Preferences help
enabled [disable] Abstract
Number of results
2013 | 60 | 3 | 417-425
Article title

Pre-analytical-related variability influencing serum peptide profiles demonstrated in a mass spectrometry-based search for colorectal and prostate cancer biomarkers

Title variants
Languages of publication
Although the degradome, which comprises proteolytic fragments of blood proteins, presents a potential source of diagnostic biomarkers, studies on cancer peptide biomarkers have provided inconsistent conclusions. In the present study, we reevaluated the usefulness of serum degradome analyses for searching peptide cancer biomarker candidates. Particular attention was paid to pre-analytical factors influencing the variability of determined peptide levels, including clotting time and control group selection. Studies were conducted on 44 and 86 serum samples collected from cancer patients and healthy individuals, respectively, using liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS)-based analyses. We identified 1373 unique peptides, nearly 40% of which originated from five blood proteins: fibrinogen alpha chain, apolipoprotein A-IV (APOA4), complement C3, apolipoprotein A-I, and alpha-1-antitrypsin. A set of 118 and 88 peptides exhibited highly significant differences (adjusted p-value ≤ 0.01 and fold change ≥ 2) in pair-wise comparisons of control vs. prostate cancer and control vs. colorectal cancer, respectively, with 37 peptides displaying a consistent direction of change for these pair-wise comparisons. The levels of 67 peptides differed significantly in serum samples collected from healthy individuals immediately prior to colonoscopy and those who underwent colonoscopic examination at least four weeks earlier. Of them, 49 peptides originated from APOA4. Whereas earlier studies, including ours, have utilized fragments of fibrinopeptide A (FPA) to distinguish cancer from healthy cases, here we show that their absolute abundance is a sensitive indicator of clotting time. These observations may have implications for future serum peptidome studies since these issues have not previously been recognized.
Physical description
  • Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
  • Institute of Radioelectronics, Warsaw University of Technology, Warsaw, Poland
  • Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
  • Department of Urology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
  • Department of Gastrointestinal Cancer, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
  • Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, and Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
  • Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
  • Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, and Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
  • Ahmad S, Ansari AA (2011) Therapeutic roles of heparin anticoagulants in cancer and related disorders. Med Chem 7: 504-517.
  • Amitrano L, Guardascione MA, Brancaccio V, Balzano A (2002) Coagulation Disorders in Liver Disease. Semin Liver Disease 22: 83-96.
  • Bakun M, Karczmarski J, Poznanski J, Rubel T, Rozga M, Malinowska A, Sands D, Hennig E, Oledzki J, Ostrowski J, Dadlez M (2009) An integrated LC-ESI-MS platform for quantitation of serum peptide ladders. Application for colon carcinoma study. Proteomics Clin Appl 3: 932-946.
  • Benjamini Y, Hochberg Y (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J Royal Statistic Soc Series B (Methodological) 57: 289-300.
  • Bertile F, Schaeffer C, Le Maho Y, Raclot T, Van Dorsselaer A (2009) A proteomic approach to identify differentially expressed plasma proteins between the fed and prolonged fasted states. Proteomics 9: 148-158.
  • Van den Broek I, Sparidans RW, Schellens JHM, Beijnen JH (2010a) Specific investigation of sample handling effects on protease activities and absolute serum concentrations of various putative peptidome cancer biomarkers. Clin Proteomics 6: 115-127.
  • Van den Broek I, Sparidans RW, Van Winden AWJ, Gast M-CW, Van Dulken EJ, Schellens JHM, Beijnen JH (2010b) The absolute quantification of eight inter-α-trypsin inhibitor heavy chain 4 (ITIH4)-derived peptides in serum from breast cancer patients. Proteomics Clin Appl 4: 931-939.
  • Cheng A-J, Chen L-C, Chien K-Y, Chen Y-J, Chang JT-C, Wang H-M, Liao C-T, Chen I-H (2005) Oral cancer plasma tumor marker identified with bead-based affinity-fractionated proteomic technology. Clin Chem 51: 2236-2244.
  • Cortes C, Vapnik V (1995) Support-vector networks. Mach Learn 20: 273-297.
  • Danese S, Papa A, Saibeni S, Repici A, Malesci A, Vecchi M (2007) Inflammation and coagulation in inflammatory bowel disease: The clot thickens. Am J Gastroenterol 102: 174-186.
  • Ebert MPA, Lamer S, Meuer J, Malfertheiner P, Reymond M, Buschmann T, Röcken C, Seibert V (2005) Identification of the thrombin light chain a as the single best mass for differentiation of gastric cancer patients from individuals with dyspepsia by proteome analysis. J Proteome Res 4: 586-590.
  • Ebert MPA, Niemeyer D, Deininger SO, Wex T, Knippig C, Hoffmann J, Sauer J, Albrecht W, Malfertheiner P, Röcken C (2006) Identification and confirmation of increased fibrinopeptide a serum protein levels in gastric cancer sera by magnet bead assisted MALDI-TOF mass spectrometry. J Proteome Res 5: 2152-2158.
  • Fung ET, Yip T-T, Lomas L, Wang Z, Yip C, Meng X-Y, Lin S, Zhang F, Zhang Z, Chan DW, Weinberger SR (2005) Classification of cancer types by measuring variants of host response proteins using SELDI serum assays. Int J Cancer 115: 783-789.
  • Gianazza E, Mainini V, Castoldi G, Chinello C, Zerbini G, Bianchi C, Galbusera C, Stella A, Mauri G, Zoppis I, Magni F, Kienle MG (2010) Different expression of fibrinopeptide A and related fragments in serum of type 1 diabetic patients with nephropathy. J Proteomics 73: 593-601.
  • Hortin GL (2006) The MALDI-TOF mass spectrometric view of the plasma proteome and peptidome. Clin Chem 52: 1223-1237.
  • Käll L, Storey JD, MacCoss MJ, Noble WS (2008) Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res 7: 29-34.
  • Koomen JM, Li D, Xiao L, Liu TC, Coombes KR, Abbruzzese J, Kobayashi R (2005) Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J Proteome Res 4: 972-981.
  • Mikula M, Gaj P, Dzwonek K, Rubel T, Karczmarski J, Paziewska A, Dzwonek A, Bragoszewski P, Dadlez M, Ostrowski J (2010) Comprehensive analysis of the palindromic motif TCTCGCGAGA: a regulatory element of the HNRNPK promoter. DNA Res 17: 245-260.
  • Muthusamy B et al. (2005) Plasma Proteome Database as a resource for proteomics research. Proteomics 5: 3531-3536.
  • Nilsson L-M, Abrahamsson A, Sahlin S, Gustafsson U, Angelin B, Parini P, Einarsson C (2007) Bile acids and lipoprotein metabolism: effects of cholestyramine and chenodeoxycholic acid on human hepatic mRNA expression. Biochem Biophys Res Commun 357: 707-711.
  • Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM, Mills GB, Simone C, Fishman DA, Kohn EC, Liotta LA (2002) Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359: 572-577.
  • Rafat M, Sattler AM, Hackler R, Soufi M, Steinmetz A, Maisch B, Schaefer JR (2004) Apolipoprotein A-IV in the Fed and Fasting States. Clin Chem 50: 1270-1271.
  • Shen L, Pearson KJ, Xiong Y, Lo C-M, Tso P, Woods SC, Davidson WS, Liu M (2008) Characterization of apolipoprotein A-IV in brain areas involved in energy homeostasis. Physiol Behav 95: 161-167.
  • Shen Y, Liu T, Tolić N, Petritis BO, Zhao R, Moore RJ, Purvine SO, Camp DG, Smith RD (2010) Strategy for degradomic-peptidomic analysis of human blood plasma. J Proteome Res 9: 2339-2346.
  • Shi Q, Harris LN, Lu X, Li X, Hwang J, Gentleman R, Iglehart JD, Miron A (2006) Declining plasma fibrinogen alpha fragment identifies HER2-positive breast cancer patients and reverts to normal levels after surgery. J Proteome Res 5: 2947-2955.
  • Song J, Patel M, Rosenzweig CN, Chan-Li Y, Sokoll LJ, Fung ET, Choi-Miura N-H, Goggins M, Chan DW, Zhang Z (2006) Quantification of fragments of human serum inter-alpha-trypsin inhibitor heavy chain 4 by a surface-enhanced laser desorption/ionization-based immunoassay. Clin Chem 52: 1045-1053.
  • Stan S, Delvin E, Lambert M, Seidman E, Levy E (2003) Apo A-IV: an update on regulation and physiologic functions. Biochim Biophys Acta 1631: 177-187.
  • Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB (2001) Missing value estimation methods for DNA microarrays. Bioinformatics 17: 520-525.
  • Ueda K, Saichi N, Takami S, Kang D, Toyama A, Daigo Y, Ishikawa N, Kohno N, Tamura K, Shuin T, Nakayama M, Sato T-A, Nakamura Y, Nakagawa H (2011) A comprehensive peptidome profiling technology for the identification of early detection biomarkers for lung adenocarcinoma. PLoS ONE 6: e18567.
  • 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 (2006) Differential exoprotease activities confer tumor-specific serum peptidome patterns. J Clin Invest 116: 271-284.
  • Vizcaíno JA, Côté R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L (2009) A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 9: 4276-4283.
  • Whiteaker JR et al. (2011) A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat Biotechnol 29: 625-634.
  • Zito F, Drummond F, Bujac SR, Esnouf MP, Morrissey JH, Humphries SE, Miller GJ (2000) Epidemiological and genetic associations of activated factor XII concentration with factor VII activity, fibrinopeptide A concentration, and risk of coronary heart disease in men. Circulation 102: 2058-2062.
Document Type
Publication order reference
YADDA identifier
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.