Charting the molecular network of the drug target Bcr-Abl

The tyrosine kinase Bcr-Abl causes chronic myeloid leukemia and is the cognate target of tyrosine kinase inhibitors like imatinib. We have charted the protein–protein interaction network of Bcr-Abl by a 2-pronged approach. Using a monoclonal antibody we have first purified endogenous Bcr-Abl protein complexes from the CML K562 cell line and characterized the set of most tightly-associated interactors by MS. Nine interactors were subsequently subjected to tandem affinity purifications/MS analysis to obtain a molecular interaction network of some hundred cellular proteins. The resulting network revealed a high degree of interconnection of 7 “core” components around Bcr-Abl (Grb2, Shc1, Crk-I, c-Cbl, p85, Sts-1, and SHIP-2), and their links to different signaling pathways. Quantitative proteomics analysis showed that tyrosine kinase inhibitors lead to a disruption of this network. Certain components still appear to interact with Bcr-Abl in a phosphotyrosine-independent manner. We propose that Bcr-Abl and other drug targets, rather than being considered as single polypeptides, can be considered as complex protein assemblies that remodel upon drug action.

[1]  N. Rosenberg,et al.  Monoclonal antibodies specific for v-abl- and c-abl-encoded molecules , 1986, Journal of virology.

[2]  G. Daley,et al.  Induction of chronic myelogenous leukemia in mice by the P210bcr/abl gene of the Philadelphia chromosome. , 1990, Science.

[3]  A. Shevchenko,et al.  Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. , 1996, Analytical chemistry.

[4]  G. Superti-Furga,et al.  An intramolecular SH3-domain interaction regulates c-Abl activity , 1998, Nature Genetics.

[5]  A novel SH2-containing phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase (SHIP2) is constitutively tyrosine phosphorylated and associated with src homologous and collagen gene (SHC) in chronic myelogenous leukemia progenitor cells. , 1999 .

[6]  H. Erdjument-Bromage,et al.  A novel SH2-containing phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase (SHIP2) is constitutively tyrosine phosphorylated and associated with src homologous and collagen gene (SHC) in chronic myelogenous leukemia progenitor cells. , 1999, Blood.

[7]  D. Stokoe,et al.  5′ Phospholipid Phosphatase SHIP-2 Causes Protein Kinase B Inactivation and Cell Cycle Arrest in Glioblastoma Cells , 2000, Molecular and Cellular Biology.

[8]  W. Langdon,et al.  Cbl: many adaptations to regulate protein tyrosine kinases , 2001, Nature Reviews Molecular Cell Biology.

[9]  R. Tibshirani,et al.  Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Gary D Bader,et al.  A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules , 2001, Science.

[11]  R. Kobayashi,et al.  Identification, cDNA Cloning, and Targeted Deletion of p70, a Novel, Ubiquitously Expressed SH3 Domain-Containing Protein , 2002, Molecular and Cellular Biology.

[12]  A. Pendergast.  The Abl family kinases: mechanisms of regulation and signaling. , 2002, Advances in cancer research.

[13]  H. Iwasaki,et al.  Critical role for Gab2 in transformation by BCR/ABL. , 2002, Cancer cell.

[14]  M. Mann,et al.  Phosphotyrosine Mapping in Bcr/Abl Oncoprotein Using Phosphotyrosine-specific Immonium Ion Scanning* , 2003, Molecular & Cellular Proteomics.

[15]  Bernhard Kuster,et al.  Profiling Core Proteomes of Human Cell Lines by One-dimensional PAGE and Liquid Chromatography-Tandem Mass Spectrometry*S , 2003, Molecular & Cellular Proteomics.

[16]  J. Griffin,et al.  Molecular mechanisms of transformation by the BCR-ABL oncogene. , 2003, Seminars in hematology.

[17]  M. Mann,et al.  Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. , 2003, Analytical chemistry.

[18]  Howard L McLeod,et al.  Pharmacogenomics--drug disposition, drug targets, and side effects. , 2003, The New England journal of medicine.

[19]  P. Schultz,et al.  Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[20]  G. Superti-Furga,et al.  Rediscovering the sweet spot in drug discovery. , 2003, Drug discovery today.

[21]  Giulio Superti-Furga,et al.  A physical and functional map of the human TNF-α/NF-κB signal transduction pathway , 2004, Nature Cell Biology.

[22]  O. Witte,et al.  The BCR-ABL story: bench to bedside and back. , 2004, Annual review of immunology.

[23]  J. Yates,et al.  A model for random sampling and estimation of relative protein abundance in shotgun proteomics. , 2004, Analytical chemistry.

[24]  Oliver Hantschel,et al.  Regulation of the c-Abl and Bcr–Abl tyrosine kinases , 2004, Nature Reviews Molecular Cell Biology.

[25]  K. Parker,et al.  Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.

[26]  E. Birney,et al.  The International Protein Index: An integrated database for proteomics experiments , 2004, Proteomics.

[27]  B. Druker,et al.  Oncogenes and Tumor Suppressors (795 articles) , 2004 .

[28]  Michael Sattler,et al.  Structural basis for the cytoskeletal association of Bcr-Abl/c-Abl. , 2005, Molecular cell.

[29]  R. Ren,et al.  Mechanisms of BCR–ABL in the pathogenesis of chronic myelogenous leukaemia , 2005, Nature Reviews Cancer.

[30]  Jacques Colinge,et al.  Differential proteomics via probabilistic peptide identification scores. , 2005, Analytical chemistry.

[31]  A. Bauch,et al.  An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells , 2006, Nature Methods.

[32]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[33]  N. Nassar,et al.  A phosphatase activity of Sts-1 contributes to the suppression of TCR signaling. , 2007, Molecular cell.

[34]  Tony Pawson,et al.  Dynamic control of signaling by modular adaptor proteins. , 2007, Current opinion in cell biology.

[35]  John Kuriyan,et al.  The origin of protein interactions and allostery in colocalization , 2007, Nature.

[36]  M. Deininger,et al.  Bcr-Abl kinase domain mutations, drug resistance, and the road to a cure for chronic myeloid leukemia. , 2007, Blood.

[37]  R. V. van Etten.  chronic myeloid , 2022 .

[38]  Gerhard Dürnberger,et al.  Chemical proteomic profiles of the BCR-ABL inhibitors imatinib, nilotinib, and dasatinib reveal novel kinase and nonkinase targets. , 2007, Blood.

[39]  A. Barabasi,et al.  Drug—target network , 2007, Nature Biotechnology.

[40]  Bernhard Kuster,et al.  Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors , 2007, Nature Biotechnology.

[41]  B. Druker,et al.  SHP-2 phosphatase is required for hematopoietic cell transformation by Bcr-Abl. , 2007, Blood.

[42]  C. Schiffer,et al.  BCR-ABL tyrosine kinase inhibitors for chronic myelogenous leukemia. , 2007, The New England journal of medicine.

[43]  Jorge Cortes,et al.  Flying under the radar: the new wave of BCR–ABL inhibitors , 2007, Nature Reviews Drug Discovery.

[44]  R. Aebersold,et al.  Analysis of protein complexes using mass spectrometry , 2007, Nature Reviews Molecular Cell Biology.

[45]  G. Superti-Furga,et al.  The Btk tyrosine kinase is a major target of the Bcr-Abl inhibitor dasatinib , 2007, Proceedings of the National Academy of Sciences.

[46]  G. Superti-Furga,et al.  The chemokine interleukin‐8 and the surface activation protein CD69 are markers for Bcr–Abl activity in chronic myeloid leukemia , 2008, Molecular oncology.

[47]  A. Jankowska,et al.  Dasatinib, a small-molecule protein tyrosine kinase inhibitor, inhibits T-cell activation and proliferation. , 2008, Blood.

[48]  L. Zhao,et al.  Class I PI3K in oncogenic cellular transformation , 2008, Oncogene.

[49]  P. Bork,et al.  Drug Target Identification Using Side-Effect Similarity , 2008, Science.

[50]  G. Superti-Furga,et al.  Target spectrum of the BCR-ABL inhibitors imatinib, nilotinib and dasatinib , 2008, Leukemia & lymphoma.