Deciphering the peptidome of urine from ovarian cancer patients and healthy controls

Clinical Proteomics

Volumn 11, Issue 1, 2014, Pages

  Smith, Christopher R ^a,b   Batruch, Ihor ^b   Bauça, Josep Miquel ^c   Kosanam, Hari ^b   Ridley, Julia ^d,e   Bernardini, Marcus Q ^f   Leung, Felix ^b,f   Diamandis, Eleftherios P ^a,b,f   Kulasingam, Vathany ^a,f  

^a UNIVERSITY HEALTH NETWORK   (Canada)

^b MOUNT SINAI HOSPITAL   (Canada)

^c HOSPITAL UNIVERSITARIO SON ESPASES   (Spain)

^d PRINCESS MARGARET HOSPITAL   (Canada)

^e UNIVERSITY OF TORONTO   (Canada)

^f UNIVERSITY OF TORONTO   (Canada)

Author keywords

Biomarker; Early diagnosis; Mass spectrometry; Ovarian cancer; Urine peptidome

Indexed keywords

ALPHA2 GLYCOPROTEIN; COLLAGEN; LEUCINE RICH ALPHA 2 GLYCOPROTEIN; PEPTIDOME; PROTEOME; TUMOR MARKER; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; CLINICAL ARTICLE; CONTROLLED STUDY; FEMALE; HUMAN; ION EXCHANGE CHROMATOGRAPHY; MASS SPECTROMETER; OVARY CANCER; PEPTIDOMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN URINE LEVEL; SOLID PHASE EXTRACTION; ULTRAFILTRATION;

EID: 84903779011     PISSN: 15426416     EISSN: 15590275     Source Type: Journal    
DOI: 10.1186/1559-0275-11-23     Document Type: Article

References (44)

1. Siegel R, Naishadham D, Jemal A: Cancer statistics, 2012. CA Cancer J Clin 2012, 62(1):10-29.
2. Bhoola S, Hoskins WJ: Diagnosis and management of epithelial ovarian cancer. Obstet Gynecol 2006, 107(6):1399-1410. (Pubitemid 44336908)
3. Leung F, Diamandis EP, Kulasingam V: From bench to bedside: discovery of ovarian cancer biomarkers using high-Throughput technologies in the past decade. Biomark Med 2012, 6(5):613-625.
4. Gelman JS, Sironi J, Castro LM, Ferro ES, Fricker LD: Peptidomic analysis of human cell lines. J Proteome Res 2011, 10(4):1583-1592.
5. Soloviev M, Finch P: Peptidomics: bridging the gap between proteome and metabolome. Proteomics 2006, 6(3):744-747. (Pubitemid 43260199)
6. Liang X, Huuskonen J, Hajivandi M, Manzanedo R, Predki P, Amshey JR, Pope RM: Identification and quantification of proteins differentially secreted by a pair of normal and malignant breast-cancer cell lines. Proteomics 2009, 9(1):182-193.
7. Makridakis M, Vlahou A: Secretome proteomics for discovery of cancer biomarkers. J Proteomics 2010, 73(12):2291-2305.
8. Koblinski JE, Ahram M, Sloane BF: Unraveling the role of proteases in cancer. Clin Chim Acta 2000, 291(2):113-135. (Pubitemid 30089760)
9. Villanueva J, Shaffer DR, Philip J, Chaparro CA, Erdjument-Bromage H, Olshen AB, Fleisher M, Lilja H, Brogi E, Boyd J, Sanchez-Carbayo M, Holland EC, Cordon-Cardo C, Scher HI, Tempst P: Differential exoprotease activities confer tumor-specific serum peptidome patterns. J Clin Invest 2006, 116(1):271-284. (Pubitemid 43121812)
10. Davis MT, Auger PL, Patterson SD: Cancer biomarker discovery via low molecular weight serum profiling-Are we following circular paths? Clin Chem 2010, 56(2):244-247.
11. Good DM, Thongboonkerd V, Novak J, Bascands JL, Schanstra JP, Coon JJ, Dominiczak A, Mischak H: Body fluid proteomics for biomarker discovery: lessons from the past hold the key to success in the future. J Proteome Res 2007, 6(12):4549-4555.
12. Fredolini C, Meani F, Luchini A, Zhou W, Russo P, Ross M, Patanarut A, Tamburro D, Gambara G, Ornstein D, Odicino F, Ragnoli M, Ravaggi A, Novelli F, Collura D, D'Urso L, Muto G, Belluco C, Pecorelli S, Liotta L, Petricoin EF III: Investigation of the ovarian and prostate cancer peptidome for candidate early detection markers using a novel nanoparticle biomarker capture technology. AAPS J 2010, 12(4):504-518.
13. Timms JF, Cramer R, Camuzeaux S, Tiss A, Smith C, Burford B, Nouretdinov I, Devetyarov D, Gentry-Maharaj A, Ford J, Luo Z, Gammerman A, Menon U, Jacobs I: Peptides generated ex vivo from serum proteins by tumorspecific exopeptidases are not useful biomarkers in ovarian cancer. Clin Chem 2010, 56(2):262-271.
14. Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM, Mills GB, Simone C, Fishman DA, Kohn EC, Liotta LA: Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002, 359(9306):572-577. (Pubitemid 34178440)
15. Petricoin EF III, Ornstein DK, Paweletz CP, Ardekani A, Hackett PS, Hitt BA, Velassco A, Trucco C, Wiegand L, Wood K, Simone CB, Levine PJ, Linehan WM, Emmert-Buck MR, Steinberg SM, Kohn EC, Liotta LA: Serum proteomic patterns for detection of prostate cancer. J Natl Cancer Inst 2002, 94(20):1576-1578. (Pubitemid 35277282)
16. Li J, Zhang Z, Rosenzweig J, Wang YY, Chan DW: Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 2002, 48(8):1296-1304. (Pubitemid 34809839)
17. Ling XB, Lau K, Deshpande C, Park JL, Milojevic D, Macaubas C, Xiao C, Lopez-Avila V, Kanegaye J, Burns JC, Cohen H, Schilling J, Mellins ED: Urine peptidomic and targeted plasma protein analyses in the diagnosis and monitoring of systemic juvenile idiopathic arthritis. Clin Proteomics 2010, 6(4):175-193.
18. Marimuthu A, O'Meally RN, Chaerkady R, Subbannayya Y, Nanjappa V, Kumar P, Kelkar DS, Pinto SM, Sharma R, Renuse S, Goel R, Christopher R, Delanghe B, Cole RN, Harsha HC, Pandey A: A comprehensive map of the human urinary proteome. J Proteome Res 2011, 10(6):2734-2743.
19. Adachi J, Kumar C, Zhang Y, Olsen JV, Mann M: The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol 2006, 7(9):R80.
20. Good DM, Zurbig P, Argiles A, Bauer HW, Behrens G, Coon JJ, Dakna M, Decramer S, Delles C, Dominiczak AF, Ehrich JH, Eitner F, Fliser D, Frommberger M, Ganser A, Girolami MA, Golovko I, Gwinner W, Haubitz M, Herget-Rosenthal S, Jankowski J, Jahn H, Jerums G, Julian BA, Kellmann M, Kliem V, Kolch W, Krolewski AS, Luppi M, Massy Z, et al: Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease. Mol Cell Proteomics 2010, 9(11):2424-2437.
21. Haubitz M, Good DM, Woywodt A, Haller H, Rupprecht H, Theodorescu D, Dakna M, Coon JJ, Mischak H: Identification and validation of urinary biomarkers for differential diagnosis and evaluation of therapeutic intervention in anti-neutrophil cytoplasmic antibody-Associated vasculitis. Mol Cell Proteomics 2009, 8(10):2296-2307.
22. Zimmerli LU, Schiffer E, Zurbig P, Good DM, Kellmann M, Mouls L, Pitt AR, Coon JJ, Schmieder RE, Peter KH, Mischak H, Kolch W, Delles C, Dominiczak AF: Urinary proteomic biomarkers in coronary artery disease. Mol Cell Proteomics 2008, 7(2):290-298. (Pubitemid 351298443)
23. Antwi K, Hostetter G, Demeure MJ, Katchman BA, Decker GA, Ruiz Y, Sielaff TD, Koep LJ, Lake DF: Analysis of the plasma peptidome from pancreas cancer patients connects a peptide in plasma to overexpression of the parent protein in tumors. J Proteome Res 2009, 8(10):4722-4731.
24. Zougman A, Pilch B, Podtelejnikov A, Kiehntopf M, Schnabel C, Kumar C, Mann M: Integrated analysis of the cerebrospinal fluid peptidome and proteome. J Proteome Res 2008, 7(1):386-399. (Pubitemid 351171153)
25. Tirumalai RS, Chan KC, Prieto DA, Issaq HJ, Conrads TP, Veenstra TD: Characterization of the low molecular weight human serum proteome. Mol Cell Proteomics 2003, 2(10):1096-1103.
26. Altelaar AF, Mohammed S, Brans MA, Adan RA, Heck AJ: Improved identification of endogenous peptides from murine nervous tissue by multiplexed peptide extraction methods and multiplexed mass spectrometric analysis. J Proteome Res 2009, 8(2):870-876.
27. Siwy J, Mullen W, Golovko I, Franke J, Zurbig P: Human urinary peptide database for multiple disease biomarker discovery. Proteomics Clin Appl 2011, 5(5-6):367-374.
28. Tabb DL, Vega-Montoto L, Rudnick PA, Variyath AM, Ham AJ, Bunk DM, Kilpatrick LE, Billheimer DD, Blackman RK, Cardasis HL, Carr SA, Clauser KR, Jaffe JD, Kowalski KA, Neubert TA, Regnier FE, Schilling B, Tegeler TJ, Wang M, Wang P, Whiteaker JR, Zimmerman LJ, Fisher SJ, Gibson BW, Kinsinger CR, Mesri M, Rodriguez H, Stein SE, Tempst P, Paulovich AG, et al: Repeatability and reproducibility in proteomic identifications by liquid chromatography-Tandem mass spectrometry. J Proteome Res 2010, 9(2):761-776.
29. Nagaraj N, Mann M: Quantitative analysis of the intra- And interindividual variability of the normal urinary proteome. J Proteome Res 2011, 10(2):637-645.
30. Lopez MF, Mikulskis A, Kuzdzal S, Golenko E, Petricoin EF III, Liotta LA, Patton WF, Whiteley GR, Rosenblatt K, Gurnani P, Nandi A, Neill S, Cullen S, O'Gorman M, Sarracino D, Lynch C, Johnson A, Mckenzie W, Fishman D: A novel, high-Throughput workflow for discovery and identification of serum carrier protein-bound peptide biomarker candidates in ovarian cancer samples. Clin Chem 2007, 53(6):1067-1074. (Pubitemid 46867523)
31. Yoshida A, Okamoto N, Tozawa-Ono A, Koizumi H, Kiguchi K, Ishizuka B, Kumai T, Suzuki N: Proteomic analysis of differential protein expression by brain metastases of gynecological malignancies. Hum Cell 2013, 26(2):56-66.
32. Maahs DM, Siwy J, Argiles A, Cerna M, Delles C, Dominiczak AF, Gayrard N, Iphofer A, Jansch L, Jerums G, Medek K, Mischak H, Navis GJ, Roob JM, Rossing K, Rossing P, Rychlik I, Schiffer E, Schmieder RE, Wascher TC, Winklhofer-Roob BM, Zimmerli LU, Zurbig P, Snell-Bergeon JK: Urinary collagen fragments are significantly altered in diabetes: A link to pathophysiology. PLoS One 2010, 5(9):e13051.
33. WOESSNER JF Jr: The determination of hydroxyproline in tissue and protein samples containing small proportions of this imino acid. Arch Biochem Biophys 1961, 93:440-447.
34. Holtta M, Zetterberg H, Mirgorodskaya E, Mattsson N, Blennow K, Gobom J: Peptidome analysis of cerebrospinal fluid by LC-MALDI MS. PLoS One 2012, 7(8):e42555.
35. Lee JE, Atkins N Jr, Hatcher NG, Zamdborg L, Gillette MU, Sweedler JV, Kelleher NL: Endogenous peptide discovery of the rat circadian clock: A focused study of the suprachiasmatic nucleus by ultrahigh performance tandem mass spectrometry. Mol Cell Proteomics 2010, 9(2):285-297.
36. Kuk C, Kulasingam V, Gunawardana CG, Smith CR, Batruch I, Diamandis EP: Mining the ovarian cancer ascites proteome for potential ovarian cancer biomarkers. Mol Cell Proteomics 2009, 8(4):661-669.
37. Chen Y, Lim BK, Peh SC, Abdul-Rahman PS, Hashim OH: Profiling of serum and tissue high abundance acute-phase proteins of patients with epithelial and germ line ovarian carcinoma. Proteome Sci 2008, 6:20.
38. Andersen JD, Boylan KL, Jemmerson R, Geller MA, Misemer B, Harrington KM, Weivoda S, Witthuhn BA, Argenta P, Vogel RI, Skubitz AP: Leucine-rich alpha-2-glycoprotein-1 is upregulated in sera and tumors of ovarian cancer patients. J Ovarian Res 2010, 3:21.
39. Kentsis A, Lin YY, Kurek K, Calicchio M, Wang YY, Monigatti F, Campagne F, Lee R, Horwitz B, Steen H, Bachur R: Discovery and validation of urine markers of acute pediatric appendicitis using high-Accuracy mass spectrometry. Ann Emerg Med 2010, 55(1):62-70.
40. Guergova-Kuras M, Kurucz I, Hempel W, Tardieu N, Kadas J, Malderez-Bloes C, Jullien A, Kieffer Y, Hincapie M, Guttman A, Csanky E, Dezso B, Karger BL, Takacs L: Discovery of lung cancer biomarkers by profiling the plasma proteome with monoclonal antibody libraries. Mol Cell Proteomics 2011, 10(12):M111.
41. Watson CJ, Ledwidge MT, Phelan D, Collier P, Byrne JC, Dunn MJ, McDonald KM, Baugh JA: Proteomic analysis of coronary sinus serum reveals leucine-rich alpha2-glycoprotein as a novel biomarker of ventricular dysfunction and heart failure. Circ Heart Fail 2011, 4(2):188-197.
42. Serada S, Fujimoto M, Terabe F, Iijima H, Shinzaki S, Matsuzaki S, Ohkawara T, Nezu R, Nakajima S, Kobayashi T, Plevy SE, Takehara T, Naka T: Serum leucine-rich alpha-2 glycoprotein is a disease activity biomarker in ulcerative colitis. Inflamm Bowel Dis 2012, 18(11):2169-2179.
43. O'Donnell LC, Druhan LJ, Avalos BR: Molecular characterization and expression analysis of leucine-rich alpha2-glycoprotein, a novel marker of granulocytic differentiation. J Leukoc Biol 2002, 72(3):478-485.
44. Takahashi N, Takahashi Y, Putnam FW: Periodicity of leucine and tandem repetition of a 24-Amino acid segment in the primary structure of leucine-rich alpha 2-glycoprotein of human serum. Proc Natl Acad Sci U S A 1985, 82(7):1906-1910. (Pubitemid 15060810)