Investigating RET RTK signaling pathways using an IAP-based activity-profiling approach

Journal of Proteome Research

Volumn 13, Issue 8, 2014, Pages 3628-3634

  Höfener, Michael ^a   Pachl, Fiona ^b   Take, Tim ^a   Fischer Von Mollard, Gabriele ^a   Kuster, Bernhard ^b,c   Sewald, Norbert ^a  

^a BIELEFELD UNIVERSITY   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c Munich Center for Integrated Protein Science   (Germany)

Author keywords

activity profiling; Chemical proteomics; kinase; mass spectrometry; RET9 signaling

Indexed keywords

ADENOSINE TRIPHOSPHATE; GLYCOGEN SYNTHASE KINASE 3BETA; HEAT SHOCK PROTEIN 70; MITOGEN ACTIVATED PROTEIN KINASE 1; MITOGEN ACTIVATED PROTEIN KINASE 11; MITOGEN ACTIVATED PROTEIN KINASE 14; MITOGEN ACTIVATED PROTEIN KINASE 3; MITOGEN ACTIVATED PROTEIN KINASE 9; PROTEIN KINASE; PROTEIN TYROSINE KINASE; PROTEIN TYROSINE KINASE 9; SERUM ALBUMIN; STRESS ACTIVATED PROTEIN KINASE; STRESS ACTIVATED PROTEIN KINASE 1; UNCLASSIFIED DRUG; IMIDAZOLE DERIVATIVE; MITOGEN ACTIVATED PROTEIN KINASE P38; PROTEIN BINDING; PROTEIN RET; PYRIMIDINE DERIVATIVE; RET PROTEIN, HUMAN; SB 218655;

AFFINITY CHROMATOGRAPHY; ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; BINDING AFFINITY; BINDING SITE; DEGENERATIVE DISEASE; ENZYME ACTIVITY; HUMAN; HUMAN CELL; INHIBITOR AFFINITY PURIFICATION; MASS SPECTROMETRY; NEUROBLASTOMA CELL; NEUROBLASTOMA CELL LINE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; PROTEOMICS; RAT; SIGNAL TRANSDUCTION; STIMULATION; STRUCTURE ACTIVITY RELATION; SYNTHESIS; ANIMAL; ANTAGONISTS AND INHIBITORS; CHEMICAL STRUCTURE; CHEMISTRY; GENE EXPRESSION PROFILING; GENETICS; LIQUID CHROMATOGRAPHY; METABOLISM; NERVE CELL; PHYSIOLOGY; PROCEDURES; TANDEM MASS SPECTROMETRY; TUMOR CELL LINE; WESTERN BLOTTING;

ANIMALS; BLOTTING, WESTERN; CELL LINE, TUMOR; CHROMATOGRAPHY, LIQUID; GENE EXPRESSION PROFILING; HUMANS; IMIDAZOLES; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NEURODEGENERATIVE DISEASES; NEURONS; P38 MITOGEN-ACTIVATED PROTEIN KINASES; PROTEIN BINDING; PROTEIN KINASES; PROTEOMICS; PROTO-ONCOGENE PROTEINS C-RET; PYRIMIDINES; RATS; SIGNAL TRANSDUCTION; TANDEM MASS SPECTROMETRY;

EID: 84905389447     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr500163r     Document Type: Article

References (36)

1. Jankovic, J. Parkinsons disease: clinical features and diagnosis J. Neurol., Neurosurg. Psychiatry 2008, 79, 368-376
2. Samii, A.; Nutt, J. G.; Ransom, B. R. Parkinsons disease Lancet 2004, 363, 1783-1793
3. Levitan, D.; Greenwald, I. Facilitation of lin-12-mediated signalling by sel-12, a Caenorhabditis elegans S182 Alzheimers disease gene Nature 1995, 377, 351-354
4. Seifert, G.; Schilling, K.; Steinhäuser, C. Astrocyte dysfunction in neurological disorders: a molecular perspective Nat. Rev. Neurosci. 2006, 7, 194-206
5. Lin, L.; Doherty, D.; Lile, J.; Bektesh, S.; Collins, F. GDNF: a glial cell line-derived neurotrophic factor for midbrain dopaminergic neurons Science 1993, 260, 1130-1132
6. Keast, J. R.; Forrest, S. L.; Osborne, P. B. Sciatic nerve injury in adult rats causes distinct changes in the central projections of sensory neurons expressing different glial cell line-derived neurotrophic factor family receptors J. Comp. Neurol. 2010, 518, 3024-3045
7. Pachnis, V.; Mankoo, B.; Costantini, F. Expression of the c-Ret proto-oncogene during mouse embryogenesis Development 1993, 119, 1005-1017
8. Avantaggiato, V.; Dathan, N. A.; Grieco, M.; Fabien, N.; Lazzaro, D.; Fusco, A.; Simeone, A.; Santoro, M. Developmental expression of the RET protooncogene Cell Growth Differ. 1994, 5, 305-311
9. Airaksinen, M. S.; Saarma, M. The GDNF family: signaling, biological functions and therapeutic value Nat. Rev. Neurosci. 2002, 3, 383-394
10. Besset, V. Signaling complexes and protein-protein interactions involved in the activation of the Ras and phosphatidylinositol 3-kinase pathways by the c-Ret receptor tyrosine kinase J. Biol. Chem. 2000, 275, 39159-39166
11. Santoro, M.; Carlomagno, F.; Melillo, R. M.; Fusco, A. Oncogenic protein tyrosine kinases Cell. Mol. Life Sci. 2004, 61, 2954-2964
12. Carter, M. T.; Yome, J. L.; Marcil, M. N.; Martin, C. A.; Vanhorne, J. B.; Mulligan, L. M. Conservation of RET proto-oncogene splicing variants and implications for RET isoform function Cytogenet. Genome Res. 2001, 95, 169-176
13. Tsui-Pierchala, B. A. The long and short isoforms of Ret function as independent signaling complexes J. Biol. Chem. 2002, 277, 34618-34625
14. Gygi, S. P.; Corthals, G. L.; Zhang, Y.; Rochon, Y.; Aebersold, R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9390-9395
15. Hagenstein, M. C.; Sewald, N. Chemical tools for activity-based proteomics J. Biotechnol. 2006, 124, 56-73
16. Pachl, F.; Plattner, P.; Ruprecht, B.; Médard, G.; Sewald, N.; Kuster, B. Characterization of a chemical affinity probe targeting Akt kinases J. Proteome Res. 2013, 12, 3792-3800
17. Bantscheff, M.; Eberhard, D.; Abraham, Y.; Bastuck, S.; Boesche, M.; Hobson, S.; Mathieson, T.; Perrin, J.; Raida, M.; Rau, C. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors Nat. Biotechnol. 2007, 25, 1035-1044
18. Schirle, M.; Bantscheff, M.; Kuster, B. Mass spectrometry-based proteomics in preclinical drug discovery Chem. Biol. 2012, 19, 72-84
19. Trott, O.; Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading J. Comput. Chem. 2010, 31, 455-461
20. Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera-a visualization system for exploratory research and analysis J. Comput. Chem. 2004, 25, 1605-1612
21. Duncan, J.; Whittle, M.; Nakamura, K.; Abell, A.; Midland, A.; Zawistowski, J.; Johnson, N.; Granger, D.; Jordan, N.; Darr, D. Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer Cell 2012, 149, 307-321
22. Okram, B.; Nagle, A.; Adrián, F. J.; Lee, C.; Ren, P.; Wang, X.; Sim, T.; Xie, Y.; Wang, X.; Xia, G. A general strategy for creating "inactive-conformation" Abl inhibitors Chem. Biol. 2006, 13, 779-786
23. Ranjitkar, P.; Perera, B.; Gayani, K.; Swaney, D. L.; Hari, S. B.; Larson, E. T.; Krishnamurty, R.; Merritt, E. A.; Villén, J.; Maly, D. J. Affinity-based probes based on type II kinase inhibitors J. Am. Chem. Soc. 2012, 134, 19017-19025
24. Wang, Z.; Canagarajah, B. J.; Boehm, J. C.; Kassisà, S.; Cobb, M. H.; Young, P. R.; Abdel-Meguid, S.; Adams, J. L.; Goldsmith, E. J. Structural basis of inhibitor selectivity in MAP kinases Structure 1998, 6, 1117-1128
25. Adams, J. L.; Boehm, J. C.; Gallagher, T. F.; Kassis, S.; Webb, E. F.; Hall, R.; Sorenson, M.; Garigipati, R.; Griswold, D. E.; Lee, J. C. Pyrimidinylimidazole inhibitors of p38: cyclic N-1 imidazole substituents enhance p38 kinase inhibition and oral activity Bioorg. Med. Chem. Lett. 2001, 11, 2867-2870
26. Van Leusen, D.; Albert, M.; Wildeman, J.; Oldenziel, O. H. Chemistry of sulfonylmethyl isocyanides. 12. Base-induced cycloaddition of sulfonylmethyl isocyanides to carbon,nitrogen double bonds. Synthesis of 1,5-disubstituted and 1,4,5-trisubstituted imidazoles from aldimines and imidoyl chlorides J. Org. Chem. 1977, 42, 1153-1159
27. Musholt, T. J.; Hanack, J.; Brehm, C.; Wasielewski, R.; Musholt, P. B. Searching for non-RET molecular alterations in medullary thyroid carcinoma: expression analysis by mRNA differential display World J. Surg. 2005, 29, 472-482
28. Drosten, M.; Pützer, B. M. Mechanisms of disease: cancer targeting and the impact of oncogenic RET for medullary thyroid carcinoma therapy Nat. Clin. Pract. Oncol. 2006, 3, 564-574
29. Lee, D.-W. Depletion of GAK/auxilin 2 inhibits receptor-mediated endocytosis and recruitment of both clathrin and clathrin adaptors J. Cell Sci. 2005, 118, 4311-4321
30. Natarajan, C.; Yao, S.-Y.; Zhang, F.; Sriram, S. Activation of NOD2/RIPK2 pathway induces mitochondrial injury to oligodendrocyte precursor cells in vitro and CNS demyelination in vivo J. Neuroimmunol. 2013, 265, 51-60
31. Knippschild, U.; Gocht, A.; Wolff, S.; Huber, N.; Löhler, J.; Stöter, M. The casein kinase 1 family: participation in multiple cellular processes in eukaryotes Cell. Signalling 2005, 17, 675-689
32. Di Cunto, F.; Imarisio, S.; Hirsch, E.; Broccoli, V.; Bulfone, A.; Migheli, A.; Atzori, C.; Turco, E.; Triolo, R.; Dotto, G. P. Defective neurogenesis in citron kinase knockout mice by altered cytokinesis and massive apoptosis Neuron 2000, 28, 115-127
33. Madaule, P.; Eda, M.; Watanabe, N.; Fujisawa, K.; Matsuoka, T.; Bito, H.; Ishizaki, T.; Narumiya, S. Role of citron kinase as a target of the small GTPase Rho in cytokinesis Nature 1998, 394, 491-494
34. Ashraf, S.; Gee, H. Y.; Woerner, S.; Xie, L. X.; Vega-Warner, V.; Lovric, S.; Fang, H.; Song, X.; Cattran, D. C.; Avila-Casado, C. ADCK4 mutations promote steroid-resistant nephrotic syndrome through CoQ10 biosynthesis disruption J. Clin. Invest. 2013, 123, 5179-5189
35. Cohen, P.; Frame, S. Timeline: the renaissance of GSK3 Nat. Rev. Mol. Cell Biol. 2001, 2, 769-776
36. Merl, J.; Ueffing, M.; Hauck, S. M.; Toerne, C. Direct comparison of MS-based label-free and SILAC quantitative proteome profiling strategies in primary retinal Müller cells Proteomics 2012, 12, 1902-1911