, Xenograft Model Antitumor Assays, Antineoplastic Agents pharmacology, Carcinoma, Non-Small-Cell Lung genetics, Lung Neoplasms genetics, Protein Kinase Inhibitors pharmacology, Proto-Oncogene Proteins c-ret antagonists & inhibitors, Signal Transduction
- Abstract
Rearranged during transfection ( RET ) rearrangements occur in 1% to 2% of lung adenocarcinomas as well as other malignancies and are now established targets for tyrosine kinase inhibitors. We developed three novel RET fusion-positive ( RET +) patient-derived cancer cell lines, CUTO22 [kinesin 5B ( KIF5B )- RET fusion], CUTO32 ( KIF5B - RET fusion), and CUTO42 (echinoderm microtubule-associated protein-like 4- RET fusion), to study RET signaling and response to therapy. We confirmed each of our cell lines expresses the RET fusion protein and assessed their sensitivity to RET inhibitors. We found that the CUTO22 and CUTO42 cell lines were sensitive to multiple RET inhibitors, whereas the CUTO32 cell line was >10-fold more resistant to three RET inhibitors. We discovered that our RET + cell lines had differential regulation of the mitogen-activated protein kinase and phosphoinositide 3-kinase/protein kinase B (AKT) pathways. After inhibition of RET, the CUTO42 cells had robust inhibition of phosphorylated AKT (pAKT), whereas CUTO22 and CUTO32 cells had sustained AKT activation. Next, we performed a drug screen, which revealed that the CUTO32 cells were sensitive (<1 nM IC
50 ) to inhibition of two cell cycle-regulating proteins, polo-like kinase 1 and Aurora kinase A. Finally, we show that two of these cell lines, CUTO32 and CUTO42, successfully establish xenografted tumors in nude mice. We demonstrated that the RET inhibitor BLU-667 was effective at inhibiting tumor growth in CUTO42 tumors but had a much less profound effect in CUTO32 tumors, consistent with our in vitro experiments. These data highlight the utility of new RET+ models to elucidate differences in response to tyrosine kinase inhibitors and downstream signaling regulation. Our RET+ cell lines effectively recapitulate the interpatient heterogeneity observed in response to RET inhibitors and reveal opportunities for alternative or combination therapies. SIGNIFICANCE STATEMENT: We have derived and characterized three novel rearranged during transfection (RET) fusion non-small cell lung cancer cell lines and demonstrated that they have differential responses to RET inhibition as well as regulation of downstream signaling, an area that has previously been limited by a lack of diverse cell line modes with endogenous RET fusions. These data offer important insight into regulation of response to RET tyrosine kinase inhibitors and other potential therapeutic targets., (Copyright © 2021 by The American Society for Pharmacology and Experimental Therapeutics.)- Published
- 2021
- Full Text
- View/download PDF
34. Targeted Therapy Given after Anti-PD-1 Leads to Prolonged Responses in Mouse Melanoma Models through Sustained Antitumor Immunity.
- Author
-
Phadke MS, Chen Z, Li J, Mohamed E, Davies MA, Smalley I, Duckett DR, Palve V, Czerniecki BJ, Forsyth PA, Noyes D, Adeegbe DO, Eroglu Z, Nguyen KT, Tsai KY, Rix U, Burd CE, Chen YA, Rodriguez PC, and Smalley KSM
- Subjects
- Animals, Antineoplastic Agents chemistry, CD8-Positive T-Lymphocytes immunology, Cell Line, Tumor, Disease Models, Animal, Female, Imidazoles chemistry, Immunotherapy, Melanoma genetics, Melanoma immunology, Mice, Mice, Inbred C3H, Mice, Inbred C57BL, Molecular Targeted Therapy, Monomeric GTP-Binding Proteins genetics, Mutation, Oximes chemistry, Programmed Cell Death 1 Receptor antagonists & inhibitors, Proto-Oncogene Proteins B-raf genetics, Pyridones chemistry, Pyrimidines chemistry, Pyrimidinones chemistry, Skin Neoplasms genetics, Skin Neoplasms immunology, Sulfones chemistry, T-Lymphocytes, Regulatory immunology, Antineoplastic Agents therapeutic use, Melanoma drug therapy, Monomeric GTP-Binding Proteins antagonists & inhibitors, Proto-Oncogene Proteins B-raf antagonists & inhibitors, Skin Neoplasms drug therapy
- Abstract
Immunotherapy (IT) and targeted therapy (TT) are both effective against melanoma, but their combination is frequently toxic. Here, we investigated whether the sequence of IT (anti-PD-1)→ TT (ceritinib-trametinib or dabrafenib-trametinib) was associated with improved antitumor responses in mouse models of BRAF- and NRAS -mutant melanoma. Mice with NRAS- mutant (SW1) or BRAF -mutant (SM1) mouse melanomas were treated with either IT, TT, or the sequence of IT→TT. Tumor volumes were measured, and samples from the NRAS -mutant melanomas were collected for immune-cell analysis, single-cell RNA sequencing (scRNA-seq), and reverse phase protein analysis (RPPA). scRNA-seq demonstrated that the IT→TT sequence modulated the immune environment, leading to increased infiltration of T cells, monocytes, dendritic cells and natural killer cells, and decreased numbers of tumor-associated macrophages, myeloid-derived suppressor cells, and regulatory T cells. Durable responses to the IT→TT sequence were dependent on T-cell activity, with depletion of CD8
+ , but not CD4+ , T cells abrogating the therapeutic response. An analysis of transcriptional heterogeneity in the melanoma compartment showed the sequence of IT→TT enriched for a population of melanoma cells with increased expression of MHC class I and melanoma antigens. RPPA analysis demonstrated that the sustained immune response induced by IT→TT suppressed tumor-intrinsic signaling pathways required for therapeutic escape. These studies establish that upfront IT improves the responses to TT in BRAF- and NRAS -mutant melanoma models., (©2021 American Association for Cancer Research.)- Published
- 2021
- Full Text
- View/download PDF
35. Cell Type-specific Adaptive Signaling Responses to KRAS G12C Inhibition.
- Author
-
Solanki HS, Welsh EA, Fang B, Izumi V, Darville L, Stone B, Franzese R, Chavan S, Kinose F, Imbody D, Koomen JM, Rix U, and Haura EB
- Subjects
- Biomarkers, Tumor metabolism, Cell Line, Tumor, Chromatography, Liquid, Computational Biology methods, Epithelial-Mesenchymal Transition genetics, Humans, Phosphoproteins metabolism, Protein Interaction Mapping methods, Protein Interaction Maps, Proteomics methods, Proto-Oncogene Proteins p21(ras) antagonists & inhibitors, Receptor, ErbB-2 metabolism, Receptor, ErbB-3 metabolism, Receptor, Fibroblast Growth Factor, Type 1 metabolism, Tandem Mass Spectrometry, Alleles, Amino Acid Substitution, Mutation, Piperazines pharmacology, Proto-Oncogene Proteins p21(ras) genetics, Proto-Oncogene Proteins p21(ras) metabolism, Quinazolines pharmacology, Signal Transduction drug effects
- Abstract
Purpose: Covalent inhibitors of KRAS
G12C specifically target tumors driven by this form of mutant KRAS, yet early studies show that bypass signaling drives adaptive resistance. Although several combination strategies have been shown to improve efficacy of KRASG12C inhibitors (KRASi), underlying mechanisms and predictive strategies for patient enrichment are less clear., Experimental Design: We performed mass spectrometry-based phosphoproteomics analysis in KRASG12C cell lines after short-term treatment with ARS-1620. To understand signaling diversity and cell type-specific markers, we compared proteome and phosphoproteomes of KRASG12C cells. Gene expression patterns of KRASG12C cell lines and lung tumor tissues were examined., Results: Our analysis suggests cell type-specific perturbation to ERBB2/3 signaling compensates for repressed ERK and AKT signaling following ARS-1620 treatment in epithelial cell type, and this subtype was also more responsive to coinhibition of SHP2 and SOS1. Conversely, both high basal and feedback activation of FGFR or AXL signaling were identified in mesenchymal cells. Inhibition of FGFR signaling suppressed feedback activation of ERK and mTOR, while AXL inhibition suppressed PI3K pathway. In both cell lines and human lung cancer tissues with KRASG12C , we observed high basal ERBB2/3 associated with epithelial gene signatures, while higher basal FGFR1 and AXL were observed in cells/tumors with mesenchymal gene signatures., Conclusions: Our phosphoproteomic study identified cell type-adaptive responses to KRASi. Markers and targets associated with ERBB2/3 signaling in epithelial subtype and with FGFR1/AXL signaling in mesenchymal subtype should be considered in patient enrichment schemes with KRASi., (©2021 American Association for Cancer Research.)- Published
- 2021
- Full Text
- View/download PDF
36. TRK xDFG Mutations Trigger a Sensitivity Switch from Type I to II Kinase Inhibitors.
- Author
-
Cocco E, Lee JE, Kannan S, Schram AM, Won HH, Shifman S, Kulick A, Baldino L, Toska E, Arruabarrena-Aristorena A, Kittane S, Wu F, Cai Y, Arena S, Mussolin B, Kannan R, Vasan N, Gorelick AN, Berger MF, Novoplansky O, Jagadeeshan S, Liao Y, Rix U, Misale S, Taylor BS, Bardelli A, Hechtman JF, Hyman DM, Elkabets M, de Stanchina E, Verma CS, Ventura A, Drilon A, and Scaltriti M
- Subjects
- Humans, Mutation, Oncogenes, Protein Kinase Inhibitors pharmacology, Neoplasms drug therapy, Neoplasms genetics, Receptor, trkA genetics
- Abstract
On-target resistance to next-generation TRK inhibitors in TRK fusion-positive cancers is largely uncharacterized. In patients with these tumors, we found that TRK xDFG mutations confer resistance to type I next-generation TRK inhibitors designed to maintain potency against several kinase domain mutations. Computational modeling and biochemical assays showed that TRKA
G667 and TRKCG696 xDFG substitutions reduce drug binding by generating steric hindrance. Concurrently, these mutations stabilize the inactive (DFG-out) conformations of the kinases, thus sensitizing these kinases to type II TRK inhibitors. Consistently, type II inhibitors impede the growth and TRK-mediated signaling of xDFG-mutant isogenic and patient-derived models. Collectively, these data demonstrate that adaptive conformational resistance can be abrogated by shifting kinase engagement modes. Given the prior identification of paralogous xDFG resistance mutations in other oncogene-addicted cancers, these findings provide insights into rational type II drug design by leveraging inhibitor class affinity switching to address recalcitrant resistant alterations. SIGNIFICANCE: In TRK fusion-positive cancers, TRK xDFG substitutions represent a shared liability for type I TRK inhibitors. In contrast, they represent a potential biomarker of type II TRK inhibitor activity. As all currently available type II agents are multikinase inhibitors, rational drug design should focus on selective type II inhibitor creation. This article is highlighted in the In This Issue feature, p. 1 ., (©2020 American Association for Cancer Research.)- Published
- 2021
- Full Text
- View/download PDF
37. Turning liabilities into opportunities: Off-target based drug repurposing in cancer.
- Author
-
Palve V, Liao Y, Remsing Rix LL, and Rix U
- Subjects
- Animals, Humans, Antineoplastic Agents therapeutic use, Drug Discovery, Drug Repositioning methods, Neoplasms drug therapy, Polypharmacology methods
- Abstract
Targeted drugs and precision medicine have transformed the landscape of cancer therapy and significantly improved patient outcomes in many cases. However, as therapies are becoming more and more tailored to smaller patient populations and acquired resistance is limiting the duration of clinical responses, there is an ever increasing demand for new drugs, which is not easily met considering steadily rising drug attrition rates and development costs. Considering these challenges drug repurposing is an attractive complementary approach to traditional drug discovery that can satisfy some of these needs. This is facilitated by the fact that most targeted drugs, despite their implicit connotation, are not singularly specific, but rather display a wide spectrum of target selectivity. Importantly, some of the unintended drug "off-targets" are known anticancer targets in their own right. Others are becoming recognized as such in the process of elucidating off-target mechanisms that in fact are responsible for a drug's anticancer activity, thereby revealing potentially new cancer vulnerabilities. Harnessing such beneficial off-target effects can therefore lead to novel and promising precision medicine approaches. Here, we will discuss experimental and computational methods that are employed to specifically develop single target and network-based off-target repurposing strategies, for instance with drug combinations or polypharmacology drugs. By illustrating concrete examples that have led to clinical translation we will furthermore examine the various scientific and non-scientific factors that cumulatively determine the success of these efforts and thus can inform the future development of new and potentially lifesaving off-target based drug repurposing strategies for cancers that constitute important unmet medical needs., (Copyright © 2020. Published by Elsevier Ltd.)
- Published
- 2021
- Full Text
- View/download PDF
38. Lowering Sample Requirements to Study Tyrosine Kinase Signaling Using Phosphoproteomics with the TMT Calibrator Approach.
- Author
-
Fang B, Izumi V, Rix LLR, Welsh E, Pike I, Reuther GW, Haura EB, Rix U, and Koomen JM
- Subjects
- Chromatography, Liquid, Humans, Protein-Tyrosine Kinases, Proteome, Proteomics, Tandem Mass Spectrometry
- Abstract
Analysis of tyrosine kinase signaling is critical for the development of targeted cancer therapy. Currently, immunoprecipitation of phosphotyrosine (pY) peptides prior to liquid chromatography-tandem mass spectrometry (LC-MS/MS) is used to profile tyrosine kinase substrates. A typical protocol requests 10 mg of total protein from ≈10
8 cells or 50-100 mg of tissue. Large sample requirements can be cost prohibitive or not feasible for certain experiments. Sample multiplexing using chemical labeling reduces the protein amount required for each sample, and newer approaches use a material-rich reference channel as a calibrator to trigger detection and quantification for smaller samples. Here, it is demonstrated that the tandem mass tag (TMT) calibrator approach reduces the sample input for pY profiling tenfold (to ≈1 mg total protein per sample from 107 cells grown in one plate), while maintaining the depth of pY proteome sampling and the biological content of the experiment. Data are available through PRIDE (PXD019764 for label-free and PXD018952 for TMT). This strategy opens more opportunities for pY profiling of large sample cohorts and samples with limited protein quantity such as immune cells, xenograft models, and human tumors., (© 2020 Wiley-VCH GmbH.)- Published
- 2020
- Full Text
- View/download PDF
39. MEK Inhibition Modulates Cytokine Response to Mediate Therapeutic Efficacy in Lung Cancer.
- Author
-
Xie M, Zheng H, Madan-Lala R, Dai W, Gimbrone NT, Chen Z, Kinose F, Blackstone SA, Smalley KSM, Cress WD, Haura EB, Rix U, and Beg AA
- Subjects
- Animals, Cell Line, Tumor, Cytokines, Humans, Mice, Protein Kinase Inhibitors, Lung Neoplasms, Proto-Oncogene Proteins B-raf
- Abstract
Activating mutations in BRAF, a key mediator of RAS signaling, are present in approximately 50% of melanoma patients. Pharmacologic inhibition of BRAF or the downstream MAP kinase MEK is highly effective in treating BRAF-mutant melanoma. In contrast, RAS pathway inhibitors have been less effective in treating epithelial malignancies, such as lung cancer. Here, we show that treatment of melanoma patients with BRAF and MEK inhibitors (MEKi) activated tumor NF-κB activity. MEKi potentiated the response to TNFα, a potent activator of NF-κB. In both melanoma and lung cancer cells, MEKi increased cell-surface expression of TNFα receptor 1 (TNFR1), which enhanced NF-κB activation and augmented expression of genes regulated by TNFα and IFNγ. Screening of 289 targeted agents for the ability to increase TNFα and IFNγ target gene expression demonstrated that this was a general activity of inhibitors of MEK and ERK kinases. Treatment with MEKi led to acquisition of a novel vulnerability to TNFα and IFNγ-induced apoptosis in lung cancer cells that were refractory to MEKi killing and augmented cell-cycle arrest. Abolishing the expression of TNFR1 on lung cancer cells impaired the antitumor efficacy of MEKi, whereas the administration of TNFα and IFNγ in MEKi-treated mice enhanced the antitumor response. Furthermore, immunotherapeutics known to induce expression of these cytokines synergized with MEKi in eradicating tumors. These findings define a novel cytokine response modulatory function of MEKi that can be therapeutically exploited. SIGNIFICANCE: Lung cancer cells are rendered sensitive to MEK inhibitors by TNFα and IFNγ, providing a strong mechanistic rationale for combining immunotherapeutics, such as checkpoint blockers, with MEK inhibitor therapy for lung cancer. See related commentary by Havel, p. 5699 ., (©2019 American Association for Cancer Research.)
- Published
- 2019
- Full Text
- View/download PDF
40. Characterization of epidermal growth factor receptor (EGFR) P848L, an unusual EGFR variant present in lung cancer patients, in a murine Ba/F3 model.
- Author
-
Sarcar B, Gimbrone NT, Wright G, Remsing Rix LL, Gordian ER, Rix U, Chiappori AA, Reuther GW, Santiago-Cardona PG, Muñoz-Antonia T, and Cress WD
- Subjects
- Animals, Cell Proliferation drug effects, Cell Survival drug effects, Cells, Cultured, ErbB Receptors genetics, ErbB Receptors metabolism, HEK293 Cells, Humans, Lung Neoplasms metabolism, Mice, Mice, Transgenic, Microscopy, Fluorescence, Mutation, Nitriles, Protein Kinase Inhibitors pharmacology, Proto-Oncogene Mas, Pyrazoles pharmacology, Pyrimidines pharmacology, Disease Models, Animal, Genetic Variation genetics, Lung Neoplasms genetics
- Abstract
Lung cancer patients with mutations in epidermal growth factor receptor (EGFR) benefit from treatments targeting tyrosine kinase inhibitors (TKIs). However, both intrinsic and acquired resistance of tumors to TKIs are common, and EGFR variants have been identified that are resistant to multiple TKIs. In the present study, we characterized selected EGFR variants previously observed in lung cancer patients and expressed in a murine bone marrow pro-B Ba/F3 cell model. Among these EGFR variants, we report that an exon 20 deletion/insertion mutation S768insVGH is resistant to erlotinib (a first-generation TKI), but sensitive to osimertinib (a third-generation TKI). We also characterized a rare exon 21 germline variant, EGFR P848L, which transformed Ba/F3 cells and conferred resistance to multiple EGFR-targeting TKIs. Our analysis revealed that P848L (a) does not bind erlotinib; (b) is turned over less rapidly than L858R (a common tumor-derived EGFR mutation); (c) is not autophosphorylated at Tyr 1045 [the major docking site for Cbl proto-oncogene (c-Cbl) binding]; and (d) does not bind c-Cbl. Using viability assays including 300 clinically relevant targeted compounds, we observed that Ba/F3 cells transduced with EGFR P848L, S768insVGH, or L858R have very different drug-sensitivity profiles. In particular, EGFR P848L, but not L858R or S768insVGH, was sensitive to multiple Janus kinase 1/2 inhibitors. In contrast, cells driven by L858R, but not by P848L, were sensitive to multikinase MAPK/extracellular-signal-regulated kinase (ERK) kinase and ERK inhibitors including EGFR-specific TKIs. These observations suggest that continued investigation of rare TKI-resistant EGFR variants is warranted to identify optimal treatments for cancer., (© 2019 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.)
- Published
- 2019
- Full Text
- View/download PDF
41. Divergent Polypharmacology-Driven Cellular Activity of Structurally Similar Multi-Kinase Inhibitors through Cumulative Effects on Individual Targets.
- Author
-
Sumi NJ, Ctortecka C, Hu Q, Bryant AT, Fang B, Remsing Rix LL, Ayaz M, Kinose F, Welsh EA, Eschrich SA, Lawrence HR, Koomen JM, Haura EB, and Rix U
- Subjects
- Antineoplastic Combined Chemotherapy Protocols metabolism, Antineoplastic Combined Chemotherapy Protocols pharmacology, Aurora Kinase B metabolism, Cell Line, Tumor, Drug Discovery, Humans, MAP Kinase Kinase 1 metabolism, MAP Kinase Kinase 2 metabolism, Organophosphates pharmacology, Protein Kinase Inhibitors chemistry, Protein-Tyrosine Kinases metabolism, Quinazolines pharmacology, Systems Analysis, Anilides pharmacology, Lung Neoplasms drug therapy, Polypharmacology, Pyridines pharmacology, Quinolines pharmacology
- Abstract
Despite recent successes of precision and immunotherapies there is a persisting need for novel targeted or multi-targeted approaches in complex diseases. Through a systems pharmacology approach, including phenotypic screening, chemical and phosphoproteomics, and RNA-seq, we elucidated the targets and mechanisms underlying the differential anticancer activity of two structurally related multi-kinase inhibitors, foretinib, and cabozantinib, in lung cancer cells. Biochemical and cellular target validation using probe molecules and RNAi revealed a polypharmacology mechanism involving MEK1/2, FER, and AURKB, which were each more potently inhibited by foretinib than cabozantinib. Based on this, we developed a synergistic combination of foretinib with barasertib, a more potent AURKB inhibitor, for MYC-amplified small-cell lung cancer. This systems pharmacology approach showed that small structural changes of drugs can cumulatively, through multiple targets, result in pronounced anticancer activity differences and that detailed mechanistic understanding of polypharmacology can enable repurposing opportunities for cancers with unmet medical need., (Copyright © 2019 Elsevier Ltd. All rights reserved.)
- Published
- 2019
- Full Text
- View/download PDF
42. HDAC Inhibition Enhances the In Vivo Efficacy of MEK Inhibitor Therapy in Uveal Melanoma.
- Author
-
Faião-Flores F, Emmons MF, Durante MA, Kinose F, Saha B, Fang B, Koomen JM, Chellappan SP, Maria-Engler SS, Rix U, Licht JD, Harbour JW, and Smalley KSM
- Subjects
- Animals, Cell Cycle Proteins metabolism, Cell Line, Tumor, Cell Survival drug effects, Disease Models, Animal, Disease Progression, Drug Resistance, Neoplasm, Drug Synergism, Humans, MAP Kinase Signaling System drug effects, Melanoma drug therapy, Melanoma pathology, Mice, Panobinostat pharmacology, Phosphatidylinositol 3-Kinases metabolism, Proteome, Proteomics methods, Proto-Oncogene Proteins c-akt metabolism, Pyridones pharmacology, Pyrimidinones pharmacology, Receptor Tyrosine Kinase-like Orphan Receptors metabolism, Receptor, IGF Type 1 metabolism, Receptors, G-Protein-Coupled metabolism, Signal Transduction drug effects, Transcription Factors metabolism, Uveal Neoplasms drug therapy, Uveal Neoplasms pathology, Xenograft Model Antitumor Assays, Histone Deacetylase Inhibitors pharmacology, Melanoma metabolism, Protein Kinase Inhibitors pharmacology, Uveal Neoplasms metabolism
- Abstract
Purpose: The clinical use of MEK inhibitors in uveal melanoma is limited by the rapid acquisition of resistance. This study has used multiomics approaches and drug screens to identify the pan-HDAC inhibitor panobinostat as an effective strategy to limit MEK inhibitor resistance. Experimental Design: Mass spectrometry-based proteomics and RNA-Seq were used to identify the signaling pathways involved in the escape of uveal melanoma cells from MEK inhibitor therapy. Mechanistic studies were performed to evaluate the escape pathways identified, and the efficacy of the MEK-HDAC inhibitor combination was demonstrated in multiple in vivo models of uveal melanoma., Results: We identified a number of putative escape pathways that were upregulated following MEK inhibition, including the PI3K/AKT pathway, ROR1/2, and IGF-1R signaling. MEK inhibition was also associated with increased GPCR expression, particularly the endothelin B receptor, and this contributed to therapeutic escape through ET-3-mediated YAP signaling. A screen of 289 clinical grade compounds identified HDAC inhibitors as potential candidates that suppressed the adaptive YAP and AKT signaling that followed MEK inhibition. In vivo , the MEK-HDAC inhibitor combination outperformed either agent alone, leading to a long-term decrease of tumor growth in both subcutaneous and liver metastasis models and the suppression of adaptive PI3K/AKT and YAP signaling., Conclusions: Together, our studies have identified GPCR-mediated YAP activation and RTK-driven AKT signaling as key pathways involved in the escape of uveal melanoma cells from MEK inhibition. We further demonstrate that HDAC inhibition is a promising combination partner for MEK inhibitors in advanced uveal melanoma., (©2019 American Association for Cancer Research.)
- Published
- 2019
- Full Text
- View/download PDF
43. An immunoproteomic approach to characterize the CAR interactome and signalosome.
- Author
-
Ramello MC, Benzaïd I, Kuenzi BM, Lienlaf-Moreno M, Kandell WM, Santiago DN, Pabón-Saldaña M, Darville L, Fang B, Rix U, Yoder S, Berglund A, Koomen JM, Haura EB, and Abate-Daga D
- Subjects
- Animals, Binding Sites immunology, Cell Line, Tumor, Humans, Mice, Inbred NOD, Mice, Knockout, Mice, SCID, Neoplasms immunology, Neoplasms pathology, Protein Binding immunology, Proteome immunology, Proteome metabolism, Receptors, Chimeric Antigen genetics, Receptors, Chimeric Antigen immunology, Signal Transduction immunology, T-Lymphocytes immunology, T-Lymphocytes transplantation, Immunotherapy, Adoptive methods, Neoplasms therapy, Proteomics methods, Receptors, Chimeric Antigen metabolism, T-Lymphocytes metabolism, Xenograft Model Antitumor Assays
- Abstract
Adoptive transfer of T cells that express a chimeric antigen receptor (CAR) is an approved immunotherapy that may be curative for some hematological cancers. To better understand the therapeutic mechanism of action, we systematically analyzed CAR signaling in human primary T cells by mass spectrometry. When we compared the interactomes and the signaling pathways activated by distinct CAR-T cells that shared the same antigen-binding domain but differed in their intracellular domains and their in vivo antitumor efficacy, we found that only second-generation CARs induced the expression of a constitutively phosphorylated form of CD3ζ that resembled the endogenous species. This phenomenon was independent of the choice of costimulatory domains, or the hinge/transmembrane region. Rather, it was dependent on the size of the intracellular domains. Moreover, the second-generation design was also associated with stronger phosphorylation of downstream secondary messengers, as evidenced by global phosphoproteome analysis. These results suggest that second-generation CARs can activate additional sources of CD3ζ signaling, and this may contribute to more intense signaling and superior antitumor efficacy that they display compared to third-generation CARs. Moreover, our results provide a deeper understanding of how CARs interact physically and/or functionally with endogenous T cell molecules, which will inform the development of novel optimized immune receptors., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
- Published
- 2019
- Full Text
- View/download PDF
44. Off-target based drug repurposing opportunities for tivantinib in acute myeloid leukemia.
- Author
-
Kuenzi BM, Remsing Rix LL, Kinose F, Kroeger JL, Lancet JE, Padron E, and Rix U
- Subjects
- Bridged Bicyclo Compounds, Heterocyclic pharmacology, Bridged Bicyclo Compounds, Heterocyclic therapeutic use, Down-Regulation drug effects, Drug Synergism, G2 Phase Cell Cycle Checkpoints drug effects, Glycogen Synthase Kinase 3 antagonists & inhibitors, Glycogen Synthase Kinase 3 metabolism, HL-60 Cells, Humans, Leukemia, Myeloid, Acute drug therapy, Leukemia, Myeloid, Acute pathology, Lithium Chloride pharmacology, Lithium Chloride therapeutic use, Myeloid Cell Leukemia Sequence 1 Protein genetics, Myeloid Cell Leukemia Sequence 1 Protein metabolism, Protein Kinase Inhibitors pharmacology, Protein Kinase Inhibitors therapeutic use, Proto-Oncogene Proteins c-met antagonists & inhibitors, Proto-Oncogene Proteins c-met metabolism, Pyrrolidinones therapeutic use, Quinolines therapeutic use, Sulfonamides pharmacology, Sulfonamides therapeutic use, bcl-X Protein genetics, bcl-X Protein metabolism, Apoptosis drug effects, Drug Repositioning, Pyrrolidinones pharmacology, Quinolines pharmacology
- Abstract
GSK3α has been identified as a new target in the treatment of acute myeloid leukemia (AML). However, most GSK3 inhibitors lack specificity for GSK3α over GSK3β and other kinases. We have previously shown in lung cancer cells that GSK3α and to a lesser extent GSK3β are inhibited by the advanced clinical candidate tivantinib (ARQ197), which was designed as a MET inhibitor. Thus, we hypothesized that tivantinib would be an effective therapy for the treatment of AML. Here, we show that tivantinib has potent anticancer activity across several AML cell lines and primary patient cells. Tivantinib strongly induced apoptosis, differentiation and G2/M cell cycle arrest and caused less undesirable stabilization of β-catenin compared to the pan-GSK3 inhibitor LiCl. Subsequent drug combination studies identified the BCL-2 inhibitor ABT-199 to synergize with tivantinib while cytarabine combination with tivantinib was antagonistic. Interestingly, the addition of ABT-199 to tivantinib completely abrogated tivantinib induced β-catenin stabilization. Tivantinib alone, or in combination with ABT-199, downregulated anti-apoptotic MCL-1 and BCL-XL levels, which likely contribute to the observed synergy. Importantly, tivantinib as single agent or in combination with ABT-199 significantly inhibited the colony forming capacity of primary patient AML bone marrow mononuclear cells. In summary, tivantinib is a novel GSK3α/β inhibitor that potently kills AML cells and tivantinib single agent or combination therapy with ABT-199 may represent attractive new therapeutic opportunities for AML.
- Published
- 2019
- Full Text
- View/download PDF
45. Targeting the BRD4-HOXB13 Coregulated Transcriptional Networks with Bromodomain-Kinase Inhibitors to Suppress Metastatic Castration-Resistant Prostate Cancer.
- Author
-
Nerlakanti N, Yao J, Nguyen DT, Patel AK, Eroshkin AM, Lawrence HR, Ayaz M, Kuenzi BM, Agarwal N, Chen Y, Gunawan S, Karim RM, Berndt N, Puskas J, Magliocco AM, Coppola D, Dhillon J, Zhang J, Shymalagovindarajan S, Rix U, Kim Y, Perera R, Lawrence NJ, Schonbrunn E, and Mahajan K
- Subjects
- Androgen Receptor Antagonists pharmacology, Androgens pharmacology, Animals, Apoptosis drug effects, Cell Cycle Proteins, Cell Line, Tumor, Cell Proliferation drug effects, Epigenesis, Genetic drug effects, Genetic Loci, Humans, Male, Mice, SCID, Neoplasm Metastasis, Up-Regulation drug effects, Xenograft Model Antitumor Assays, Gene Expression Regulation, Neoplastic drug effects, Gene Regulatory Networks drug effects, Homeodomain Proteins metabolism, Nuclear Proteins metabolism, Prostatic Neoplasms, Castration-Resistant genetics, Prostatic Neoplasms, Castration-Resistant pathology, Protein Kinase Inhibitors pharmacology, Transcription Factors metabolism
- Abstract
Resistance to androgen receptor (AR) antagonists is a significant problem in the treatment of castration-resistant prostate cancers (CRPC). Identification of the mechanisms by which CRPCs evade androgen deprivation therapies (ADT) is critical to develop novel therapeutics. We uncovered that CRPCs rely on BRD4-HOXB13 epigenetic reprogramming for androgen-independent cell proliferation. Mechanistically, BRD4, a member of the BET bromodomain family, epigenetically promotes HOXB13 expression. Consistently, genetic disruption of HOXB13 or pharmacological suppression of its mRNA and protein expression by the novel dual-activity BET bromodomain-kinase inhibitors directly correlates with rapid induction of apoptosis, potent inhibition of tumor cell proliferation and cell migration, and suppression of CRPC growth. Integrative analysis revealed that the BRD4-HOXB13 transcriptome comprises a proliferative gene network implicated in cell-cycle progression, nucleotide metabolism, and chromatin assembly. Notably, although the core HOXB13 target genes responsive to BET inhibitors (HOTBIN10) are overexpressed in metastatic cases, in ADT-treated CRPC cell lines and patient-derived circulating tumor cells (CTC) they are insensitive to AR depletion or blockade. Among the HOTBIN10 genes, AURKB and MELK expression correlates with HOXB13 expression in CTCs of mCRPC patients who did not respond to abiraterone (ABR), suggesting that AURKB inhibitors could be used additionally against high-risk HOXB13-positive metastatic prostate cancers. Combined, our study demonstrates that BRD4-HOXB13-HOTBIN10 regulatory circuit maintains the malignant state of CRPCs and identifies a core proproliferative network driving ADT resistance that is targetable with potent dual-activity bromodomain-kinase inhibitors., (©2018 American Association for Cancer Research.)
- Published
- 2018
- Full Text
- View/download PDF
46. Functional Proteomics and Deep Network Interrogation Reveal a Complex Mechanism of Action of Midostaurin in Lung Cancer Cells.
- Author
-
Ctortecka C, Palve V, Kuenzi BM, Fang B, Sumi NJ, Izumi V, Novakova S, Kinose F, Remsing Rix LL, Haura EB, Koomen JM, and Rix U
- Subjects
- Biomarkers, Tumor antagonists & inhibitors, Cell Cycle drug effects, Cell Line, Tumor, Cell Survival drug effects, Drug Discovery, Drug Synergism, Humans, RNA Interference, Signal Transduction drug effects, Staurosporine pharmacology, Polo-Like Kinase 1, Aurora Kinase A antagonists & inhibitors, Carcinoma, Non-Small-Cell Lung metabolism, Cell Cycle Proteins antagonists & inhibitors, Lung Neoplasms metabolism, Protein Serine-Threonine Kinases antagonists & inhibitors, Protein-Tyrosine Kinases antagonists & inhibitors, Proteomics methods, Proto-Oncogene Proteins antagonists & inhibitors, Staurosporine analogs & derivatives
- Abstract
Lung cancer is associated with high prevalence and mortality, and despite significant successes with targeted drugs in genomically defined subsets of lung cancer and immunotherapy, the majority of patients currently does not benefit from these therapies. Through a targeted drug screen, we found the recently approved multi-kinase inhibitor midostaurin to have potent activity in several lung cancer cells independent of its intended target, PKC, or a specific genomic marker. To determine the underlying mechanism of action we applied a layered functional proteomics approach and a new data integration method. Using chemical proteomics, we identified multiple midostaurin kinase targets in these cells. Network-based integration of these targets with quantitative tyrosine and global phosphoproteomics data using protein-protein interactions from the STRING database suggested multiple targets are relevant for the mode of action of midostaurin. Subsequent functional validation using RNA interference and selective small molecule probes showed that simultaneous inhibition of TBK1, PDPK1 and AURKA was required to elicit midostaurin's cellular effects. Immunoblot analysis of downstream signaling nodes showed that combined inhibition of these targets altered PI3K/AKT and cell cycle signaling pathways that in part converged on PLK1. Furthermore, rational combination of midostaurin with the potent PLK1 inhibitor BI2536 elicited strong synergy. Our results demonstrate that combination of complementary functional proteomics approaches and subsequent network-based data integration can reveal novel insight into the complex mode of action of multi-kinase inhibitors, actionable targets for drug discovery and cancer vulnerabilities. Finally, we illustrate how this knowledge can be used for the rational design of synergistic drug combinations with high potential for clinical translation., (© 2018 Ctortecka et al.)
- Published
- 2018
- Full Text
- View/download PDF
47. Bidirectional Adaptive Signaling between cancer and stromal cells: mechanisms and therapeutics.
- Author
-
Boutchueng-Djidjou M, Rix U, and Haura EB
- Subjects
- Humans, Isotope Labeling, Protein Processing, Post-Translational, Proteomics, Stromal Cells metabolism, Stromal Cells pathology, Neoplasms metabolism, Neoplasms pathology, Signal Transduction
- Published
- 2018
- Full Text
- View/download PDF
48. Unraveling the rewired network.
- Author
-
Palve V, Kuenzi BM, and Rix U
- Subjects
- Computational Biology
- Published
- 2018
- Full Text
- View/download PDF
49. Comparison of Quantitative Mass Spectrometry Platforms for Monitoring Kinase ATP Probe Uptake in Lung Cancer.
- Author
-
Hoffman MA, Fang B, Haura EB, Rix U, and Koomen JM
- Subjects
- Adenosine Triphosphate pharmacokinetics, Drug Monitoring methods, Humans, Lung Neoplasms metabolism, Phosphotransferases pharmacokinetics, Protein Kinase Inhibitors pharmacology, Proteomics methods, Data Collection methods, Data Collection standards, Mass Spectrometry methods
- Abstract
Recent developments in instrumentation and bioinformatics have led to new quantitative mass spectrometry platforms including LC-MS/MS with data-independent acquisition (DIA) and targeted analysis using parallel reaction monitoring mass spectrometry (LC-PRM), which provide alternatives to well-established methods, such as LC-MS/MS with data-dependent acquisition (DDA) and targeted analysis using multiple reaction monitoring mass spectrometry (LC-MRM). These tools have been used to identify signaling perturbations in lung cancers and other malignancies, supporting the development of effective kinase inhibitors and, more recently, providing insights into therapeutic resistance mechanisms and drug repurposing opportunities. However, detection of kinases in biological matrices can be challenging; therefore, activity-based protein profiling enrichment of ATP-utilizing proteins was selected as a test case for exploring the limits of detection of low-abundance analytes in complex biological samples. To examine the impact of different MS acquisition platforms, quantification of kinase ATP uptake following kinase inhibitor treatment was analyzed by four different methods: LC-MS/MS with DDA and DIA, LC-MRM, and LC-PRM. For discovery data sets, DIA increased the number of identified kinases by 21% and reduced missingness when compared with DDA. In this context, MRM and PRM were most effective at identifying global kinome responses to inhibitor treatment, highlighting the value of a priori target identification and manual evaluation of quantitative proteomics data sets. We compare results for a selected set of desthiobiotinylated peptides from PRM, MRM, and DIA and identify considerations for selecting a quantification method and postprocessing steps that should be used for each data acquisition strategy.
- Published
- 2018
- Full Text
- View/download PDF
50. Ceritinib Enhances the Efficacy of Trametinib in BRAF/NRAS -Wild-Type Melanoma Cell Lines.
- Author
-
Verduzco D, Kuenzi BM, Kinose F, Sondak VK, Eroglu Z, Rix U, and Smalley KSM
- Subjects
- Antineoplastic Agents pharmacology, Cell Line, Tumor, Humans, Melanoma pathology, Pyridones pharmacology, Pyrimidines pharmacology, Pyrimidinones pharmacology, Sulfones pharmacology, Antineoplastic Agents therapeutic use, Melanoma drug therapy, Melanoma genetics, Proto-Oncogene Proteins B-raf genetics, Pyridones therapeutic use, Pyrimidines therapeutic use, Pyrimidinones therapeutic use, Sulfones therapeutic use
- Abstract
Targeted therapy options are currently lacking for the heterogeneous population of patients whose melanomas lack BRAF or NRAS mutations (∼35% of cases). We undertook a chemical biology screen to identify potential novel drug targets for this understudied group of tumors. Screening a panel of 8 BRAF/NRAS -WT melanoma cell lines against 240 targeted drugs identified ceritinib and trametinib as potential hits with single-agent activity. Ceritinib enhanced the efficacy of trametinib across the majority of the BRAF/NRAS -WT cell lines, and the combination showed increased cytotoxicity in both three-dimensional spheroid culture and long-term colony formation experiments. Coadministration of ceritinib and trametinib led to robust inhibition of tumor growth in an in vivo xenograft BRAF/NRAS -WT melanoma model; this was not due to ALK inhibition by ceritinib. Mechanistic studies showed the ceritinib-trametinib combination to increase suppression of MAPK and TORC1 signaling. Similar results were seen when BRAF/NRAS -WT melanoma cells were treated with a combination of trametinib and the TORC1/2 inhibitor INK128. We next used mass spectrometry-based chemical proteomics and identified known and new ceritinib targets, such as IGF1R and ACK1, respectively. Validation studies suggested that ceritinib could suppress mTORC1 signaling in the presence of trametinib through inhibition of IGF1R and/or ACK1 in a cell line-dependent manner. Together, our studies demonstrated that combining a specific inhibitor (trametinib) with a more broadly targeted agent (ceritinib) has efficacy against tumors with heterogeneous mutational profiles. Mol Cancer Ther; 17(1); 73-83. ©2017 AACR ., (©2017 American Association for Cancer Research.)
- Published
- 2018
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.