An informatics-assisted label-free approach for personalized tissue membrane proteomics: Case study on colorectal cancer

Molecular and Cellular Proteomics

Volumn 10, Issue 4, 2011, Pages

  Han, Chia Li ^a   Chen, Jinn Shiun ^b,c   Chan, Err Cheng ^d   Wu, Chien Peng ^a   Yu, Kun Hsing ^e   Chen, Kuei Tien ^d   Tsou, Chih Chiang ^f   Tsai, Chia Feng ^a   Chien, Chih Wei ^g   Kuo, Yung Bin ^h   Lin, Pei Yi ^a   Yu, Jau Song ^d   Hsueh, Chuen ^b,d   Chen, Min Chi ^d   Chan, Chung Chuan ⁱ   Chang, Yu Sun ^c,d   Chen, Yu Ju ^a,j  

^a INSTITUTE OF CHEMISTRY   (Taiwan)

^b CHANG GUNG MEMORIAL HOSPITAL   (Taiwan)

^c CHANG GUNG UNIVERSITY   (Taiwan)

^d CHANG GUNG UNIVERSITY   (Taiwan)

^e NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^f ACADEMIA SINICA   (Taiwan)

^g NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^h NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

ⁱ CATHAY GENERAL HOSPITAL   (Taiwan)

^j NATIONAL TAIWAN UNIVERSITY   (Taiwan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA DEFENSIN; ANNEXIN; CARCINOEMBRYONIC ANTIGEN; CLAUDIN 3; MEMBRANE PROTEIN; STOMATIN; STOMATIN LIKE 2; TUMOR MARKER; UNCLASSIFIED DRUG; DEFENSIN 1; LIPOCORTIN 4; PEPTIDE; PLASMA PROTEIN; PROTEOME; STOML2 PROTEIN, HUMAN;

ACCURACY; ADULT; ARTICLE; BIOINFORMATICS; CANCER DIAGNOSIS; CANCER RECURRENCE; CANCER SURVIVAL; COLORECTAL CANCER; CONTROLLED STUDY; EARLY DIAGNOSIS; ENZYME LINKED IMMUNOSORBENT ASSAY; FEMALE; FRACTIONATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; MALE; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; SEROLOGY; ADENOCARCINOMA; AGED; AMINO ACID SEQUENCE; BIOSYNTHESIS; BLOOD; CHEMISTRY; COLORECTAL TUMOR; GENE EXPRESSION REGULATION; KAPLAN MEIER METHOD; METABOLISM; METHODOLOGY; MIDDLE AGED; MOLECULAR DIAGNOSIS; MULTIVARIATE ANALYSIS; PATHOLOGY; PROGNOSIS; PROPORTIONAL HAZARDS MODEL; RECEIVER OPERATING CHARACTERISTIC; TANDEM MASS SPECTROMETRY;

ADENOCARCINOMA; ADULT; AGED; AGED, 80 AND OVER; ALPHA-DEFENSINS; AMINO ACID SEQUENCE; ANNEXIN A4; BLOOD PROTEINS; CARCINOEMBRYONIC ANTIGEN; COLORECTAL NEOPLASMS; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; KAPLAN-MEIER ESTIMATE; MALE; MEMBRANE PROTEINS; MIDDLE AGED; MOLECULAR DIAGNOSTIC TECHNIQUES; MULTIVARIATE ANALYSIS; PEPTIDES; PROGNOSIS; PROPORTIONAL HAZARDS MODELS; PROTEOME; ROC CURVE; TANDEM MASS SPECTROMETRY; TUMOR MARKERS, BIOLOGICAL;

EID: 79953303839     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M110.003087     Document Type: Article

References (62)

1. Weitz, J., Koch, M., Debus, J., Höhler, T., Galle, P. R., and Büchler, M. W. (2005) Colorectal cancer. Lancet 365, 153-165
2. Jemal, A., Siegel, R., Ward, E., Murray, T., Xu, J., and Thun, M. J. (2007) Cancer statistics, 2007. CA Cancer J. Clin. 57, 43-66
3. Kronborg, O., Fenger, C., Olsen, J., Jørgensen, O. D., and Søndergaard, O. (1996) Randomised study of screening for colorectal cancer with faecaloccult- blood test. Lancet 348, 1467-1471 (Pubitemid 26400241)
4. Walsh, J. M., and Terdiman, J. P. (2003) Colorectal cancer screening: scientific review. JAMA 289, 1288-1296 (Pubitemid 37432910)
5. Smith, R. A., Cokkinides, V., and Eyre, H. J. American Cancer Society guidelines for the early detection of cancer, 2006. CA Cancer J. Clin. 56:11-25, 2006; quiz 49-50
6. Thompson, J. A., Grunert, F., and Zimmermann, W. (1991) Carcinoembryonic antigen gene family: molecular biology and clinical perspectives. J. Clin. Lab. Anal. 5, 344-366
7. Kim, H. J., Yu, M. H., Kim, H., Byun, J., and Lee, C. (2008) Noninvasive molecular biomarkers for the detection of colorectal cancer. BMB Rep. 41, 685-692
8. Wanebo, H. J., Rao, B., Pinsky, C. M., Hoffman, R. G., Stearns, M., Schwartz, M. K., and Oettgen, H. F. (1978) Preoperative carcinoembryonic antigen level as a prognostic indicator in colorectal cancer. N. Engl. J. Med. 299, 448-451
9. Minton, O., and Stone, P. C. (2010) Review: the use of proteomics as a research methodology for studying cancer-related fatigue: a review. Palliat. Med. 24, 310-316
10. Leth-Larsen, R., Lund, R. R., and Ditzel, H. J. (2010) Plasma membrane proteomics and its application in clinical cancer biomarker discovery. Mol. Cell Proteomics 9, 1369-1382
11. Simpson, R. J., Bernhard, O. K., Greening, D. W., and Moritz, R. L. (2008) Proteomics-driven cancer biomarker discovery: looking to the future. Curr. Opin. Chem. Biol. 12, 72-77
12. Sprung, R. W., Jr., Brock, J. W., Tanksley, J. P., Li, M., Washington, M. K., Slebos, R. J., and Liebler, D. C. (2009) Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol. Cell Proteomics 8, 1988-1998
13. Hwang, S. I., Thumar, J., Lundgren, D. H., Rezaul, K., Mayya, V., Wu, L., Eng, J., Wright, M. E., and Han, D. K. (2007) Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene 26, 65-76
14. Zielinska, D. F., Gnad, F., Wiśniewski, J. R., and Mann, M. (2010) Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell 141, 897-907
15. Uhlén, M., Björling, E., Agaton, C., Szigyarto, C. A., Amini, B., Andersen, E., Andersson, A. C., Angelidou, P., Asplund, A., Asplund, C., Berglund, L., Bergström, K., Brumer, H., Cerjan, D., Ekström, M., Elobeid, A., Eriksson, C., Fagerberg, L., Falk, R., Fall, J., Forsberg, M., Björklund, M. G., Gumbel, K., Halimi, A., Hallin, I., Hamsten, C., Hansson, M., Hedhammar, M., Hercules, G., Kampf, C., Larsson, K., Lindskog, M., Lodewyckx, W., Lund, J., Lundeberg, J., Magnusson, K., Malm, E., Nilsson, P., Odling, J., Oksvold, P., Olsson, I., Oster, E., Ottosson, J., Paavilainen, L., Persson, A., Rimini, R., Rockberg, J., Runeson, M., Sivertsson, A., Sköllermo, A., Steen, J., Stenvall, M., Sterky, F., Strömberg, S., Sundberg, M., Tegel, H., Tourle, S., Wahlund, E., Walden, A., Wan, J., Wernérus, H., Westberg, J., Wester, K., Wrethagen, U., Xu, L. L., Hober, S., and Pontén, F. (2005) A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell Proteomics 4, 1920-1932
16. Björling, E., Lindskog, C., Oksvold, P., Linné, J., Kampf, C., Hober, S., Uhlén, M., and Pontén, F. (2008) A web-based tool for in silico biomarker discovery based on tissue-specific protein profiles in normal and cancer tissues. Mol. Cell Proteomics 7, 825-844
17. Roessler, M., Rollinger, W., Palme, S., Hagmann, M. L., Berndt, P., Engel, A. M., Schneidinger, B., Pfeffer, M., Andres, H., Karl, J., Bodenmüller, H., Rüschoff, J., Henkel, T., Rohr, G., Rossol, S., Rösch, W., Langen, H., Zolg, W., and Tacke, M. (2005) Identification of nicotinamide N-methyl-transferase as a novel serum tumor marker for colorectal cancer. Clin. Cancer Res. 11, 6550-6557
18. Alfonso, P., Núñez, A., Madoz-Gurpide, J., Lombardia, L., Sánchez, L., and Casal, J. I. (2005) Proteomic expression analysis of colorectal cancer by two-dimensional differential gel electrophoresis. Proteomics 5, 2602-2611 (Pubitemid 40966487)
19. Rho, J. H., Qin, S., Wang, J. Y., and Roehrl, M. H. (2008) Proteomic expression analysis of surgical human colorectal cancer tissues: upregulation of PSB7, PRDX1, and SRP9 and hypoxic adaptation in cancer. J. Proteome Res. 7, 2959-2972
20. Ma, Y., Peng, J., Liu, W., Zhang, P., Huang, L., Gao, B., Shen, T., Zhou, Y., Chen, H., Chu, Z., Zhang, M., and Qin, H. (2009) Proteomics identification of desmin as a potential oncofetal diagnostic and prognostic biomarker in colorectal cancer. Mol. Cell Proteomics 8, 1878-1890
21. Xing, X., Lai, M., Gartner, W., Xu, E., Huang, Q., Li, H., and Chen, G. (2006) Identification of differentially expressed proteins in colorectal cancer by proteomics: down-regulation of secretagogin. Proteomics 6, 2916-2923
22. Pei, H., Zhu, H., Zeng, S., Li, Y., Yang, H., Shen, L., Chen, J., Zeng, L., Fan, J., Li, X., Gong, Y., and Shen, H. (2007) Proteome analysis and tissue microarray for profiling protein markers associated with lymph node metastasis in colorectal cancer. J. Proteome Res. 6, 2495-2501 (Pubitemid 47122346)
23. Ma, Y. L., Peng, J. Y., Zhang, P., Huang, L., Liu, W. J., Shen, T. Y., Chen, H. Q., Zhou, Y. K., Zhang, M., Chu, Z. X., and Qin, H. L. (2009) Heterogeneous nuclear ribonucleoprotein A1 is identified as a potential biomarker for colorectal cancer based on differential proteomics technology. J. Proteome Res. 8, 4525-4535
24. Krasnov, G. S., Oparina, N., Khankin, S. L., Mashkova, T. D., Ershov, A. N., Zatsepina, O. G., Karpov, V. L., and Beresten, S. F. (2009) [Colorectal cancer 2D-proteomics: identification of altered protein expression]. Mol. Biol. 43, 348-356
25. Alfonso, P., Cañamero, M., Fernández-Carbonié, F., Núñez, A., and Casal, J. I. (2008) Proteome analysis of membrane fractions in colorectal carcinomas by using 2D-DIGE saturation labeling. J. Proteome Res. 7, 4247-4255
26. Prenzel, N., Zwick, E., Leserer, M., and Ullrich, A. (2000) Tyrosine kinase signalling in breast cancer. Epidermal growth factor receptor: convergence point for signal integration and diversification. Breast Cancer Res.. 2, 184-190
27. Kufe, D. W. (2009) Mucins in cancer: function, prognosis and therapy. Nat. Rev. Cancer 9, 874-885
28. Hopkins, A. L., and Groom, C. R. (2002) The druggable genome. Nat. Rev. Drug Discov. 1, 727-730
29. Rajcevic, U., Petersen, K., Knol, J. C., Loos, M., Bougnaud, S., Klychnikov, O., Li, K. W., Pham, T. V., Wang, J., Miletic, H., Peng, Z., Bjerkvig, R., Jimenez, C. R., and Niclou, S. P. (2009) iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype. Mol. Cell Proteomics 8, 2595-2612
30. Kristiansen, T. Z., Harsha, H. C., Grønborg, M., Maitra, A., and Pandey, A. (2008) Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma. J. Proteome Res. 7, 4670-4677
31. Han, C. L., Chien, C. W., Chen, W. C., Chen, Y. R., Wu, C. P., Li, H., and Chen, Y. J. (2008) A multiplexed quantitative strategy for membrane proteomics: opportunities for mining therapeutic targets for autosomal dominant polycystic kidney disease. Mol. Cell Proteomics 7, 1983-1997
32. Tsou, C. C., Tsai, C. F., Tsui, Y. H., Sudhir, P. R., Wang, Y. T., Chen, Y. J., Chen, J. Y., Sung, T. Y., and Hsu, W. L. (2010) IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation. Mol. Cell Proteomics 9, 131-144
33. Wu, C. C., Hsu, C. W., Chen, C. D., Yu, C. J., Chang, K. P., Tai, D. I., Liu, H. P., Su, W. H., Chang, Y. S., and Yu, J. S. (2010) Candidate serological biomarkers for cancer identified from the secretomes of 23 cancer cell lines and the human protein atlas. Mol. Cell Proteomics 9, 1100-1117
34. Kersey, P. J., Duarte, J., Williams, A., Karavidopoulou, Y., Birney, E., and Apweiler, R. (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics 4, 1985-1988 (Pubitemid 38880363)
35. Bendtsen, J. D., Nielsen, H., von Heijne, G., and Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783-795
36. Cattoretti, G., Pileri, S., Parravicini, C., Becker, M. H., Poggi, S., Bifulco, C., Key, G., D'Amato, L., Sabattini, E., Feudale, E., and et al. (1993) Antigen unmasking on formalin-fixed, paraffin-embedded tissue sections. J. Pathol. 171, 83-98 (Pubitemid 23309729)
37. Cao, W. F., Zhang, L. Y., Liu, M. B., Tang, P. Z., Liu, Z. H., and Sun, B. C. (2007) Prognostic significance of stomatin-like protein 2 overexpression in laryngeal squamous cell carcinoma: clinical, histologic, and immunohistochemistry analyses with tissue microarray. Hum. Pathol. 38, 747-752
38. Feng Han, Q., Zhao, W., Bentel, J., Shearwood, A. M., Zeps, N., Joseph, D., Iacopetta, B., and Dharmarajan, A. (2006) Expression of sFRP-4 and beta-catenin in human colorectal carcinoma. Cancer Lett. 231, 129-137 (Pubitemid 41779461)
39. Ravn, V., Rasmussen, B. B., Højholt, L., Barfoed, M., Heiberg, I., and Thorpe, S. M. (1993) Reproducibility of subjective immunohistochemical estrogen- and progesterone receptor determination in human endometrium. Pathol. Res. Pract. 189, 1015-1022
40. Callister, S. J., Barry, R. C., Adkins, J. N., Johnson, E. T., Qian, W. J., Webb-Robertson, B. J., Smith, R. D., and Lipton, M. S. (2006) Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. J. Proteome Res. 5, 277-286 (Pubitemid 43222296)
41. Ono, M., Shitashige, M., Honda, K., Isobe, T., Kuwabara, H., Matsuzuki, H., Hirohashi, S., and Yamada, T. (2006) Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry. Mol. Cell Proteomics 5, 1338-1347 (Pubitemid 44103403)
42. Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G., Mendoza, A., Sevinsky, J. R., Resing, K. A., and Ahn, N. G. (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell Proteomics 4, 1487-1502
43. Zhang, L., Ding, F., Cao, W., Liu, Z., Liu, W., Yu, Z., Wu, Y., Li, W., Li, Y., and Liu, Z. (2006) Stomatin-like protein 2 is overexpressed in cancer and involved in regulating cell growth and cell adhesion in human esophageal squamous cell carcinoma. Clin. Cancer Res. 12, 1639-1646
44. Cao, W., Zhang, B., Liu, Y., Li, H., Zhang, S., Fu, L., Niu, Y., Ning, L., Cao, X., Liu, Z., and Sun, B. (2007) High-level SLP-2 expression and HER-2/ neu protein expression are associated with decreased breast cancer patient survival. Am. J. Clin. Pathol. 128, 430-436
45. Cui, Z., Zhang, L., Hua, Z., Cao, W., Feng, W., and Liu, Z. (2007) Stomatin-like protein 2 is overexpressed and related to cell growth in human endometrial adenocarcinoma. Oncol. Rep. 17, 829-833
46. DeSouza, L. V., Grigull, J., Ghanny, S., Dubé, V., Romaschin, A. D., Colgan, T. J., and Siu, K. W. (2007) Endometrial carcinoma biomarker discovery and verification using differentially tagged clinical samples with multidimensional liquid chromatography and tandem mass spectrometry. Mol. Cell Proteomics 6, 1170-1182
47. Elschenbroich, S., Ignatchenko, V., Sharma, P., Schmitt-Ulms, G., Gramolini, A. O., and Kislinger, T. (2009) Peptide separations by on-line MudPIT compared to isoelectric focusing in an off-gel format: application to a membrane-enriched fraction from C2C12 mouse skeletal muscle cells. J. Proteome Res. 8, 4860-4869
48. Slebos, R. J., Brock, J. W., Winters, N. F., Stuart, S. R., Martinez, M. A., Li, M., Chambers, M. C., Zimmerman, L. J., Ham, A. J., Tabb, D. L., and Liebler, D. C. (2008) Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography- tandem mass spectrometry. J. Proteome Res. 7, 5286-5294
49. Zimmermann, U., Balabanov, S., Giebel, J., Teller, S., Junker, H., Schmoll, D., Protzel, C., Scharf, C., Kleist, B., and Walther, R. (2004) Increased expression and altered location of annexin IV in renal clear cell carcinoma: a possible role in tumour dissemination. Cancer Lett. 209, 111-118 (Pubitemid 38625750)
50. Kim, A., Enomoto, T., Serada, S., Ueda, Y., Takahashi, T., Ripley, B., Miyatake, T., Fujita, M., Lee, C. M., Morimoto, K., Fujimoto, M., Kimura, T., and Naka, T. (2009) Enhanced expression of Annexin A4 in clear cell carcinoma of the ovary and its association with chemoresistance to carboplatin. Int. J. Cancer 125, 2316-2322
51. Baris, O., Mirebeau-Prunier, D., Savagner, F., Rodien, P., Ballester, B., Loriod, B., Granjeaud, S., Guyetant, S., Franc, B., Houlgatte, R., Reynier, P., and Malthiery, Y. (2005) Gene profiling reveals specific oncogenic mechanisms and signaling pathways in oncocytic and papillary thyroid carcinoma. Oncogene 24, 4155-4161 (Pubitemid 40897060)
52. Shen, J., Person, M. D., Zhu, J., Abbruzzese, J. L., and Li, D. (2004) Protein expression profiles in pancreatic adenocarcinoma compared with normal pancreatic tissue and tissue affected by pancreatitis as detected by two-dimensional gel electrophoresis and mass spectrometry. Cancer Res. 64, 9018-9026 (Pubitemid 39665512)
53. Liu, L., Wang, S., Zhang, Q., and Ding, Y. (2008) Identification of potential genes/proteins regulated by Tiam1 in colorectal cancer by microarray analysis and proteome analysis. Cell Biol. Int. 32, 1215-1222
54. Zou, H., Harrington, J. J., Sugumar, A., Klatt, K. K., Smyrk, T. C., and Ahlquist, D. A. (2007) Detection of colorectal disease by stool defensin assay: an exploratory study. Clin. Gastroenterol. Hepatol. 5, 865-868
55. Mothes, H., Melle, C., Ernst, G., Kaufmann, R., von Eggeling, F., and Settmacher, U. (2008) Human Neutrophil Peptides 1-3-early markers in development of colorectal adenomas and carcinomas. Dis. Markers 25, 123-129
56. Hewitt, K. J., Agarwal, R., and Morin, P. J. (2006) The claudin gene family: expression in normal and neoplastic tissues. BMC Cancer 6, 186
57. Wang, Y., and Morrow, J. S. (2000) Identification and characterization of human SLP-2, a novel homologue of stomatin (band 7.2b) present in erythrocytes and other tissues. J. Biol. Chem. 275, 8062-8071
58. Kinzler, K. W., and Vogelstein, B. (1996) Lessons from hereditary colorectal cancer. Cell 87, 159-170 (Pubitemid 26358996)
59. Dowling, P., Meleady, P., Dowd, A., Henry, M., Glynn, S., and Clynes, M. (2007) Proteomic analysis of isolated membrane fractions from superinvasive cancer cells. Biochim. Biophys. Acta 1774, 93-101
60. Winawer, S., Fletcher, R., Rex, D., Bond, J., Burt, R., Ferrucci, J., Ganiats, T., Levin, T., Woolf, S., Johnson, D., Kirk, L., Litin, S., and Simmang, C. (2003) Colorectal cancer screening and surveillance: clinical guidelines and rationale-Update based on new evidence. Gastroenterology 124, 544-560 (Pubitemid 36169269)
61. Inger, D. B. (1999) Colorectal cancer screening. Prim. Care 26, 179-187
62. Huber, K., Kirchheimer, J. C., Sedlmayer, A., Bell, C., Ermler, D., and Binder, B. R. (1993) Clinical value of determination of urokinase-type plasminogen activator antigen in plasma for detection of colorectal cancer: comparison with circulating tumor-associated antigens CA 19-9 and carcinoembryonic antigen. Cancer Res. 53, 1788-1793