Facile discovery of cell-surface protein targets of cancer cell aptamers

Molecular and Cellular Proteomics

Volumn 14, Issue 10, 2015, Pages 2692-2700

  Bing, Tao ^a,b   Shangguan, Dihua ^a   Wang, Yinsheng ^b  

^a INSTITUTE OF CHEMISTRY   (China)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA4 INTEGRIN; APTAMER; BINDING PROTEIN; CELL SURFACE PROTEIN; L SELECTIN; OLIGODEOXYNUCLEOTIDE; SMALL INTERFERING RNA; ARGININE; CARBON; LYSINE; NITROGEN;

ARTICLE; CANCER CELL; CELL SURFACE; ELECTROSPRAY MASS SPECTROMETRY; FLOW CYTOMETRY; HUMAN; HUMAN CELL; LIMIT OF QUANTITATION; LIQUID CHROMATOGRAPHY; LYMPHOMA; MYELOMA; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CROSS LINKING; PROTEIN DEPLETION; PROTEIN EXPRESSION; PROTEIN TARGETING; PROTEOMICS; QUANTITATIVE ANALYSIS; TANDEM MASS SPECTROMETRY; VALIDATION STUDY; ISOTOPE LABELING; METABOLISM; TUMOR CELL LINE;

APTAMERS, NUCLEOTIDE; ARGININE; CARBON ISOTOPES; CELL LINE, TUMOR; FLOW CYTOMETRY; HUMANS; INTEGRIN ALPHA4; ISOTOPE LABELING; L-SELECTIN; LYSINE; NITROGEN ISOTOPES; PROTEOMICS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TANDEM MASS SPECTROMETRY;

EID: 84942910177     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M115.051243     Document Type: Article

References (37)

1. Stewart, B., and Wild, C. P. (2014) World Cancer Report 2014 IARC Nonserial Publication, International Agency for Research on Cancer, Lyon, France
2. Mäbert, K., Cojoc, M., Peitzsch, C., Kurth, I., Souchelnytskyi, S., and Dubrovska, A. (2014) Cancer biomarker discovery: Current status and future perspectives. Int. J. Radiat. Biol. 90, 659-677
3. Anderson, N. L., Polanski, M., Pieper, R., Gatlin, T., Tirumalai, R. S., Conrads, T. P., Veenstra, T. D., Adkins, J. N., Pounds, J. G., and Fagan, R. (2004) The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol. Cell. Proteomics 3, 311-326
4. Ellington, A. D., and Szostak, J. W. (1990) Invitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822
5. Tuerk, C., and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510
6. Shangguan, D., Li, Y., Tang, Z., Cao, Z. C., Chen, H. W., Mallikaratchy, P., Sefah, K., Yang, C. J., and Tan, W. (2006) Aptamers evolved from live cells as effective molecular probes for cancer study. Proc. Natl. Acad. Sci. U.S.A. 103, 11838-11843
7. Ye, M., Hu, J., Peng, M., Liu, J., Liu, J., Liu, H., Zhao, X., and Tan, W. (2012) Generating aptamers by cell-SELEX for applications in molecular medicine. Int. J. Mol. Sci. 13, 3341-3353
8. Shangguan, D., Cao, Z., Meng, L., Mallikaratchy, P., Sefah, K., Wang, H., Li, Y., and Tan, W. (2008) Cell-specific aptamer probes for membrane protein elucidation in cancer cells. J. Proteome Res. 7, 2133-2139
9. Yang, M., Jiang, G., Li, W., Qiu, K., Zhang, M., Carter, C. M., Al-Quran, S. Z., and Li, Y. (2014) Developing aptamer probes for acute myelogenous leukemia detection and surface protein biomarker discovery. J. Hematol. Oncol. 7:5
10. Berezovski, M. V., Lechmann, M., Musheev, M. U., Mak, T. W., and Krylov, S. N. (2008) Aptamer-facilitated biomarker discovery (AptaBiD). J. Am. Chem. Soc. 130, 9137-9143
11. Mallikaratchy, P., Tang, Z., Kwame, S., Meng, L., Shangguan, D., and Tan, W. (2007) Aptamer directly evolved from live cells recognizes membrane bound immunoglobin heavy mu chain in Burkitt's lymphoma cells. Mol. Cell. Proteomics 6, 2230-2238
12. Van Simaeys, D., Turek, D., Champanhac, C., Vaizer, J., Sefah, K., Zhen, J., Sutphen, R., and Tan, W. (2014) Identification of cell membrane protein stress-induced phosphoprotein 1 as a potential ovarian cancer biomarker using aptamers selected by cell systematic evolution of ligands by exponential enrichment. Anal. Chem. 86, 4521-4527
13. Mann, M. (2006) Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol. 7, 952-958
14. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., and 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
15. Shangguan, D., Cao, Z. C., Li, Y., and Tan, W. (2007) Aptamers evolved from cultured cancer cells reveal molecular differences of cancer cells in patient samples. Clin. Chem. 53, 1153-1155
16. Chaar, V., Laurance, S., Lapoumeroulie, C., Cochet, S., De Grandis, M., Colin, Y., Elion, J., Le Van Kim, C., and El Nemer, W. (2014) Hydroxycarbamide decreases sickle reticulocyte adhesion to resting endothelium by inhibiting endothelial lutheran/basal cell adhesion molecule (Lu/ BCAM) through phosphodiesterase 4A activation. J. Biol. Chem. 289, 11512-11521
17. Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V., and Mann, M. (2006) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protocols 1, 2856-2860
18. Chandler, C. S., and Ballard, F. J. (1986) Multiple biotin-containing proteins in 3T3-L1 cells. Biochem. J. 237, 123-130
19. Raffler, N. A., Rivera-Nieves, J., and Ley, K. (2005) L-selectin in inflammation, infection and immunity. Drug Disc. Today Ther. Strateg. 2, 213-220
20. Yang, S., Liu, F., Wang, Q. J., Rosenberg, S. A., and Morgan, R. A. (2011) The shedding of CD62L (L-selectin) regulates the acquisition of lytic activity in human tumor reactive T lymphocytes. PLoS One 6, e22560
21. Schlesinger, M., and Bendas, G. (2015) Contribution of very late antigen-4 (VLA-4) integrin to cancer progression and metastasis. Cancer Metastasis Rev. 1-17
22. Jin, J. K., Tien, P. C., Cheng, C. J., Song, J. H., Huang, C., Lin, S. H., and Gallick, G. E. (2015) Talin1 phosphorylation activates beta1 integrins: A novel mechanism to promote prostate cancer bone metastasis. Oncogene 34, 1811-1821
23. Calderwood, D. A., Zent, R., Grant, R., Rees, D. J., Hynes, R. O., and Ginsberg, M. H. (1999) The Talin head domain binds to integrin beta subunit cytoplasmic tails and regulates integrin activation. J. Biol. Chem. 274, 28071-28074
24. Tan, W., Donovan, M. J., and Jiang, J. (2013) Aptamers from cell-based selection for bioanalytical applications. Chem. Rev. 113, 2842-2862
25. Tang, Z., Shangguan, D., Wang, K., Shi, H., Sefah, K., Mallikratchy, P., Chen, H. W., Li, Y., and Tan, W. (2007) Selection of aptamers for molecular recognition and characterization of cancer cells. Anal. Chem. 79, 4900-4907
26. Chen, H. W., Medley, C. D., Sefah, K., Shangguan, D., Tang, Z., Meng, L., Smith, J. E., and Tan, W. (2008) Molecular recognition of small-cell lung cancer cells using aptamers. ChemMedChem 3, 991-1001
27. Shangguan, D., Meng, L., Cao, Z. C., Xiao, Z., Fang, X., Li, Y., Cardona, D., Witek, R. P., Liu, C., and Tan, W. (2008) Identification of liver cancerspecific aptamers using whole live cells. Anal. Chem. 80, 721-728
28. Fang, X., and Tan, W. (2010) Aptamers generated from cell-SELEX for molecular medicine: A chemical biology approach. Acc. Chem. Res. 43, 48-57
29. Wang, Y., Luo, Y., Bing, T., Chen, Z., Lu, M., Zhang, N., Shangguan, D., and Gao, X. (2014) DNA aptamer evolved by cell-SELEX for recognition of prostate cancer. PLoS One 9, e100243
30. Li, W. M., Bing, T., Wei, J. Y., Chen, Z. Z., Shangguan, D. H., and Fang, J. (2014) Cell-SELEX-based selection of aptamers that recognize distinct targets on metastatic colorectal cancer cells. Biomaterials 35, 6998-7007
31. Sefah, K., Bae, K. M., Phillips, J. A., Siemann, D. W., Su, Z., McClellan, S., Vieweg, J., and Tan, W. (2013) Cell-based selection provides novel molecular probes for cancer stem cells. Int. J. Cancer 132, 2578-2588
32. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., Purkayastha, S., Juhasz, P., Martin, S., Bartlet-Jones, M., He, F., Jacobson, A., and Pappin, D. J. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154-1169
33. Thompson, A., Schäfer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., Neumann, T., Johnstone, R., Mohammed, A. K., and Hamon, C. (2003) Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75, 1895-1904
34. Burgess, M., Gill, D., Singhania, R., Cheung, C., Chambers, L., Renyolds, B. A., Smith, L., Mollee, P., Saunders, N., and McMillan, N. A. (2013) CD62L as a therapeutic target in chronic lymphocytic leukemia. Clin. Cancer Res. 19, 5675-5685
35. Majid, A., Lin, T. T., Best, G., Fishlock, K., Hewamana, S., Pratt, G., Yallop, D., Buggins, A. G., Wagner, S., Kennedy, B. J., Miall, F., Hills, R., Devereux, S., Oscier, D. G., Dyer, M. J., Fegan, C., and Pepper, C. (2011) CD49d is an independent prognostic marker that is associated with CXCR4 expression in CLL. Leukemia Res. 35, 750-756
36. Polman, C. H., O'Connor, P. W., Havrdova, E., Hutchinson, M., Kappos, L., Miller, D. H., Phillips, J. T., Lublin, F. D., Giovannoni, G., Wajgt, A., Toal, M., Lynn, F., Panzara, M. A., Sandrock, A. W., and Investigators, A. (2006) A randomized, placebo-controlled trial of natalizumab for relapsing multiple sclerosis. N. Engl. J. Med. 354, 899-910
37. Esposito, C. L., Catuogno, S., de Franciscis, V., and Cerchia, L. (2011) New insight into clinical development of nucleic acid aptamers. Discov. Med. 11, 487-496