Abstract
Chronic myeloid leukemia (CML) is driven by the oncogenic fusion kinase Bcr-Abl, which organizes its own signaling network with various proteins. These proteins, their interactions, and their role in relevant signaling pathways can be analyzed by quantitative mass spectrometry (MS) approaches in various models systems, e.g., in cell culture models. In this chapter, we describe in detail immunoprecipitations and quantitative proteomics analysis using stable isotope labeling by amino acids in cell culture (SILAC) of components of the Bcr-Abl signaling pathway in the human CML cell line K562.
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References
Faderl S, Talpaz M, Estrov Z, Kantarjian HM (1999) Chronic myelogenous leukemia: biology and therapy. Ann Intern Med 131:207–219
Hantschel O, Superti-Furga G (2004) Regulation of the c-Abl and Bcr-Abl tyrosine kinases. Nat Rev Mol Cell Biol 5:33–44
Wohrle FU, Daly RJ, Brummer T (2009) Function, regulation and pathological roles of the Gab/DOS docking proteins. Cell Commun Signal 7:22
Donato NJ, Wu JY, Stapley J, Gallick G, Lin H, Arlinghaus R, Talpaz M (2003) BCR-ABL independence and LYN kinase overexpression in chronic myelogenous leukemia cells selected for resistance to STI571. Blood 101:690–698
Wilson-Rawls J, Liu J, Laneuville P, Arlinghaus RB (1997) P210 Bcr-Abl interacts with the interleukin-3 beta c subunit and constitutively activates Jak2. Leukemia 11(Suppl 3):428–431
Halbach S, Rigbolt KT, Wohrle FU, Diedrich B, Gretzmeier C, Brummer T, Dengjel J (2013) Alterations of Gab2 signalling complexes in imatinib and dasatinib treated chronic myeloid leukaemia cells. Cell Commun Signal 11:30
Wohrle FU, Halbach S, Aumann K, Schwemmers S, Braun S, Auberger P, Schramek D, Penninger JM, Laßmann S, Werner M, Waller CF, Pahl HL, Zeiser R, Daly RJ, Brummer T (2013) Gab2 signaling in chronic myeloid leukemia cells confers resistance to multiple Bcr-Abl inhibitors. Leukemia 27:118–129
Preisinger C, Schwarz JP, Bleijerveld OB, Corradini E, Muller PJ, Anderson KI, Kolch W, Scholten A, Heck AJ (2013) Imatinib-dependent tyrosine phosphorylation profiling of Bcr-Abl-positive chronic myeloid leukemia cells. Leukemia 27:743–746
Druker BJ (2008) Translation of the Philadelphia chromosome into therapy for CML. Blood 112:4808–4817
Sawyers CL (2009) Shifting paradigms: the seeds of oncogene addiction. Nat Med 15:1158–1161
Hunter T (2007) Treatment for chronic myelogenous leukemia: the long road to imatinib. J Clin Invest 117:2036–2043
Burchert A (2007) Roots of imatinib resistance: a question of self-renewal? Drug Resist Updat 10:152–161
von Bubnoff N, Duyster J (2010) Chronic myelogenous leukemia: treatment and monitoring. Dtsch Arztebl Int 107:114–121
Druker BJ, Guilhot F, O‘Brien SG, Gathmann I, Kantarjian H, Gattermann N, Deininger MW, Silver RT, Goldman JM, Stone RM, Cervantes F, Hochhaus A, Powell BL, Gabrilove JL, Rousselot P, Reiffers J, Cornelissen JJ, Hughes T, Agis H, Fischer T, Verhoef G, Shepherd J, Saglio G, Gratwohl A, Nielsen JL, Radich JP, Simonsson B, Taylor BM, So C, Letvak L, Larson RA, IRIS Investigators (2006) Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. N Engl J Med 355:2408–2417
O‘Hare T, Eide CA, Deininger MW (2007) Bcr-Abl kinase domain mutations, drug resistance, and the road to a cure for chronic myeloid leukemia. Blood 110:2242–2249
O‘Hare T, Eide CA, Deininger MW (2008) New Bcr-Abl inhibitors in chronic myeloid leukemia: keeping resistance in check. Expert Opin Investig Drugs 17:865–878
Weisberg E, Manley PW, Cowan-Jacob SW, Hochhaus A, Griffin JD (2007) Second generation inhibitors of BCR-ABL for the treatment of imatinib-resistant chronic myeloid leukaemia. Nat Rev Cancer 7:345–356
O‘Hare T, Deininger MW, Eide CA, Clackson T, Druker BJ (2011) Targeting the BCR-ABL signaling pathway in therapy-resistant Philadelphia chromosome-positive leukemia. Clin Cancer Res 17:212–221
Bixby D, Talpaz M (2011) Seeking the causes and solutions to imatinib-resistance in chronic myeloid leukemia. Leukemia 25:7–22
Sprenger A, Weber S, Zarai M, Engelke R, Nascimento JM, Gretzmeier C, Hilpert M, Boerries M, Has C, Busch H, Bruckner-Tuderman L, Dengjel J (2013) Consistency of the proteome in primary human keratinocytes with respect to gender, age, and skin localization. Mol Cell Proteomics 12:2509–2521
Dengjel J, Akimov V, Olsen JV, Bunkenborg J, Mann M, Blagoev B, Andersen JS (2007) Quantitative proteomic assessment of very early cellular signaling events. Nat Biotechnol 25:566–568
Kuttner V, Mack C, Gretzmeier C, Bruckner-Tuderman L, Dengjel J (2014) Loss of collagen VII is associated with reduced transglutaminase 2 abundance and activity. J Invest Dermatol 134:2381–2389
Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1:376–386
Hsu JL, Huang SY, Chow NH, Chen SH (2003) Stable-isotope dimethyl labeling for quantitative proteomics. Anal Chem 75:6843–6852
Zimmermann AC, Zarei M, Eiselein S, Dengjel J (2010) Quantitative proteomics for the analysis of spatio-temporal protein dynamics during autophagy. Autophagy 6:1009–1016
Dengjel J, Kratchmarova I, Blagoev B (2010) Mapping protein-protein interactions by quantitative proteomics. Methods Mol Biol 658:267–278
Kristensen AR, Schandorff S, Hoyer-Hansen M, Nielsen MO, Jaattela M, Dengjel J, Andersen JS (2008) Ordered organelle degradation during starvation-induced autophagy. Mol Cell Proteomics 7:2419–2428
Kruger M, Moser M, Ussar S, Thievessen I, Luber CA, Forner F, Schmidt S, Zanivan S, Fässler R, Mann M (2008) SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134:353–364
Sury MD, Chen JX, Selbach M (2010) The SILAC fly allows for accurate protein quantification in vivo. Mol Cell Proteomics 9:2173–2183
Blagoev B, Mann M (2006) Quantitative proteomics to study mitogen-activated protein kinases. Methods 40:243–250
Lossner C, Warnken U, Pscherer A, Schnolzer M (2011) Preventing arginine-to-proline conversion in a cell-line-independent manner during cell cultivation under stable isotope labeling by amino acids in cell culture (SILAC) conditions. Anal Biochem 412:123–125
Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M (2006) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 1:2856–2860
Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2:1896–1906
Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26:1367–1372
Cox J, Mann M (2012) 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. BMC Bioinformatics 13(Suppl 16):S12
Lozzio CB, Lozzio BB (1975) Human chronic myelogenous leukemia cell-line with positive Philadelphia chromosome. Blood 45:321–334
Klein E, Ben-Bassat H, Neumann H, Ralph P, Zeuthen J, Polliack A, Vanky F (1976) Properties of the K562 cell line, derived from a patient with chronic myeloid leukemia. Int J Cancer 18:421–431
Andersson LC, Nilsson K, Gahmberg CG (1979) K562--a human erythroleukemic cell line. Int J Cancer 23:143–147
Schlosser A, Vanselow JT, Kramer A (2005) Mapping of phosphorylation sites by a multi-protease approach with specific phosphopeptide enrichment and NanoLC-MS/MS analysis. Anal Chem 77:5243–5250
Acknowledgments
This study was supported in part by the Excellence Initiative of the German Research Foundation (GSC-4, Spemann Graduate School) and the José Carreras Leukämie Stiftung e.V. (project 13/12). TB is also supported by the Emmy-Noether and Heisenberg programs of the German Research Foundation (DFG).
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Halbach, S., Dengjel, J., Brummer, T. (2016). Quantitative Proteomics Analysis of Leukemia Cells. In: Li, S., Zhang, H. (eds) Chronic Myeloid Leukemia. Methods in Molecular Biology, vol 1465. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-4011-0_12
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DOI: https://doi.org/10.1007/978-1-4939-4011-0_12
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