Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP)

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Wang, Jigang ^a   Zhang, Chong Jing ^b   Zhang, Jianbin ^c   He, Yingke ^d   Lee, Yew Mun ^a   Chen, Songbi ^b   Lim, Teck Kwang ^a   Ng, Shukie ^c   Shen, Han Ming ^c   Lin, Qingsong ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b INSTITUTE OF TROPICAL BIOSCIENCE AND BIOTECHNOLOGY   (China)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^d SINGAPORE GENERAL HOSPITAL   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLSALICYLIC ACID; PEPTIDE;

ACETYLATION; BINDING SITE; CHEMISTRY; DRUG DEVELOPMENT; DRUG EFFECTS; HUMAN; ISOLATION AND PURIFICATION; METABOLISM; PROTEIN MICROARRAY; PROTEOMICS;

ACETYLATION; ASPIRIN; BINDING SITES; DRUG DISCOVERY; HUMANS; PEPTIDES; PROTEIN ARRAY ANALYSIS; PROTEOMICS;

EID: 84939439840     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep07896     Document Type: Article

References (51)

1. Eggert, U. S. The why and how of phenotypic small-molecule screens. Nat. Chem. Biol. 9, 206-9 (2013).
2. Ziegler, S., Pries, V., Hedberg, C.,Waldmann, H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew. Chem. Int. Ed. Engl. 52, 2744-92 (2013).
3. Speers, A. E., Adam, G. C., Cravatt, B. F. Activity-based protein profiling in vivo using a copper(i)-catalyzed azide-alkyne [3 12] cycloaddition. J. Am. Chem. Soc. 125, 4686-4687 (2003).
4. Ovaa, H. et al. Chemistry in Living Cells: Detection of Active Proteasomes by a Two-Step Labeling Strategy. Angew. Chem. Int. Ed. 115, 3754-3757 (2003).
5. Evans, M. J., Cravatt, B. F. Mechanism-based profiling of enzyme families. Chem. Rev. 106, 3279-3301 (2006).
6. Paulick, M., Bogyo, M. Application of activity-based probes to the study of enzymes involved in cancer progression. Curr. Opin. Genet. Dev. 18, 97-106 (2008).
7. Fonović,M., Bogyo, M. Activity Based Probes as a tool for Functional Proteomic Analysis of Proteases. Expert Rev. Proteomics. 5, 721-730 (2008).
8. Böttcher, T., Pitscheider, M., Sieber, S. A. Natural products and their biological targets: proteomic and metabolomic labeling strategies. Angew. Chem. Int. Ed. 49, 2680-2698 (2010).
9. Willems, L. I. et al. Bioorthogonal chemistry: applications in activity-based protein profiling. Acc. Chem. Res. 44, 718-729 (2011).
10. Su, Y. et al. Target identification of biologically active small molecules via in situ methods. Curr. Opin. Chem. Biol. 17, 768-75 (2013).
11. Wirth, T., Schmuck, K. Duocarmycin analogues target aldehyde dehydrogenase 1 in lung cancer cells. Angew. Chemie 51, 2874-2877 (2012).
12. Okerberg, E. S. et al. High-resolution functional proteomics by active-site peptide profiling. Proc. Natl. Acad. Sci. U. S. A. 102, 4996-5001 (2005).
13. Adam, G. C., Burbaum, J., Kozarich, J. W., Patricelli, M. P., Cravatt, B. F. Mapping enzyme active sites in complex proteomes. J. Am. Chem. Soc. 126, 1363-8 (2004).
14. Hekmat, O., Kim, Y.-W., Williams, S. J., He, S., Withers, S. G. Active-site peptide "fingerprinting" of glycosidases in complex mixtures by mass spectrometry. Discovery of a novel retaining beta-1,4-glycanase in Cellulomonas fimi. J. Biol. Chem. 280, 35126-35 (2005).
15. Speers, A. E., Cravatt, B. F. A tandem orthogonal proteolysis strategy for highcontent chemical proteomics. J. Am. Chem. Soc. 127, 10018-9 (2005).
16. Weerapana, E., Speers, A. E., Cravatt, B. F. Tandem orthogonal proteolysisactivity-based protein profiling (TOP-ABPP)-a general method for mapping sites of probe modification in proteomes. Nat. protoc. 2, 1414-25 (2007).
17. Bantscheff, M. et al. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotechnol. 25, 1035-1044 (2007).
18. Sharma, K. et al. Proteomics strategy for quantitative protein interaction profiling in cell extracts. Nat. Methods 6, 741-744 (2009).
19. Ong, S. et al. Identifying the proteins to which small-molecule probes and drugs bind in cells. Proc. Natl. Acad. Sci. USA 106, 4617-4622 (2009).
20. Li, X. et al. Quantitative chemical proteomics approach to identify posttranslational modification-mediated protein-protein interactions. J. Am. Chem. Soc. 134, 1982-1985 (2012).
21. Rudolf, G. C.,Heydenreuter, W., Sieber, S. A. Chemical proteomics: ligation and cleavage of protein modifications. Curr. Opin. Chem. Biol. 17, 110-7 (2013).
22. Szychowski, J. et al. Cleavable biotin probes for labeling of biomolecules via azidealkyne cycloaddition. J. Am. Chem. Soc. 132, 18351-60 (2010).
23. Fonović,M., Verhelst, S. H. L., Sorum,M. T.&Bogyo, M. Proteomics evaluation of chemically cleavable activity-based probes. Mol. Cell. Proteomics 6, 1761-70 (2007).
24. Geurink, P. P. et al. A cleavable linker based on the levulinoyl ester for activitybased protein profiling. Angew. Chem. Int. Ed. Engl. 49, 6802-5 (2010).
25. Nishihara, R. et al. Aspirin use and risk of colorectal cancer according to BRAF mutation status. JAMA 309, 2563-71 (2013).
26. Liao, X. et al. Aspirin use, tumor PIK3CA mutation, and colorectal-cancer survival. N. Engl. J. Med. 367, 1596-606 (2012).
27. Marimuthu, S. et al. Aspirin acetylates multiple cellular proteins in HCT-116 colon cancer cells: Identification of novel targets. Int. J. Oncol. 39, 1273-83 (2011).
28. Alfonso, L. F., Srivenugopal, K. S., Bhat, G. J. Does aspirin acetylate multiple cellular proteins (Review) Mol. Med. Rep. 2, 533-537 (2009).
29. Yang, Y.-Y., Ascano, J. M., Hang, H. C. Bioorthogonal chemical reporters for monitoring protein acetylation. J. Am. Chem. Soc. 132, 3640-1 (2010).
30. Din, F. V. N. et al. Aspirin inhibits mTOR signaling, activates AMP-activated protein kinase, and induces autophagy in colorectal cancer cells. Gastroenterology 142, 1504-15.e3 (2012).
31. Hardwick, J. C. H., van Santen, M., van den Brink, G. R., van Deventer, S. J. H., Peppelenbosch,M. P. DNA array analysis of the effects of aspirin on colon cancer cells: involvement of Rac1. Carcinogenesis 25, 1293-8 (2004).
32. Pathi, S. et al. Aspirin inhibits colon cancer cell and tumor growth and downregulates specificity protein (Sp) transcription factors. PLoS One 7, e48208 (2012).
33. Wang, J. et al. A quantitative chemical proteomics approach to profile the specific cellular targets of andrographolide, a promising anticancer agent that suppresses tumor metastasis. Mol. Cell. Proteomics 13, 876-86 (2014).
34. Ross, P. L. et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics. 3, 1154-1169 (2004).
35. Strahl, B. D., Allis, C. D. The language of covalent histone modifications. Nature 403, 41-45 (2000).
36. Jenuwein, T., Allis, C. D. Translating the histone code. Science 293, 1074-80 (2001).
37. Dieterich, D. C. et al. Labeling, detection and identification of newly synthesized proteomes with bioorthogonal non-canonical amino-acid tagging. Nat. Protoc. 2, 532-40 (2007).
38. Zoncu, R., Efeyan, A., Sabatini, D. M. mTOR: from growth signal integration to cancer, diabetes and ageing. Nat. Rev. Mol. Cell Biol. 12, 21-35 (2011).
39. Inoki, K., Guan, K.-L. Complexity of the TOR signaling network. Trends Cell Biol. 16, 206-12 (2006).
40. Sengupta, S., Peterson, T. R., Sabatini, D. M. Regulation of the mTOR complex 1 pathway by nutrients, growth factors, and stress. Mol. Cell 40, 310-22 (2010).
41. Mizushima, N. The role of the Atg1/ULK1 complex in autophagy regulation. Curr. Opin. Cell Biol. 22, 132-9 (2010).
42. Hosokawa, N. et al. Nutrient-dependent mTORC1 Association with the ULK1-Atg13-FIP200 Complex Required for Autophagy. Mol Biol Cell 20, 1981-1991 (2009).
43. Luzio, J. P., Pryor, P. R., Bright, N. A. Lysosomes: fusion and function. Nat. Rev. Mol. Cell Biol. 8, 622-32 (2007).
44. Saftig, P., Klumperman, J. Lysosome biogenesis and lysosomal membrane proteins: trafficking meets function. Nat. Rev. Mol. Cell Biol. 10, 623-35 (2009).
45. Eskelinen, E.-L., Saftig, P. Autophagy: a lysosomal degradation pathway with a central role in health and disease. Biochim. Biophys. Acta 1793, 664-73 (2009).
46. Zhou, J. et al. Activation of lysosomal function in the course of autophagy via mTORC1 suppression and autophagosome-lysosome fusion. Cell Res. 23, 508-23 (2013).
47. Shen, H.-M., Mizushima, N. At the end of the autophagic road: an emerging understanding of lysosomal functions in autophagy. Trends Biochem. Sci. 39, 61-71 (2013).
48. Bateman, L., Zaro, B. An Alkyne-Aspirin Chemical Reporter for the Detection of Aspirin-Dependent Protein Modification in Living Cells. J. Am. Chem. Soc. 135, 14568-14573 (2013).
49. Lu, J.-J., Pan, W., Hu, Y.-J., Wang, Y.-T. Multi-target drugs: the trend of drug research and development. PLoS One 7, e40262 (2012).
50. Tang, L. A. L. et al. High-performance graphene-titania platform for detection of phosphopeptides in cancer cells. Anal. Chem. 84, 6693-6700 (2012).
51. Ghosh, D. et al. Identification of Key Players for Colorectal Cancer Metastasis by iTRAQ Quantitative Proteomics Profiling of Isogenic SW480 and SW620 Cell Lines. J. Proteome Res. 10, 4373-4387 (2011).