The role of quantitative mass spectrometry in the discovery of pancreatic cancer biomarkers for translational science
详细信息 查看全文
- 作者：Daniel Ansari (1)
Linus Aronsson (1)
Agata Sasor (2)
Charlotte Welinder (3)
Melinda Rezeli (4)
Gy枚rgy Marko-Varga (4)
Roland Andersson (1)
1. Department of Surgery ; Clinical Sciences Lund ; Lund University ; and Sk氓ne University Hospital ; SE-221 85 ; Lund ; Sweden
2. Department of Pathology ; Clinical Sciences Lund ; Lund University ; and Sk氓ne University Hospital ; Lund ; Sweden
3. Department of Oncology ; Clinical Sciences Lund ; Lund University ; Lund ; Sweden
4. Clinical Protein Science & Imaging ; Biomedical Center ; Department of Measurement Technology and Industrial Electrical Engineering ; Lund University ; Lund ; Sweden - 关键词：Biomarker ; Mass spectrometry ; Diagnostics ; Pancreatic cancer ; Proteomics
- 刊名：Journal of Translational Medicine
- 出版年：2014
- 出版时间：December 2014
- 年：2014
- 卷：12
- 期：1
- 全文大小：436 KB
- 参考文献：1. Anderson, NL (2005) The roles of multiple proteomic platforms in a pipeline for new diagnostics. Mol Cell Proteomics 4: pp. 1441-1444
2. Vegvari, A, Marko-Varga, G (2010) Clinical protein science and bioanalytical mass spectrometry with an emphasis on lung cancer. Chem Rev 110: pp. 3278-3298
3. V茅gv谩ri, 脕, Rezeli, M, D枚me, B, Fehniger, TE, Marko-Varga, G (2011) Translation Science for Targeted Personalized Medicine Treatments in "Selected Presentations from the 2011 Sino-American Symposium on Clinical and Translational Medicine". Science/AAAS, Washington, DC
4. Zolg, JW, Langen, H (2004) How industry is approaching the search for new diagnostic markers and biomarkers. Mol Cell Proteomics 3: pp. 345-354
5. Siegel, R, Naishadham, D, Jemal, A (2013) Cancer statistics, 2013. CA Cancer J Clin 63: pp. 11-30
6. Vincent, A, Herman, J, Schulick, R, Hruban, RH, Goggins, M (2011) Pancreatic cancer. Lancet 378: pp. 607-620
7. Ferlay, J, Shin, HR, Bray, F, Forman, D, Mathers, C, Parkin, DM (2010) Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer 127: pp. 2893-2917
8. Tingstedt, B, Andersson, E, Flink, A, Bolin, K, Lindgren, B, Andersson, R (2011) Pancreatic cancer, healthcare cost, and loss of productivity: a register-based approach. World J Surg 35: pp. 2298-2305
9. Egawa, S, Takeda, K, Fukuyama, S, Motoi, F, Sunamura, M, Matsuno, S (2004) Clinicopathological aspects of small pancreatic cancer. Pancreas 28: pp. 235-240
10. Ariyama, J, Suyama, M, Satoh, K, Sai, J (1998) Imaging of small pancreatic ductal adenocarcinoma. Pancreas 16: pp. 396-401
11. Glenn, JSW, Kurtzman, SH, Steinberg, SM, Sindelar, WF (1988) Evaluation of the utility of a radioimmunoassay for serum CA 19鈥? levels in patients before and after treatment of carcinoma of the pancreas. J Clin Oncol 6: pp. 462-468
12. Goonetilleke, KSSA (2007) Systematic review of carbohydrate antigen (CA 19鈥?) as a biochemical marker in the diagnosis of pancreatic cancer. Eur J Surg Oncol 33: pp. 266-270
Bosman, FT, Carneiro, F, Hruban, RH, Theise, ND eds. (2010) World Health Organization Classification of Tumours of the Digestive System. IARC Press, Lyon
13. Kl枚ppel, G, Hruban, RH, Longnecker, DS, Adler, G, Kern, SE, Partanen, TJ (2000) Ductal adenocarcinoma of the pancreas. In: Hamilton SR, Aaltonen LA, eds. World Health Organization Classification of Tumours. Pathology and Genetics of Tumours of the Digestive System. IARC Press, Lyon
14. Kim, JELK, Lee, JK, Paik, SW, Rhee, JC, Choi, KW (2004) Clinical usefulness of carbohydrate antigen 19鈥? as a screening test for pancreatic cancer in an asymptomatic population. J Gastroenterol Hepatol 19: pp. 182-186
15. Kawai, S, Suzuki, K, Nishio, K, Ishida, Y, Okada, R, Goto, Y, Naito, M, Wakai, K, Ito, Y, Hamajima, N (2008) Smoking and serum CA19-9 levels according to Lewis and secretor genotypes. Int J Cancer 123: pp. 2880-2884
16. Duffy, MJ, Sturgeon, C, Lamerz, R, Haglund, C, Holubec, VL, Klapdor, R, Nicolini, A, Topolcan, O, Heinemann, V (2010) Tumor markers in pancreatic cancer: a European Group on Tumor Markers (EGTM) status report. Ann Oncol 21: pp. 441-447
17. Wulfkuhle, JD, Liotta, LA, Petricoin, EF (2003) Proteomic applications for the early detection of cancer. Nat Rev Cancer 3: pp. 267-275
18. Paik, YK, Jeong, SK, Omenn, GS, Uhlen, M, Hanash, S, Cho, SY, Lee, HJ, Na, K, Choi, EY, Yan, F, Zhang, F, Zhang, Y, Snyder, M, Cheng, Y, Chen, R, Marko-Varga, G, Deutsch, EW, Kim, H, Kwon, JY, Aebersold, R, Bairoch, A, Taylor, AD, Kim, KY, Lee, EY, Hochstrasser, D, Legrain, P, Hancock, WS (2012) The chromosome-centric human proteome project for cataloging proteins encoded in the genome. Nat Biotechnol 30: pp. 221-223
19. Kondo, T, Tasaka, T, Sano, F, Matsuda, K, Kubo, Y, Matsuhashi, Y, Nakanishi, H, Sadahira, Y, Wada, H, Sugihara, T, Tohyama, K (2009) Philadelphia chromosome-positive acute myeloid leukemia (Ph+AML) treated with imatinib mesylate (IM): a report with IM plasma concentration and bcr-abl transcripts. Leuk Res 33: pp. e137-e138
20. Campbell, PJ, Yachida, S, Mudie, LJ, Stephens, PJ, Pleasance, ED, Stebbings, LA, Morsberger, LA, Latimer, C, McLaren, S, Lin, ML, McBride, DJ, Varela, I, Nik-Zainal, SA, Leroy, C, Jia, M, Menzies, A, Butler, AP, Teague, JW, Griffin, CA, Burton, J, Swerdlow, H, Quail, MA, Stratton, MR, Iacobuzio-Donahue, C, Futreal, PA (2010) The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467: pp. 1109-1113
21. Jones, S, Zhang, X, Parsons, DW, Lin, JC, Leary, RJ, Angenendt, P, Mankoo, P, Carter, H, Kamiyama, H, Jimeno, A, Hong, SM, Fu, B, Lin, MT, Calhoun, ES, Kamiyama, M, Walter, K, Nikolskaya, T, Nikolsky, Y, Hartigan, J, Smith, DR, Hidalgo, M, Leach, SD, Klein, AP, Jaffee, EM, Goggins, M, Maitra, A, Iacobuzio-Donahue, C, Eshleman, JR, Kern, SE, Hruban, RH (2008) Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321: pp. 1801-1806
22. Fenn, JB, Mann, M, Meng, CK, Wong, SF, Whitehouse, CM (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246: pp. 64-71
23. Karas, M, Bahr, U, Hillenkamp, F (1989) UV laser matrix desorption/ionization mass spectrometry of proteins in the 100 000 dalton range. Int J Mass Spectrom Ion Processes 92: pp. 231-242
24. Tanaka, K, Waki, H, Ido, Y, Akita, S, Yoshida, Y, Yoshida, T, Matsuo, T (1988) Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2: pp. 151-153
Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clin Pharmacol Ther 69: pp. 89-95
25. Winter, JM, Yeo, CJ, Brody, JR (2013) Diagnostic, prognostic, and predictive biomarkers in pancreatic cancer. J Surg Oncol 107: pp. 15-22
26. Baumgart, S, Ellenrieder, V, Fernandez-Zapico, ME (2013) Oncogenic transcription factors: cornerstones of inflammation-linked pancreatic carcinogenesis. Gut 62: pp. 310-316
27. Donnarumma, F, V茅gv谩ri, A, Rezeli, M, Welinder, C, Jansson, B, Marko-Varga, G (2013) Accessing microenvironment compartments in FFPE-tissues by protein expression analysis. Bioanalysis.
28. Takadate, T, Onogawa, T, Fukuda, T, Motoi, F, Suzuki, T, Fujii, K, Kihara, M, Mikami, S, Bando, Y, Maeda, S, Ishida, K, Minowa, T, Hanagata, N, Ohtsuka, H, Katayose, Y, Egawa, S, Nishimura, T, Unno, M (2013) Novel prognostic protein markers of resectable pancreatic cancer identified by coupled shotgun and targeted proteomics using formalin-fixed paraffin-embedded tissues. Int J Cancer 132: pp. 1368-1382
29. Marko-Varga, GA, Fehniger, TE (2004) Microscale protein expression profiling during disease evolvement. J Chromatogr A 1053: pp. 279-290
30. Honda, K, Ono, M, Shitashige, M, Masuda, M, Kamita, M, Miura, N, Yamada, T (2013) Proteomic approaches to the discovery of cancer biomarkers for early detection and personalized medicine. Jpn J Clin Oncol 43: pp. 103-109
31. Anderson, NL, Anderson, NG (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 1: pp. 845-867
32. O'Farrell, PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250: pp. 4007-4021
33. Gronborg, M, Bunkenborg, J, Kristiansen, TZ, Jensen, ON, Yeo, CJ, Hruban, RH, Maitra, A, Goggins, MG, Pandey, A (2004) Comprehensive proteomic analysis of human pancreatic juice. J Proteome Res 3: pp. 1042-1055
34. Zhou, L, Lu, Z, Yang, A, Deng, R, Mai, C, Sang, X, Faber, KN, Lu, X (2007) Comparative proteomic analysis of human pancreatic juice: methodological study. Proteomics 7: pp. 1345-1355
35. Abdallah, CD-GE, Renaut, J, Sergeant, K (2012) Gel-based and gel-free quantitative proteomics approaches at a glance. Int J Plant Genomics.
36. Cox, J, Mann, M (2007) Is proteomics the new genomics?. Cell 130: pp. 395-398
37. Mann, M (2009) Comparative analysis to guide quality improvements in proteomics. Nat Methods 6: pp. 717-719
38. Nilsson, T, Mann, M, Aebersold, R, Yates, JR, Bairoch, A, Bergeron, JJ (2010) Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods 7: pp. 681-685
39. Rezeli, M, Vegvari, A, Fehniger, TE, Laurell, T, Marko-Varga, G (2011) Moving towards high density clinical signature studies with a human proteome catalogue developing multiplexing mass spectrometry assay panels. J Clin Bioinforma 1: pp. 7
40. Choudhary, C, Mann, M (2010) Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol 11: pp. 427-439
41. Bondarenko, PV, Chelius, D, Shaler, TA (2002) Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal Chem 74: pp. 4741-4749
42. Wang, W, Zhou, H, Lin, H, Roy, S, Shaler, TA, Hill, LR, Norton, S, Kumar, P, Anderle, M, Becker, CH (2003) Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem 75: pp. 4818-4826
43. Lundgren, DH, Hwang, SI, Wu, L, Han, DK (2010) Role of spectral counting in quantitative proteomics. Expert Rev Proteomics 7: pp. 39-53
44. Liu, H, Sadygov, RG, Yates, JR (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76: pp. 4193-4201
45. Searle, BC (2010) Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies. Proteomics 10: pp. 1265-1269
46. Richter, R, Schulz-Knappe, P, Schrader, M, Standker, L, Jurgens, M, Tammen, H, Forssmann, WG (1999) Composition of the peptide fraction in human blood plasma: database of circulating human peptides. J Chromatogr B Biomed Sci Appl 726: pp. 25-35
47. Turtoi, A, Musmeci, D, Wang, Y, Dumont, B, Somja, J, Bevilacqua, G, De Pauw, E, Delvenne, P, Castronovo, V (2011) Identification of novel accessible proteins bearing diagnostic and therapeutic potential in human pancreatic ductal adenocarcinoma. J Proteome Res 10: pp. 4302-4313
48. Golembieski, WA, Rempel, SA (2002) cDNA array analysis of SPARC-modulated changes in glioma gene expression. J Neurooncol 60: pp. 213-226
49. Ivanov, SV, Ivanova, AV, Salnikow, K, Timofeeva, O, Subramaniam, M, Lerman, MI (2008) Two novel VHL targets, TGFBI (BIGH3) and its transactivator KLF10, are up-regulated in renal clear cell carcinoma and other tumors. Biochem Biophys Res Commun 370: pp. 536-540
50. Ma, C, Rong, Y, Radiloff, DR, Datto, MB, Centeno, B, Bao, S, Cheng, AW, Lin, F, Jiang, S, Yeatman, TJ, Wang, XF (2008) Extracellular matrix protein betaig-h3/TGFBI promotes metastasis of colon cancer by enhancing cell extravasation. Genes Dev 22: pp. 308-321
51. Yamanaka, M, Kimura, F, Kagata, Y, Kondoh, N, Asano, T, Yamamoto, M, Hayakawa, M (2008) BIGH3 is overexpressed in clear cell renal cell carcinoma. Oncol Rep 19: pp. 865-874
52. Ahmed, W, Kucich, U, Abrams, W, Bashir, M, Rosenbloom, J, Segade, F, Mecham, R, Rosenbloom, J (1998) Signaling pathway by which TGF-beta1 increases expression of latent TGF-beta binding protein-2 at the transcriptional level. Connect Tissue Res 37: pp. 263-276
53. Vehvilainen, P, Hyytiainen, M, Keski-Oja, J (2003) Latent transforming growth factor-beta-binding protein 2 is an adhesion protein for melanoma cells. J Biol Chem 278: pp. 24705-24713
54. Nakajima, M, Kizawa, H, Saitoh, M, Kou, I, Miyazono, K, Ikegawa, S (2007) Mechanisms for asporin function and regulation in articular cartilage. J Biol Chem 282: pp. 32185-32192
55. Zhang, J, Song, M, Wang, J, Sun, M, Wang, B, Li, R, Huang, Y, Hou, L, Jin, Y, Wang, M, Tang, J (2011) Enoyl coenzyme A hydratase 1 is an important factor in the lymphatic metastasis of tumors. Biomed Pharmacother 65: pp. 157-162
56. Yu, L, Wang, L, Chen, S (2011) Olfactomedin 4, a novel marker for the differentiation and progression of gastrointestinal cancers. Neoplasma 58: pp. 9-13
57. Zhang, L, Ding, F, Cao, W, Liu, Z, Liu, W, Yu, Z, Wu, Y, Li, W, Li, Y, 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: pp. 1639-1646
58. Cao, W, Zhang, B, Ding, F, Zhang, W, Sun, B, Liu, Z (2013) Expression of SLP-2 was associated with invasion of esophageal squamous cell carcinoma. PLoS One 8: pp. e63890
59. Cui, Z, Zhang, L, Hua, Z, Cao, W, Feng, W, Liu, Z (2007) Stomatin-like protein 2 is overexpressed and related to cell growth in human endometrial adenocarcinoma. Oncol Rep 17: pp. 829-833
60. Chan, DA, Sutphin, PD, Nguyen, P, Turcotte, S, Lai, EW, Banh, A, Reynolds, GE, Chi, JT, Wu, J, Solow-Cordero, DE, Bonnet, M, Flanagan, JU, Bouley, DM, Graves, EE, Denny, WA, Hay, MP, Giaccia, AJ (2011) Targeting GLUT1 and the Warburg effect in renal cell carcinoma by chemical synthetic lethality. Sci Transl Med 3: pp. 94ra70
61. Pizzi, S, Porzionato, A, Pasquali, C, Guidolin, D, Sperti, C, Fogar, P, Macchi, V, De Caro, R, Pedrazzoli, S, Parenti, A (2009) Glucose transporter-1 expression and prognostic significance in pancreatic carcinogenesis. Histol Histopathol 24: pp. 175-185
62. Ito, H, Duxbury, M, Zinner, MJ, Ashley, SW, Whang, EE (2004) Glucose transporter-1 gene expression is associated with pancreatic cancer invasiveness and MMP-2 activity. Surgery 136: pp. 548-556
63. Paulo, JA, Lee, LS, Banks, PA, Steen, H, Conwell, DL (2012) Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry. Pancreas 41: pp. 175-185
64. Mogami, T, Yokota, N, Asai-Sato, M, Yamada, R, Koizume, S, Sakuma, Y, Yoshihara, M, Nakamura, Y, Takano, Y, Hirahara, F, Miyagi, Y, Miyagi, E (2013) Annexin A4 is involved in proliferation, chemo-resistance and migration and invasion in ovarian clear cell adenocarcinoma cells. PLoS One 8: pp. e80359
65. Deng, S, Wang, J, Hou, L, Li, J, Chen, G, Jing, B, Zhang, X, Yang, Z (2013) Annexin A1, A2, A4 and A5 play important roles in breast cancer, pancreatic cancer and laryngeal carcinoma, alone and/or synergistically. Oncol Lett 5: pp. 107-112
66. Schwarz, RE, Awasthi, N, Konduri, S, Caldwell, L, Cafasso, D, Schwarz, MA (2010) Antitumor effects of EMAP II against pancreatic cancer through inhibition of fibronectin-dependent proliferation. Cancer Biol Ther 9: pp. 632-639
67. Matsubara, J, Honda, K, Ono, M, Tanaka, Y, Kobayashi, M, Jung, G, Yanagisawa, K, Sakuma, T, Nakamori, S, Sata, N, Nagai, H, Ioka, T, Okusaka, T, Kosuge, T, Tsuchida, A, Shimahara, M, Yasunami, Y, Chiba, T, Hirohashi, S, Yamada, T (2011) Reduced plasma level of CXC chemokine ligand 7 in patients with pancreatic cancer. Cancer Epidemiol Biomarkers Prev 20: pp. 160-171
68. 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: pp. 271-284
69. Van den Steen, PE, Proost, P, Wuyts, A, Van Damme, J, Opdenakker, G (2000) Neutrophil gelatinase B potentiates interleukin-8 tenfold by aminoterminal processing, whereas it degrades CTAP-III, PF-4, and GRO-alpha and leaves RANTES and MCP-2 intact. Blood 96: pp. 2673-2681
70. Tian, M, Cui, YZ, Song, GH, Zong, MJ, Zhou, XY, Chen, Y, Han, JX (2008) Proteomic analysis identifies MMP-9, DJ-1 and A1BG as overexpressed proteins in pancreatic juice from pancreatic ductal adenocarcinoma patients. BMC Cancer 8: pp. 241
71. Gevaert, K, Impens, F, Ghesquiere, B, Van Damme, P, Lambrechts, A, Vandekerckhove, J (2008) Stable isotopic labeling in proteomics. Proteomics 8: pp. 4873-4885
72. Picotti, P, Aebersold, R (2012) Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods 9: pp. 555-566
73. Colzani, M, Schutz, F, Potts, A, Waridel, P, Quadroni, M (2008) Relative protein quantification by isobaric SILAC with immonium ion splitting (ISIS). Mol Cell Proteomics 7: pp. 927-937
74. Pan, S, Brentnall, TA, Kelly, K, Chen, R (2013) Tissue proteomics in pancreatic cancer study: discovery, emerging technologies, and challenges. Proteomics 13: pp. 710-721
75. Amanchy, R, Kalume, DE, Pandey, A (2005) Stable isotope labeling with amino acids in cell culture (SILAC) for studying dynamics of protein abundance and posttranslational modifications. Sci STKE 2005 267: pp. pl2
76. Everley, PA, Krijgsveld, J, Zetter, BR, Gygi, SP (2004) Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Mol Cell Proteomics 3: pp. 729-735
77. Ong, SEBB, Kratchmarova, I, Kristensen, DB, Steen, H, Pandey, A, Mann, M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1: pp. 376-386
78. Geiger, T, Cox, J, Ostasiewicz, P, Wisniewski, JR, Mann, M (2010) Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods 7: pp. 383-385
79. Gronborg, M, Kristiansen, TZ, Iwahori, A, Chang, R, Reddy, R, Sato, N, Molina, H, Jensen, ON, Hruban, RH, Goggins, MG, Maitra, A, Pandey, A (2006) Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol Cell Proteomics 5: pp. 157-171
80. Wang, HX, Li, Q, Sharma, C, Knoblich, K, Hemler, ME (2011) Tetraspanin protein contributions to cancer. Biochem Soc Trans 39: pp. 547-552
81. Sho, M, Adachi, M, Taki, T, Hashida, H, Konishi, T, Huang, CL, Ikeda, N, Nakajima, Y, Kanehiro, H, Hisanaga, M, Nakano, H, Miyake, M (1998) Transmembrane 4 superfamily as a prognostic factor in pancreatic cancer. Int J Cancer 79: pp. 509-516
82. Whitelock, JM, Melrose, J, Iozzo, RV (2008) Diverse cell signaling events modulated by perlecan. Biochemistry 47: pp. 11174-11183
83. Jiang, X, Multhaupt, H, Chan, E, Schaefer, L, Schaefer, RM, Couchman, JR (2004) Essential contribution of tumor-derived perlecan to epidermal tumor growth and angiogenesis. J Histochem Cytochem 52: pp. 1575-1590
84. Mahley, RW (1988) Apolipoprotein E: cholesterol transport protein with expanding role in cell biology. Science 240: pp. 622-630
85. Hui, DY, Basford, JE (2005) Distinct signaling mechanisms for apoE inhibition of cell migration and proliferation. Neurobiol Aging 26: pp. 317-323
86. Zhang, H, Wu, LM, Wu, J (2011) Cross-talk between apolipoprotein E and cytokines. Mediators Inflamm 2011: pp. 949072
87. Chen, J, Chen, LJ, Yang, RB, Xia, YL, Zhou, HC, Wu, W, Lu, Y, Hu, LW, Zhao, Y (2013) Expression and clinical significance of apolipoprotein E in pancreatic ductal adenocarcinoma. Med Oncol 30: pp. 583
88. Chen, J, Wu, W, Zhen, C, Zhou, H, Yang, R, Chen, L, Hu, L (2013) Expression and clinical significance of complement C3, complement C4b1 and apolipoprotein E in pancreatic cancer. Oncol Lett 6: pp. 43-48
89. Martinez-Clemente, M, Ferre, N, Gonzalez-Periz, A, Lopez-Parra, M, Horrillo, R, Titos, E, Moran-Salvador, E, Miquel, R, Arroyo, V, Funk, CD, Claria, J (2010) 5-lipoxygenase deficiency reduces hepatic inflammation and tumor necrosis factor alpha-induced hepatocyte damage in hyperlipidemia-prone ApoE-null mice. Hepatology 51: pp. 817-827
90. Liang, JJ, Zhu, S, Bruggeman, R, Zaino, RJ, Evans, DB, Fleming, JB, Gomez, HF, Zander, DS, Wang, H (2010) High levels of expression of human stromal cell-derived factor-1 are associated with worse prognosis in patients with stage II pancreatic ductal adenocarcinoma. Cancer Epidemiol Biomarkers Prev 19: pp. 2598-2604
91. Walsh, N, Clynes, M, Crown, J, O'Donovan, N (2009) Alterations in integrin expression modulates invasion of pancreatic cancer cells. J Exp Clin Cancer Res 28: pp. 140
92. Yu, KH, Barry, CG, Austin, D, Busch, CM, Sangar, V, Rustgi, AK, Blair, IA (2009) Stable isotope dilution multidimensional liquid chromatography-tandem mass spectrometry for pancreatic cancer serum biomarker discovery. J Proteome Res 8: pp. 1565-1576
93. Roland, CL, Dineen, SP, Toombs, JE, Carbon, JG, Smith, CW, Brekken, RA, Barnett, CC (2010) Tumor-derived intercellular adhesion molecule-1 mediates tumor-associated leukocyte infiltration in orthotopic pancreatic xenografts. Exp Biol Med (Maywood) 235: pp. 263-270
94. Tempia-Caliera, AA, Horvath, LZ, Zimmermann, A, Tihanyi, TT, Korc, M, Friess, H, Buchler, MW (2002) Adhesion molecules in human pancreatic cancer. J Surg Oncol 79: pp. 93-100
95. Kikkawa, Y, Miner, JH (2005) Review: Lutheran/B-CAM: a laminin receptor on red blood cells and in various tissues. Connect Tissue Res 46: pp. 193-199
96. Gygi, SPRB, Gerber, SA, Turecek, F, Gelb, MH, Aebersold, R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17: pp. 994-999
97. Yi, ECLX, Cooke, K, Lee, H, Raught, B, Page, A, Aneliunas, V, Hieter, P, Goodlett, DR, Aebersold, R (2005) Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics 5: pp. 380-387
98. Chen, R, Yi, EC, Donohoe, S, Pan, S, Eng, J, Cooke, K, Crispin, DA, Lane, Z, Goodlett, DR, Bronner, MP, Aebersold, R, Brentnall, TA (2005) Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape. Gastroenterology 129: pp. 1187-1197
99. Zheng, L, Foley, K, Huang, L, Leubner, A, Mo, G, Olino, K, Edil, BH, Mizuma, M, Sharma, R, Le, DT, Anders, RA, Illei, PB, Van Eyk, JE, Maitra, A, Laheru, D, Jaffee, EM (2011) Tyrosine 23 phosphorylation-dependent cell-surface localization of annexin A2 is required for invasion and metastases of pancreatic cancer. PLoS One 6: pp. e19390
100. Zhang, X, Liu, S, Guo, C, Zong, J, Sun, MZ (2012) The association of annexin A2 and cancers. Clin Transl Oncol 14: pp. 634-640
101. Chen, R, Pan, S, Yi, EC, Donohoe, S, Bronner, MP, Potter, JD, Goodlett, DR, Aebersold, R, Brentnall, TA (2006) Quantitative proteomic profiling of pancreatic cancer juice. Proteomics 6: pp. 3871-3879
102. Busund, LT, Richardsen, E, Busund, R, Ukkonen, T, Bjornsen, T, Busch, C, Stalsberg, H (2005) Significant expression of IGFBP2 in breast cancer compared with benign lesions. J Clin Pathol 58: pp. 361-366
103. Hsieh, D, Hsieh, A, Stea, B, Ellsworth, R (2010) IGFBP2 promotes glioma tumor stem cell expansion and survival. Biochem Biophys Res Commun 397: pp. 367-372
104. Pan, S, Chen, R, Crispin, DA, May, D, Stevens, T, McIntosh, MW, Bronner, MP, Ziogas, A, Anton-Culver, H, Brentnall, TA (2011) Protein alterations associated with pancreatic cancer and chronic pancreatitis found in human plasma using global quantitative proteomics profiling. J Proteome Res 10: pp. 2359-2376
105. Bloomston, M, Shafii, A, Zervos, EE, Rosemurgy, AS (2002) TIMP-1 overexpression in pancreatic cancer attenuates tumor growth, decreases implantation and metastasis, and inhibits angiogenesis. J Surg Res 102: pp. 39-44
106. Thompson, ASJ, Kuhn, K, Kienle, S, Schwarz, J, Schmidt, G, Neumann, T, Johnstone, R, Mohammed, AK, Hamon, C (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75: pp. 1895-1904
107. Dayon, LHA, Licker, V, Turck, N, Kuhn, K, Hochstrasser, DF, Burkhard, PR, Sanchez, JC (2008) Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal Chem 80: pp. 2921-2931
108. Sinclair, J, Timms, JF (2011) Quantitative profiling of serum samples using TMT protein labelling, fractionation and LC-MS/MS. Methods 54: pp. 361-369
109. Ni, XG, Zhou, L, Wang, GQ, Liu, SM, Bai, XF, Liu, F, Peppelenbosch, MP, Zhao, P (2008) The ubiquitin-proteasome pathway mediates gelsolin protein downregulation in pancreatic cancer. Mol Med 14: pp. 582-589
110. Abulaizi, M, Tomonaga, T, Satoh, M, Sogawa, K, Matsushita, K, Kodera, Y, Obul, J, Takano, S, Yoshitomi, H, Miyazaki, M, Nomura, F (2011) The application of a three-step proteome analysis for identification of new biomarkers of pancreatic cancer. Int J Proteomics 2011: pp. 628787
111. Wang, R, Zhang, T, Ma, Z, Wang, Y, Cheng, Z, Xu, H, Li, W, Wang, X (2010) The interaction of coagulation factor XII and monocyte/macrophages mediating peritoneal metastasis of epithelial ovarian cancer. Gynecol Oncol 117: pp. 460-466
112. Fedail, SS, Harvey, RF, Salmon, PR, Brown, P, Read, AE (1979) Trypsin and lactoferrin levels in pure pancreatic juice in patients with pancreatic disease. Gut 20: pp. 983-986
113. Deng, M, Zhang, W, Tang, H, Ye, Q, Liao, Q, Zhou, Y, Wu, M, Xiong, W, Zheng, Y, Guo, X, Qin, Z, He, W, Zhou, M, Xiang, J, Li, X, Ma, J, Li, G (2013) Lactotransferrin acts as a tumor suppressor in nasopharyngeal carcinoma by repressing AKT through multiple mechanisms. Oncogene 32: pp. 4273-4283
114. Beck, F, Burkhart, JM, Geiger, J, Zahedi, RP, Sickmann, A (2012) Robust workflow for iTRAQ-based peptide and protein quantification. Methods Mol Biol 893: pp. 101-113
115. Ting, L, Rad, R, Gygi, SP, Haas, W (2011) MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods 8: pp. 937-940
116. Ow, SY, Salim, M, Noirel, J, Evans, C, Rehman, I, Wright, PC (2009) iTRAQ underestimation in simple and complex mixtures: "the good, the bad and the ugly". J Proteome Res 8: pp. 5347-5355
117. Pan, S, Chen, R, Reimel, BA, Crispin, DA, Mirzaei, H, Cooke, K, Coleman, JF, Lane, Z, Bronner, MP, Goodlett, DR, McIntosh, MW, Traverso, W, Aebersold, R, Brentnall, TA (2009) Quantitative proteomics investigation of pancreatic intraepithelial neoplasia. Electrophoresis 30: pp. 1132-1144
118. Sawai, H, Okada, Y, Funahashi, H, Takahashi, H, Matsuo, Y, Yasuda, A, Ochi, N, Takeyama, H, Manabe, T (2008) Basement membrane proteins play an important role in the invasive processes of human pancreatic cancer cells. J Surg Res 144: pp. 117-123
119. Fitzner, B, Walzel, H, Sparmann, G, Emmrich, J, Liebe, S, Jaster, R (2005) Galectin-1 is an inductor of pancreatic stellate cell activation. Cell Signal 17: pp. 1240-1247
120. Masamune, A, Satoh, M, Hirabayashi, J, Kasai, K, Satoh, K, Shimosegawa, T (2006) Galectin-1 induces chemokine production and proliferation in pancreatic stellate cells. Am J Physiol Gastrointest Liver Physiol 290: pp. G729-G736
121. Kikuchi, S, Honda, K, Tsuda, H, Hiraoka, N, Imoto, I, Kosuge, T, Umaki, T, Onozato, K, Shitashige, M, Yamaguchi, U, Ono, M, Tsuchida, A, Aoki, T, Inazawa, J, Hirohashi, S, Yamada, T (2008) Expression and gene amplification of actinin-4 in invasive ductal carcinoma of the pancreas. Clin Cancer Res 14: pp. 5348-5356
122. Welsch, T, Keleg, S, Bergmann, F, Bauer, S, Hinz, U, Schmidt, J (2009) Actinin-4 expression in primary and metastasized pancreatic ductal adenocarcinoma. Pancreas 38: pp. 968-976
123. Hayashida, Y, Honda, K, Idogawa, M, Ino, Y, Ono, M, Tsuchida, A, Aoki, T, Hirohashi, S, Yamada, T (2005) E-cadherin regulates the association between beta-catenin and actinin-4. Cancer Res 65: pp. 8836-8845
124. Anderson, L, Hunter, CL (2006) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics 5: pp. 573-588
125. Whiteaker, JR, Zhao, L, Abbatiello, SE, Burgess, M, Kuhn, E, Lin, C, Pope, ME, Razavi, M, Anderson, NL, Pearson, TW, Carr, SA, Paulovich, AG (2011) Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry. Mol Cell Proteomics 10: pp. M110 005645
126. Whiteaker, JR, Zhao, L, Anderson, L, Paulovich, AG (2010) An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers. Mol Cell Proteomics 9: pp. 184-196
127. Kamiie, J, Ohtsuki, S, Iwase, R, Ohmine, K, Katsukura, Y, Yanai, K, Sekine, Y, Uchida, Y, Ito, S, Terasaki, T (2008) Quantitative atlas of membrane transporter proteins: development and application of a highly sensitive simultaneous LC/MS/MS method combined with novel in-silico peptide selection criteria. Pharm Res 25: pp. 1469-1483
128. Scherl, A, Shaffer, SA, Taylor, GK, Kulasekara, HD, Miller, SI, Goodlett, DR (2008) Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides. Anal Chem 80: pp. 1182-1191
129. Lange, V, Picotti, P, Domon, B, Aebersold, R (2008) Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 4: pp. 222
130. Unwin, RD, Griffiths, JR, Leverentz, MK, Grallert, A, Hagan, IM, Whetton, AD (2005) Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity. Mol Cell Proteomics 4: pp. 1134-1144
131. Griffiths, JR, Unwin, RD, Evans, CA, Leech, SH, Corfe, BM, Whetton, AD (2007) The application of a hypothesis-driven strategy to the sensitive detection and location of acetylated lysine residues. J Am Soc Mass Spectrom 18: pp. 1423-1428
132. Duncan, MWYA, Patterson, SD (2009) Quantifying proteins by mass spectrometry: the selectivity of SRM is only part of the problem. Proteomics 9: pp. 1124-1127
133. MacLean, B, Tomazela, DM, Shulman, N, Chambers, M, Finney, GL, Frewen, B, Kern, R, Tabb, DL, Liebler, DC, MacCoss, MJ (2010) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26: pp. 966-968
134. Martin, DB, Holzman, T, May, D, Peterson, A, Eastham, A, Eng, J, McIntosh, M (2008) MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol Cell Proteomics 7: pp. 2270-2278
135. Sherwood, CA, Eastham, A, Lee, LW, Risler, J, Mirzaei, H, Falkner, JA, Martin, DB (2009) Rapid optimization of MRM-MS instrument parameters by subtle alteration of precursor and product m/z targets. J Proteome Res 8: pp. 3746-3751
136. Abbatiello, SE, Mani, DR, Keshishian, H, Carr, SA (2010) Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry. Clin Chem 56: pp. 291-305
137. Whiteaker, JR, Lin, C, Kennedy, J, Hou, L, Trute, M, Sokal, I, Yan, P, Schoenherr, RM, Zhao, L, Voytovich, UJ, Kelly-Spratt, KS, Krasnoselsky, A, Gafken, PR, Hogan, JM, Jones, LA, Wang, P, Amon, L, Chodosh, LA, Nelson, PS, McIntosh, MW, Kemp, CJ, Paulovich, AG (2011) A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat Biotechnol 29: pp. 625-634
138. Yoneyama, T, Ohtsuki, S, Ono, M, Ohmine, K, Uchida, Y, Yamada, T, Tachikawa, M, Terasaki, T (2013) Quantitative targeted absolute proteomics-based large-scale quantification of proline-hydroxylated alpha-fibrinogen in plasma for pancreatic cancer diagnosis. J Proteome Res 12: pp. 753-762
139. Baker, M (2012) Biorepositories: Building better biobanks. Nature 486: pp. 141-146
140. Marko-Varga, G, Omenn, GS, Paik, YK, Hancock, WS (2013) A first step toward completion of a genome-wide characterization of the human proteome. J Proteome Res 12: pp. 1-5
141. Liang, WS, Craig, DW, Carpten, J, Borad, MJ, Demeure, MJ, Weiss, GJ, Izatt, T, Sinari, S, Christoforides, A, Aldrich, J, Kurdoglu, A, Barrett, M, Phillips, L, Benson, H, Tembe, W, Braggio, E, Kiefer, JA, Legendre, C, Posner, R, Hostetter, GH, Baker, A, Egan, JB, Han, H, Lake, D, Stites, EC, Ramanathan, RK, Fonseca, R, Stewart, AK, Von Hoff, D (2012) Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing. PLoS One 7: pp. e43192
142. Fagerberg, L, Oksvold, P, Skogs, M, Algenas, C, Lundberg, E, Ponten, F, Sivertsson, A, Odeberg, J, Klevebring, D, Kampf, C, Asplund, A, Sj枚stedt, E, Al-Khalili Szigyarto, C, Edqvist, PH, Olsson, I, Rydberg, U, Hudson, P, Ottosson Takanen, J, Berling, H, Bj枚rling, L, Tegel, H, Rockberg, J, Nilsson, P, Navani, S, Jirstr枚m, K, Mulder, J, Schwenk, JM, Zwahlen, M, Hober, S, Forsberg, M (2013) Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP). J Proteome Res 12: pp. 2439-2448
143. Lane, L, Argoud-Puy, G, Britan, A, Cusin, I, Duek, PD, Evalet, O, Gateau, A, Gaudet, P, Gleizes, A, Masselot, A, Zwahlen, C, Bairoch, A (2012) neXtProt: a knowledge platform for human proteins. Nucleic Acids Res 40: pp. D76-D83
144. Harsha, HC, Jimeno, A, Molina, H, Mihalas, AB, Goggins, MG, Hruban, RH, Schulick, RD, Kamath, U, Maitra, A, Hidalgo, M, Pandey, A (2008) Activated epidermal growth factor receptor as a novel target in pancreatic cancer therapy. J Proteome Res 7: pp. 4651-4658
145. Ritchie, SA, Akita, H, Takemasa, I, Eguchi, H, Pastural, E, Nagano, H, Monden, M, Doki, Y, Mori, M, Jin, W, Sajobi, TT, Jayasinghe, D, Chitou, B, Yamazaki, Y, White, T, Goodenowe, DB (2013) Metabolic system alterations in pancreatic cancer patient serum: potential for early detection. BMC Cancer 13: pp. 416
146. Krastins, B, Prakash, A, Sarracino, DA, Nedelkov, D, Niederkofler, EE, Kiernan, UA, Nelson, R, Vogelsang, MS, Vadali, G, Garces, A, Sutton, JN, Peterman, S, Byram, G, Darbouret, B, P茅russe, JR, Seidah, NG, Coulombe, B, Gobom, J, Portelius, E, Pannee, J, Blennow, K, Kulasingam, V, Couchman, L, Moniz, C, Lopez, MF (2013) Rapid development of sensitive, high-throughput, quantitative and highly selective mass spectrometric targeted immunoassays for clinically important proteins in human plasma and serum. Clin Biochem 46: pp. 399-410
147. Addona, TA, Abbatiello, SE, Schilling, B, Skates, SJ, Mani, DR, Bunk, DM, Spiegelman, CH, Zimmerman, LJ, Ham, A-JL, Keshishian, H, Hall, SC, Allen, S, Blackman, RK, Borchers, CH, Buck, C, Cardasis, HL, Cusack, MP, Dodder, NG, Gibson, BW, Held, JM, Hiltke, T, Jackson, A, Johansen, EB, Kinsinger, CR, Li, J, Mesri, M, Neubert, TA, Niles, RK, Pulsipher, TC, Ransohoff, D (2009) Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotech 27: pp. 633-641
148. Paik, YK, Hancock, WS (2012) Uniting ENCODE with genome-wide proteomics. Nat Biotechnol 30: pp. 1065-1067
149. Lichti, CF, Liu, H, Shavkunov, AS, Mostovenko, E, Sulman, EP, Ezhilarasan, R, Wang, Q, Kroes, RA, Moskal, JC, Fenyo, D, Oksuz, BA, Conrad, CA, Lang, FF, Berven, FS, V茅gv谩ri, A, Rezeli, M, Marko-Varga, G, Hober, S, Nilsson, CL (2014) Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines. J Proteome Res 13: pp. 191-199 - 刊物主题：Biomedicine general; Medicine/Public Health, general;
- 出版者：BioMed Central
- ISSN：1479-5876
文摘
In the post-genomic era, it has become evident that genetic changes alone are not sufficient to understand most disease processes including pancreatic cancer. Genome sequencing has revealed a complex set of genetic alterations in pancreatic cancer such as point mutations, chromosomal losses, gene amplifications and telomere shortening that drive cancerous growth through specific signaling pathways. Proteome-based approaches are important complements to genomic data and provide crucial information of the target driver molecules and their post-translational modifications. By applying quantitative mass spectrometry, this is an alternative way to identify biomarkers for early diagnosis and personalized medicine. We review the current quantitative mass spectrometric technologies and analyses that have been developed and applied in the last decade in the context of pancreatic cancer. Examples of candidate biomarkers that have been identified from these pancreas studies include among others, asporin, CD9, CXC chemokine ligand 7, fibronectin 1, galectin-1, gelsolin, intercellular adhesion molecule 1, insulin-like growth factor binding protein 2, metalloproteinase inhibitor 1, stromal cell derived factor 4, and transforming growth factor beta-induced protein. Many of these proteins are involved in various steps in pancreatic tumor progression including cell proliferation, adhesion, migration, invasion, metastasis, immune response and angiogenesis. These new protein candidates may provide essential information for the development of protein diagnostics and targeted therapies. We further argue that new strategies must be advanced and established for the integration of proteomic, transcriptomic and genomic data, in order to enhance biomarker translation. Large scale studies with meta data processing will pave the way for novel and unexpected correlations within pancreatic cancer, that will benefit the patient, with targeted treatment.