Antibody-based detection of protein phosphorylation status to track the efficacy of novel therapies using nanogram protein quantities from stem cells and cell lines

Nature Protocols

Volumn 10, Issue 1, 2015, Pages 149-168

  Aspinall O'Dea, Mark ^a   Pierce, Andrew ^a   Pellicano, Francesca ^b   Williamson, Andrew J ^a   Scott, Mary T ^b   Walker, Michael J ^a   Holyoake, Tessa L ^b   Whetton, Anthony D ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BCR ABL PROTEIN; CRK LIKE PROTEIN; ISOPROTEIN; PROTEIN TYROSINE KINASE; PROTEIN TYROSINE KINASE INHIBITOR; PROTEIN TYROSINE PHOSPHATASE; ANTIBODY; CD45 ANTIGEN; NUCLEAR PROTEIN; PROTEIN; PTPRC PROTEIN, HUMAN; SIGNAL TRANSDUCING ADAPTOR PROTEIN; TYROSINE;

ANTIBODY DETECTION; ARTICLE; CELL LYSATE; CELL POPULATION; CHRONIC MYELOID LEUKEMIA; HIGH THROUGHPUT SCREENING; HUMAN; IN VITRO STUDY; ISOELECTRIC FOCUSING; LIMIT OF DETECTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STEM CELL; TREATMENT RESPONSE; DIAGNOSTIC USE; FLOW CYTOMETRY; METABOLISM; PHOSPHORYLATION; PROCEDURES; WESTERN BLOTTING;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; ANTIBODIES; ANTIGENS, CD45; BLOTTING, WESTERN; FLOW CYTOMETRY; FUSION PROTEINS, BCR-ABL; HIGH-THROUGHPUT SCREENING ASSAYS; ISOELECTRIC FOCUSING; LEUKEMIA, MYELOGENOUS, CHRONIC, BCR-ABL POSITIVE; NUCLEAR PROTEINS; PHOSPHORYLATION; PROTEINS; STEM CELLS; TYROSINE;

EID: 84925959802     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2015.007     Document Type: Article

References (56)

1. O'Neill, R.A. et al. Isoelectric focusing technology quantifies protein signaling in 25 cells. Proc. Natl. Acad. Sci. USA 103, 16153-16158 (2006).
2. Fan, A.C. et al. Nanofluidic proteomic assay for serial analysis of oncoprotein activation in clinical specimens. Nat. Med. 15, 566-571 (2009).
3. Maiso, P. et al. Defining the role of TORC1/2 in multiple myeloma. Blood 118, 6860-6870 (2011).
4. Kentsis, A. et al. Autocrine activation of the MET receptor tyrosine kinase in acute myeloid leukemia. Nat. Med. 18, 1118-1122 (2012).
5. Williamson, A.J.K. et al. A specific PTPRC/CD45 phosphorylation event governed by stem cell chemokine CXCL12 regulates primitive hematopoietic cell motility. Mol. Cell. Proteom. 12, 3319-3329 (2013).
6. Brown, S. et al. Monocyte-derived dendritic cells from chronic myeloid leukaemia have abnormal maturation and cytoskeletal function that is associated with defective localisation and signalling by normal ABL1 protein. Eur. J. Haematol. 93, 96-102 (2014).
7. Al-Hajj, M., Wicha, M.S., Benito-Hernandez, A., Morrison, S.J., Clarke, M.F. Prospective identification of tumorigenic breast cancer cells. Proc. Natl. Acad. Sci. USA 100, 3983-3988 (2003).
8. Li, C. et al. Identification of pancreatic cancer stem cells. Cancer Res. 67, 1030-1037 (2007).
9. Prince, M. et al. Identification of a subpopulation of cells with cancer stem cell properties in head and neck squamous cell carcinoma. Proc. Natl. Acad. Sci. USA 104, 973-981 (2007).
10. Mitelman, F., Johansson, B., Mertens, F. The impact of translocations and gene fusions on cancer causation. Nat. Rev. Cancer 7, 233-245 (2007).
11. Sanz, M., Burnett, A., Lo-Coco, F., Lowenberg, B. FLT3 inhibition as a targeted therapy for acute myeloid leukemia. Curr. Opin. Oncol. 21, 594-600 (2009).
12. Verstovsek, S. Therapeutic potential of JAK2 inhibitors. Hematol. Am. Soc. Hematol. Educ. Prog. 2009, 636-642 (2009).
13. Rowley, J.D. Letter: a new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature 243, 290-293 (1973).
14. Groffen, J. et al. Philadelphia chromosomal breakpoints are clustered within a limited region, bcr, on chromosome 22. Cell 36, 93-99 (1984).
15. Druker, B.J. et al. Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr-Abl-positive cells. Nat. Med. 2, 561-566 (1996).
16. Gambacorti-Passerini, C. et al. Inhibition of the ABL kinase activity blocks the proliferation of BCR/ABL+ leukemic cells and induces apoptosis. Blood Cells Mol. Dis. 23, 380-394 (1997).
17. Hamilton, A. et al. BCR-ABL activity and its response to drugs can be determined in CD34+ CML stem cells by CrkL phosphorylation status using flow cytometry. Leukemia 20, 1035-1039 (2006).
18. Copland, M. et al. Dasatinib (BMS-354825) targets an earlier progenitor population than imatinib in primary CML but does not eliminate the quiescent fraction. Blood 107, 4532-4539 (2006).
19. Hochhaus, A. et al. Six-year follow-up of patients receiving imatinib for the first-line treatment of chronic myeloid leukemia. Leukemia 23, 1054-1061 (2009).
20. Hochhaus, A. et al. Favorable long-term follow-up results over 6 years for response, survival, and safety with imatinib mesylate therapy in chronic-phase chronic myeloid leukemia after failure of interferon-? treatment. Blood 111, 1039-1043 (2008).
21. O'Hare, T., Zabriskie, M.S., Eiring, A.M., Deininger, M.W. Pushing the limits of targeted therapy in chronic myeloid leukaemia. Nat. Rev. Cancer 12, 513-526 (2012).
22. Graham, S.M. et al. Primitive, quiescent, Philadelphia-positive stem cells from patients with chronic myeloid leukemia are insensitive to STI571. Blood 99, 319-325 (2002).
23. Holtz, M.S. Imatinib mesylate (STI571) inhibits growth of primitive malignant progenitors in chronic myelogenous leukemia through reversal of abnormally increased proliferation. Blood 99, 3792-3800 (2002).
24. Mahon, F.X. et al. Discontinuation of imatinib in patients with chronic myeloid leukaemia who have maintained complete molecular remission for at least 2 years: the prospective, multicentre Stop Imatinib (STIM) trial. Lancet Oncol. 11, 1029-1035 (2010).
25. Chu, S. et al. Persistence of leukemia stem cells in chronic myelogenous leukemia patients in prolonged remission with imatinib treatment. Blood 118, 5565-5572 (2011).
26. Rousselot, P. et al. Imatinib mesylate discontinuation in patients with chronic myelogenous leukemia in complete molecular remission for more than 2 years. Blood 109, 58-60 (2007).
27. Druker, B.J. et al. Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. N. Engl. J. Med. 355, 2408-2417 (2006).
28. Addona, T.A. et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 27, 633-641 (2009).
29. Hjelle, S.M. et al. Clinical proteomics of myeloid leukemia. Genome Med. 2, 41 (2010).
30. de Jong, R., ten Hoeve, J., Heisterkamp, N., Groffen, J. Tyrosine 207 in CRKL is the BCR/ABL phosphorylation site. Oncogene 14, 507-513 (1997).
31. Seo, J.H. et al. A specific need for CRKL in p210BCR-ABL-induced transformation of mouse hematopoietic progenitors. Cancer Res. 70, 7325-7335 (2010).
32. Konig, H. et al. Effects of dasatinib on SRC kinase activity and downstream intracellular signaling in primitive chronic myelogenous leukemia hematopoietic cells. Cancer Res. 68, 9624-9633 (2008).
33. Oda, T. et al. Crkl is the major tyrosine-phosphorylated protein in neutrophils from patients with chronic myelogenous leukemia. J. Biol. Chem. 269, 22925-22928 (1994).
34. Liu, X. et al. Constrained selected reaction monitoring: quantification of selected post-translational modifications and protein isoforms. Methods 61, 304-312 (2013).
35. Maxwell, S.A. et al. Analysis of p210bcr-abl tyrosine protein kinase activity in various subtypes of Philadelphia chromosome-positive cells from chronic myelogenous leukemia patients. Cancer Res. 47, 1731-1739 (1987).
36. Copland, M., Hamilton, A., Holyoake, T.L. Response: conventional western blotting techniques will not reliably quantify p210 BCR-ABL. Blood 109, 1336 (2007).
37. Bendall, S.C., Nolan, G.P. From single cells to deep phenotypes in cancer. Nat. Biotechnol. 30, 639-647 (2012).
38. Irish, J.M. et al. Single-cell profiling of potentiated phospho-protein networks in cancer cells. Cell 118, 217-228 (2004).
39. Bendall, S.C., Nolan, G.P., Roederer, M., Chattopadhyay, P.K. A deep profiler's guide to cytometry. Trends Immunol. 33, 323-332 (2012).
40. Hamilton, A., Alhashimi, F., Myssina, S., Jorgensen, H.G., Holyoake, T.L. Optimization of methods for the detection of BCR-ABL activity in Philadelphia-positive cells. Exp. Hematol. 37, 395-401 (2009).
41. Protein Simple, Inc. Application Brief, Vol. 1023 http://www.proteinsimple.com/technical-library.html?product=simplewestern&def-list=list (Protein Simple, 2010).
42. Hamilton, A. et al. Chronic myeloid leukemia stem cells are not dependent on Bcr-Abl kinase activity for their survival. Blood 119, 1501-1511 (2012).
43. Hornbeck, P.V. et al. PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40, D261-D270 (2012).
44. Konopka, J.B., Watanabe, S.M., Witte, O.N. An alteration of the human c-abl protein in K562 leukemia cells unmasks associated tyrosine kinase activity. Cell 37, 1035-1042 (1984).
45. Golub, T.R., Barker, G.F., Lovett, M., Gilliland, D.G. Fusion of PDGF receptor ? to a novel ets-like gene, tel, in chronic myelomonocytic leukemia with t(5;12) chromosomal translocation. Cell 77, 307-316 (1994).
46. Cools, J. et al. A tyrosine kinase created by fusion of the PDGFRA and FIP1L1 genes as a therapeutic target of imatinib in idiopathic hypereosinophilic syndrome. N. Engl. J. Med. 348, 1201-1214 (2003).
47. Morris, S.W. et al. Fusion of a kinase gene, ALK, to a nucleolar protein gene, NPM, in non-Hodgkin's lymphoma. Science 263, 1281-1284 (1994).
48. Nagata, H. et al. Identification of a point mutation in the catalytic domain of the proto-oncogene c-kit in peripheral blood mononuclear cells of patients who have mastocytosis with an associated hematologic disorder. Proc. Natl. Acad. Sci. USA 92, 10560-10564 (1995).
49. Ziegler, S. et al. A novel protein kinase D phosphorylation site in the tumor suppressor Rab interactor 1 is critical for coordination of cell migration. Mol. Biol. Cell 22, 570-580 (2011).
50. Shah, N.P. et al. Transient potent BCR-ABL inhibition is sufficient to commit chronic myeloid leukemia cells irreversibly to apoptosis. Cancer Cell 14, 485-493 (2008).
51. Young, M.A. et al. Structure of the kinase domain of an imatinib-resistant Abl mutant in complex with the Aurora kinase inhibitor VX-680. Cancer Res. 66, 1007-1014 (2006).
52. Zipfel, P.A., Zhang, W., Quiroz, M., Pendergast, A.M. Requirement for Abl kinases in T cell receptor signaling. Curr. Biol. 14, 1222-1231 (2004).
53. Uemura, N., Griffin, J.D. The adapter protein Crkl links Cbl to C3G after integrin ligation and enhances cell migration. J. Biol. Chem. 274, 37525-37532 (1999).
54. Senechal, K., Heaney, C., Druker, B., Sawyers, C.L. Structural requirements for function of the Crkl adapter protein in fibroblasts and hematopoietic cells. Mol. Cell Biol. 18, 5082-5090 (1998).
55. Nichols, G.L. et al. Identification of CRKL as the constitutively phosphorylated 39-kDa tyrosine phosphoprotein in chronic myelogenous leukemia cells. Blood 84, 2912-2918 (1994).
56. ten Hoeve, J., Arlinghaus, R.B., Guo, J.Q., Heisterkamp, N., Groffen, J. Tyrosine phosphorylation of CRKL in Philadelphia+ leukemia. Blood 84, 1731-1736 (1994).