Activity-based proteomics: Identification of ABHD11 and ESD activities as potential biomarkers for human lung adenocarcinoma

Journal of Proteomics

Volumn 74, Issue 10, 2011, Pages 1884-1894

  Wiedl, T ^a,b   Arni, S ^a   Roschitzki, B ^c   Grossmann, J ^c   Collaud, S ^a   Soltermann, A ^d   Hillinger, S ^a   Aebersold, R ^b,e   Weder, W ^a  

^a UNIVERSITY HOSPITAL ZURICH   (Switzerland)

^b ETH ZURICH   (Switzerland)

^c FUNCTIONAL GENOMICS CENTER ZURICH   (Switzerland)

^d UHZ   (Switzerland)

^e UZH   (Switzerland)

Author keywords

Activity based proteomics; Biomarker; Non small cell lung cancer (NSCLC)

Indexed keywords

ESTERASE; SERINE DEHYDRATASE; TUMOR MARKER;

ADULT; AGED; ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; DISTANT METASTASIS; ENZYME ACTIVITY; FEMALE; FOLLOW UP; HUMAN; HUMAN TISSUE; LUNG ADENOCARCINOMA; LUNG PARENCHYMA; MALE; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS;

ADENOCARCINOMA; CARBOXYLESTERASE; HUMANS; LUNG NEOPLASMS; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SERINE PROTEASES; TUMOR MARKERS, BIOLOGICAL;

EID: 80052032307     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2011.04.030     Document Type: Article

References (57)

1. Parkin D.M., Pisani P., Ferlay J. Global cancer statistics. CA Cancer J Clin 1999, 49:33-64. 1.
2. Garcia M., Jemal A., Ward E.M., Center M.M., Hao Y., Siegel R.L., et al. Global Cancer Facts & Figures 2007, American Cancer Society 2007, Atlanta, GA.
3. Brambilla E., L, Sylvie Histopathology of lung tumors. Textbook of lung cancer 2008, 61-74. Informa Healthcare, London, UK. second ed. H. Hanson (Ed.).
4. Chen G., Gharib T.G., Wang H., Huang C.C., Kuick R., Thomas D.G., et al. Protein profiles associated with survival in lung adenocarcinoma. Proc Natl Acad Sci U S A 2003, 100:13537-13542.
5. Kaira K., Oriuchi N., Imai H., Shimizu K., Yanagitani N., Sunaga N., et al. Prognostic significance of L-type amino acid transporter 1 expression in resectable stage I-III nonsmall cell lung cancer. Br J Cancer 2008, 98:742-748.
6. Dusmet M., G, Peter Staging, classification, and prognosis. Textbook of lung cancer 2008, 97-122. Informa Healthcare, London, UK. second ed. H. Hanson (Ed.).
7. Mullon J., O, Eric Clinical diagnosis and basic evaluation. Textbook of lung cancer 2008, 75-96. Informa Healthcare, London, UK. H. Hanson (Ed.).
8. Gas Selvaggi, Vittorio Giorgio The future. Textbook of lung cancer 2008, 264-274. Informa Healthcare, London, UK. second ed. H. Hanson (Ed.).
9. Sugimura H., Nichols F.C., Yang P., Allen M.S., Cassivi S.D., Deschamps C., et al. Survival after recurrent nonsmall-cell lung cancer after complete pulmonary resection. Ann Thorac Surg 2007, 83:409-417. discussioin 17-8.
10. Ji P., Diederichs S., Wang W., Boing S., Metzger R., Schneider P.M., et al. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 2003, 22:8031-8041.
11. Haugen A., M, Steen Etiology of lung cancer. Textbook of lung cancer 2008, 61-74. Informa Healthcare, London, UK. second ed. H. Hanson (Ed.).
12. Sawyers C.L. The cancer biomarker problem. Nature 2008, 452:548-552.
13. Rodriguez-Pineiro A.M., Blanco-Prieto S., Sanchez-Otero N., Rodriguez-Berrocal F.J., de la Cadena M.P. On the identification of biomarkers for non-small cell lung cancer in serum and pleural effusion. J Proteomics 2010, 73:1511-1522.
14. Gygi S.P., Rochon Y., Franza B.R., Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 1999, 19:1720-1730.
15. Alaiya A.A., Franzen B., Auer G., Linder S. Cancer proteomics: from identification of novel markers to creation of artifical learning models for tumor classification. Electrophoresis 2000, 21:1210-1217.
16. Sieber S.A., Cravatt B.F. Analytical platforms for activity-based protein profiling - exploiting the versatility of chemistry for functional proteomics. Chem Commun (Camb) 2006, 2311-2319.
17. Sieber S.A., Niessen S., Hoover H.S., Cravatt B.F. Proteomic profiling of metalloprotease activities with cocktails of active-site probes. Nat Chem Biol 2006, 2:274-281.
18. Jessani N., Niessen S., Wei B.Q., Nicolau M., Humphrey M., Ji Y., et al. A streamlined platform for high-content functional proteomics of primary human specimens. Nat Methods 2005, 2:691-697.
19. Liu Y., Patricelli M.P., Cravatt B.F. Activity-based protein profiling: the serine hydrolases. Proc Natl Acad Sci U S A 1999, 96:14694-14699.
20. Jessani N., Liu Y., Humphrey M., Cravatt B.F. Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness. Proc Natl Acad Sci U S A 2002, 99:10335-10340.
21. Orita H., Coulter J., Lemmon C., Tully E., Vadlamudi A., Medghalchi S.M., et al. Selective inhibition of fatty acid synthase for lung cancer treatment. Clin Cancer Res 2007, 13:7139-7145.
22. Hernandez J., Thompson I.M. Prostate-specific antigen: a review of the validation of the most commonly used cancer biomarker. Cancer 2004, 101:894-904.
23. Kobe B., Kemp B.E. Active site-directed protein regulation. Nature 1999, 402:373-376.
24. Silverman G.A., Bird P.I., Carrell R.W., Church F.C., Coughlin P.B., Gettins P.G., et al. The serpins are an expanding superfamily of structurally similar but functionally diverse proteins. Evolution, mechanism of inhibition, novel functions, and a revised nomenclature. J Biol Chem 2001, 276:33293-33296.
25. Steu S., Baucamp M., von Dach G., Bawohl M., Dettwiler S., Storz M., et al. A procedure for tissue freezing and processing applicable to both intra-operative frozen section diagnosis and tissue banking in surgical pathology. Virchows Arch 2008, 452:305-312.
26. Creighton T.E. Proteins: structure and molecular properties 1993, Freeman, New York. 2nd ed.
27. Walsh C.T. Enzymatic reaction mechanisms 1979, Freeman, New York.
28. Higson A.P., Ferguson M.A.J., Nikolaev A.V. Synthesis of 6-N-Biotinylaminohexyl isopropyl phosphorofluoridate: A potent tool for the inhibition/isolation of serine esterases and proteases. Synthesis 1999, 407-409.
29. Nomura D.K., Leung D., Chiang K.P., Quistad G.B., Cravatt B.F., Casida J.E. A brain detoxifying enzyme for organophosphorus nerve poisons. Proc Natl Acad Sci U S A 2005, 102:6195-6200.
30. Quistad G.B., Casida J.E. Lysophospholipase inhibition by organophosphorus toxicants. Toxicol Appl Pharmacol 2004, 196:319-326.
31. Desiere F., Deutsch E.W., Nesvizhskii A.I., Mallick P., King N.L., Eng J.K., et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol 2005, 6:R9.
32. Li X.J., Pedrioli P.G., Eng J., Martin D., Yi E.C., Lee H., et al. A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. Anal Chem 2004, 76:3856-3860.
33. Marchler-Bauer A., Anderson J.B., Chitsaz F., Derbyshire M.K., DeWeese-Scott C., Fong J.H., et al. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 2009, 37:D205-D210.
34. Marchler-Bauer A., Anderson J.B., Derbyshire M.K., DeWeese-Scott C., Gonzales N.R., Gwadz M., et al. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res 2007, 35:D237-D240.
35. Marchler-Bauer A., Panchenko A.R., Shoemaker B.A., Thiessen P.A., Geer L.Y., Bryant S.H. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 2002, 30:281-283.
36. Grossmann J., Roschitzki B., Panse C., Fortes C., Barkow-Oesterreicher S., Rutishauser D., et al. Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods. J Proteomics 2010, 73:1740-1746.
37. Malmstrom J., Beck M., Schmidt A., Lange V., Deutsch E.W., Aebersold R. Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 2009, 460:762-765.
38. Silva J.C., Gorenstein M.V., Li G.Z., Vissers J.P., Geromanos S.J. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol Cell Proteomics 2006, 5:144-156.
39. Peng C.Y.J., Lee K.L., Ingersoll G.M. An introduction to logistic regression analysis and reporting. J Educ Res 2002, 96.
40. Loong T.W. Understanding sensitivity and specificity with the right side of the brain. BMJ 2003, 327:716-719.
41. Haws C., Finkbeiner W.E., Widdicombe J.H., Wine J.J. CFTR in Calu-3 human airway cells: channel properties and role in cAMP-activated Cl-conductance. Am J Physiol 1994, 266:L502-L512.
42. Minna J. Neoplasms of the Lung. Harrison's principles of internal medicine 2005, 506-515. 16 ed. D.L. Kasper (Ed.).
43. Suster SaM C. Tumors of the lung and pleura. Cancer grading manual 2007, 23-31. Springer, New York. I. Fan (Ed.).
44. Barletta J.A., Yeap B.Y., Chirieac L.R. Prognostic significance of grading in lung adenocarcinoma. Cancer 2010, 116:659-669.
45. Mountain C.F., Dresler C.M. Regional lymph node classification for lung cancer staging. Chest 1997, 111:1718-1723.
46. Marian A.J. Nature's genetic gradients and the clinical phenotype. Circ Cardiovasc Genet 2009, 2:537-539.
47. Sieber S.A., Mondala T.S., Head S.R., Cravatt B.F. Microarray platform for profiling enzyme activities in complex proteomes. J Am Chem Soc 2004, 126:15640-15641.
48. Weerapana E., Speers A.E., Cravatt B.F. Tandem orthogonal proteolysis-activity-based protein profiling (TOP-ABPP) - a general method for mapping sites of probe modification in proteomes. Nat Protoc 2007, 2:1414-1425.
49. Gillet L.C., Namoto K., Ruchti A., Hoving S., Boesch D., Inverardi B., et al. In-cell selectivity profiling of serine protease inhibitors by activity-based proteomics. Mol Cell Proteomics 2008, 7:1241-1253.
50. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17:994-999.
51. Wu D., Li Y., Song G., Zhang D., Shaw N., Liu Z.J. Crystal structure of human esterase D: a potential genetic marker of retinoblastoma. FASEB J 2009, 23:1441-1446.
52. Eiberg H., Mohr J. Identity of the polymorphisms for esterase D and S-formylglutathione hydrolase in red blood cells. Hum Genet 1986, 74:174-175.
53. Kilpinen S., Autio R., Ojala K., Iljin K., Bucher E., Sara H., et al. Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. Genome Biol 2008, 9:R139.
54. Gonzalez C.F., Proudfoot M., Brown G., Korniyenko Y., Mori H., Savchenko A.V., et al. Molecular basis of formaldehyde detoxification. Characterization of two S-formylglutathione hydrolases from Escherichia coli, FrmB and YeiG. J Biol Chem 2006, 281:14514-14522.
55. Merla G., Ucla C., Guipponi M., Reymond A. Identification of additional transcripts in the Williams-Beuren syndrome critical region. Hum Genet 2002, 110:429-438.
56. Collaud S., Wiedl T., Cattaneo E., Soltermann A., Hillinger S., Weder W., et al. Laser-capture microdissection impairs activity-based protein profiles for serine hydrolase in human lung adenocarcinoma. J Biomol Tech 2010, 21:25-28.
57. Cravatt B.F., Wright A.T., Kozarich J.W. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu Rev Biochem 2008, 77:383-414.