A mouse to human search for plasma proteome changes associated with pancreatic tumor development

PLoS Medicine

Volumn 5, Issue 6, 2008, Pages 0953-0967

  Faca, Vitor M ^a   Song, Kenneth S ^a   Wang, Hong ^a   Zhang, Qing ^a   Krasnoselsky, Alexei L ^a   Newcomb, Lisa F ^a   Plentz, Ruben R ^b   Gurumurthy, Sushma ^b   Redston, Mark S ^c   Pitteri, Sharon J ^a   Pereira Faca, Sandra R ^a   Ireton, Renee C ^a   Katayama, Hiroyuki ^a   Glukhova, Veronika ^a   Phanstiel, Douglas ^a   Brenner, Dean E ^d   Anderson, Michelle A ^d   Misek, David ^d   Scholler, Nathalie ^a   Urban, Nicole D ^a   Barnett, Matt J ^a   Edelstein, Cim ^a   Goodman, Gary E ^a   Thornquist, Mark D ^a   Mcintosh, Martin W ^a   DePinho, Ronald A ^e   Bardeesy, Nabeel ^b   Hanash, Samir M ^a   more..

^a Fred Hutchinson Cancer Center and University of Washington   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c BRIGHAM AND WOMEN S HOSPITAL   (United States)

^d UNIVERSITY OF MICHIGAN   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; RNA; MESSENGER RNA; TUMOR MARKER;

ADVANCED CANCER; ANIMAL TISSUE; ARTICLE; BLOOD SAMPLING; CANCER PATIENT; CANCER STAGING; COHORT ANALYSIS; CONTROLLED STUDY; EARLY CANCER; FRACTIONATION; GENE EXPRESSION; HUMAN; HUMAN TISSUE; MOUSE; NONHUMAN; PANCREAS CANCER; PROTEIN EXPRESSION; PROTEOMICS; SYMPTOMATOLOGY; TECHNOLOGY; TUMOR GROWTH; ANIMAL; BLOOD; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; PANCREAS TUMOR;

ANIMALS; HUMANS; MASS SPECTROMETRY; MICE; PANCREATIC NEOPLASMS; PROTEOME; PROTEOMICS; RNA, MESSENGER; TUMOR MARKERS, BIOLOGICAL;

EID: 46349104324     PISSN: 15491277     EISSN: 15491676     Source Type: Journal    
DOI: 10.1371/journal.pmed.0050123     Document Type: Article

References (68)

1. Hanash S (2003) Disease proteomics. Nature 422: 226-232.
2. Hanash SM, Pitteri SJ, Faca VM (2008) Mining the plasma proteome for cancer biomarkers. Nature 452: 571-579.
3. Faca V, Pitteri SJ, Newcomb L, Glukhova V, Phanstiel D, et al. (2007) Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J Proteome Res 6: 3558-3565.
4. States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, et al. (2006) Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol 24: 333-338.
5. Sweet-Cordero A, Mukherjee S, Subramanian A, You H, Roix JJ, et al. (2005) An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis, Nat Genet 37: 48-55.
6. Zender L, Spector MS, Xue W, Flemming P, Cordon-Cardo C, et al. (2006) Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach. Cell 125: 1253-1267.
7. Kim M, Cans JD, Xogueira C, Wang A, Paik JH, et al. (2006) Comparative oncogenomics identifies NEDD9 as a melanoma metastasis gene. Cell 125: 1269-1281.
8. Maser RS, Choudhury B, Campbell PJ, Feng B, Wong KK, et al. (2007) Chromosomally unstable mouse tumours have genomic alterations similar to diverse human cancel's. Nature 447: 966-971.
9. Hingorani SR, Petricoin EF, Maitra A, Rajapakse V, King C, et al. (2003) Preinvasive and invasive ductal pancreatic cancer and its early detection in the mouse. Cancer Cell 4: 437-450.
10. Hezel AF, Kimmehnan AC, Stanger BZ, Bardeesy N, Depinho RA (2006) Genetics and biology of pancreatic ductal adenocarcinoma. Genes Bev 20: 1218-1249.
11. Moskaluk CA. Hruban RH, Kern SE (1997) p 16 and K-ras gene mutations in the intraductal precursors of human pancreatic adenocarcinoma. Cancer Res 57: 2140-2143.
12. DiGiuseppe JA, Hruban RH, Goodman SN, Polak M, van den Berg FM, et al. (1994) Overexpression of p53 protein in adenocarcinoma of the pancreas. Am J Clin Pathol 101: 684-688.
13. Aguirre AJ, Bardeesy N, Sinha M, Lopez L, Tuveson DA, et al. (2003) Activated Kras and Ink4a/Arf deficiency cooperate to produce metastatic pancreatic ductal adenocarcinoma. Genes Dev 17: 3112-3126.
14. Bardeesy N, Aguirre AJ, Chu GC, Cheng KH, Lopez LV, et al. (2006) Both p16(Ink4a) and the p19(Arf)-p53 pathway constrain progression of pancreatic adenocarcinoma in the mouse. Proc Natl Acad Sci U S A 103: 5947-5952.
15. Hingorani SR, Wang L, Multani AS, Combs C, Deramaudt IB, et al. (2005) Trp53R172H and KrasG12D cooperate to promote chromosomal instability and widely metastatic pancreatic ductal adenocarcinoma in mice. Cancer Cell 7: 469-483.
16. Faca V, Coram M, Phanstiel D, Glukhova V, Zhang Q, et al. (2006) Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS. J Proteome Res 5: 2009-2018.
17. Misek BE, Kuick R, Wang H, Galchev V, Deng B, et al. (2005) A wide range of protein isoforms in serum and plasma uncovered by a quantitative intact protein analysis system. Proteomics 5: 3343-3352.
18. Wang H. Clouthier SG, Galchev V, Misek DF, Duffner U, et al. (2005) Intact-protein-based high-resolution three-dimensional quantitative analysis system for proteome profiling of biological fluids. Mol Cell Proteomics 4: 618-625.
19. Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, et al. (2006) Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J Proteome Res 5: 112-121.
20. MacLean B Eng JK, Beavis RC, McIntosh M (2006) General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics 22: 2830-2832.
21. Keller A, Nesvizhskii AI, Kolker E, Aebersold R (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74: 5383-5392.
22. Nesvizhskii AI, Keller A, Kolker E, Aebersold R (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75: 4646-4658.
23. Scholler X, Crawford M, Sato A, Drescher CW, O'Briant KC, et al. (2006) Bead-based ELISA for validation of ovarian cancer early detection market's. Clin Cancer Res 12: 2117-2124.
24. McIntosh MW, Drescher C, Karlan B, Scholler X, Urban X, et al. (2004) Combining CA 125 and SMR serum markers for diagnosis and early detection of ovarian carcinoma. Gynecol Oncol 95: 9-15.
25. Pepe MS, Longton G (2005) Standardizing diagnostic markers to evaluate and compare their performance. Epidemiology 16: 598-603.
26. DeLong ER, DeLong DM, Clarke-Pearson DL (1988) Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics 44: 837-845.
27. Su AL Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101: 6062-6067.
28. Logsdon CD, Simeone DM, Binkley C, Arumugam T, Greenson JK, et al. (2003) Molecular profiling of pancreatic adenocarcinoma and chronic pancreatitis identifies multiple genes differentially regulated in pancreatic cancer. Cancer Res 68: 2649-2657.
29. Hood BL, Zhou M, Chan KG, Lucas DA, Kim GJ, et al, (2005) Investigation of the mouse serum proteome, J Proteome Res 4: 1561-1568.
30. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, et al. (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4: 1487-1502.
31. Eoster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, et al. (2006) A mammalian organelle map by protein correlation profiling. Cell 125: 187-199.
32. Kislinger T, Cox B, Kannan A, Chung C, Hu P, et al. (2006) Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 125: 173-186.
33. Goonetilleke KS, Siriwardena AK (2007) Systematic review of carbohydrate antigen (CA 19-9) as a biochemical marker in the diagnosis of pancreatic cancer. Eur J Surg Oncol 33: 266-270.
34. Goodman GE, Thornquist MD, Balmes J, Cullen MR, Meyskens FL Jr., et al. (2004) The Beta-Carotene and Retinol Efficacy Trial: incidence of lung cancer and cardiovascular disease mortality during 6-year follow-up after stopping beta-carotene and retinol supplements, J Natl Cancer Inst 96: 1743-1750.
35. Bardeesy N, DePinho RA (2002) Pancreatic cancer biology and genetics. Nat Rev Cancer 2: 897-909.
36. Shiio Y, Aebersold R (2006) Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nat Protoc 1: 139-145.
37. Gong YL, Xu GM, Huang WD, Chen LB (2000) Expression of matrix metalloproteinases and the tissue inhibitors of metalloproteinases and their local invasiveness and metastasis in Chinese human pancreatic cancer. J Surg Oncol 73: 95-99.
38. Okamoto H (1999) The Reg gene family and Reg proteins: with special attention to the regeneration of pancreatic beta-cells. J Hepatobiliary Pancreat Surg 6: 254-262.
39. Esposito I, Penzel R, Chaib-Harrireche M. Barcena U, Bergmann F, et al. (2006) Tenascin C and annexin II expression in the process of pancreatic carcinogenesis. J Pathol 208: 673-685.
40. Markocka-Maczka K (2003) [Concentration of serum soluble forms of ICAM-1 (sVCAM-1) and VCAM-1 (sVCAM-1) in patients with chronic pancreatitis and in patients with pancreatic carcinoma], Wiad Lek 56: 147-151.
41. Barber MD, Fearon KC, Ross JA (1999) Relationship of serum levels of interleukin-6, soluble interleukin-6 receptor and tumour necrosis factor receptors to the acute-phase protein response in advanced pancreatic cancer. Clin Sci (Lond) 96: 83-87.
42. Ofori-Acquah SF, King JA (2008) Activated leukocyte cell adhesion molecule: a new paradox in cancer. Transl Res 151: 122-128.
43. Rosso O, Piazza T, Bongarzone I, Rossello A, Mezzanzanica D, et al. (2007) The ALCAM shedding by the metalloprotease ADAM17/TACE is involved in motility of ovarian carcinoma cells. Mol Cancer Res 5: 1246-1253.
44. Durai R, Davies M, Yang W, Yang SY, Seifalian A, et al. (2006) Biology of insulin-like growth factor binding protein-4 and its role in cancer (review). Int J Oncol 28: 1317-1325.
45. Lee HJ, Lee EK, Lee KJ, Hong SW, Yoon Y, et al. (2006) Ectopic expression of neutrophil gelatinase-associated lipocalin suppresses the invasion and liver metastasis of colon cancer cells. Int J Cancer 118: 2490-2497.
46. Laurell H, Bouisson M, Berthelemy P, Rochaix P, Dejean S, et al. (2006) Identification of biomarkers of human pancreatic adenocarcinomas by expression profiling and validation with gene expression analysis in endoscopic ultrasound-guided fine needle aspiration samples. World J Gastroenterol 12: 3344-3351.
47. Hellstrom I, Raycraft J, Hayden-Ledbetter M, Ledbetter JA, Schummer M, et al. (2003) The HE4 (WEDC2) protein is a biomarker for ovarian carcinoma. Cancer Res 63: 3695-3700.
48. Galgano MT, Hampton GM, Frierson HE Jr. (2006) Comprehensive analysis of HE4 expression in normal and malignant human tissues. Mod Pathol 19: 847-853.
49. Bouchard D, Morisset D, Bourbonnais Y, Tremblay GM (2006) Proteins with whey-acidic-protein motifs and cancer. Lancet Oncol 7: 167-174,
50. Wang JF, Dai DQ (2007) Metastatic suppressor genes inactivated by aberrant methylation in gastric cancer. World J Gastroenterol 13: 5692-5698.
51. Koopmann J, Rosenzweig CX, Zhang Z, Canto ML Brown DA, et al. (2006) Serum markers in patients with resectable pancreatic adenocarcinoma: macrophage inhibitory cytokine 1 versus CA19-9. Clin Cancer Res 12: 442-446.
52. Chen R, Yi EC, Donohoe S, Pan S, Eng J, et al. (2005) Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape. Gastroenterology 129: 1187-1197.
53. Chen R, Pan S, Cooke K, Moyes KW, Bronner MP, et al. (2007) Comparison of pancreas juice proteins from cancer versus pancreatitis using quantitative proteomic analysis. Pancreas 34: 70-79.
54. Gronborg M, Bunkenborg J, Kristiansen TZ, Jensen ON, Yeo GJ, et al. (2004) Comprehensive proteomic analysis of human pancreatic juice. J Proteome Res 3: 1042-1055.
55. Zhou L, Lu Z, Yang A, Deng R, Mai C, et al. (2007) Comparative proteomic analysis of human pancreatic juice: methodological study, Proteomics 7: 1345-1355.
56. Kakisaka T, Kondo T, Okano T, Fujii K, Honda K, et al, (2007) Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leueine-rich alpha-2-glycoprotein in pancreatic cancer. J Chromatogr B Analyt Technol Biomed Life Sci 852: 257-267.
57. Motoo Y, Satomura Y, Mouri I, Mouri H, Ohtsubo K, et al. (1999) Serum levels of pancreatitis-associated protein in digestive diseases with special reference to gastrointestinal cancers. Dig Dis Sci 44: 1142-1147.
58. Satomura Y, Sawabu N. Mouri I, Yamakawa O, Watanabe H, et al. (1995) Measurement of serum PSP/reg-protein concentration in various diseases with a newly developed enzyme-linked immunosorbent assay. J Gastroenterol 30: 643-650.
59. Chen R, Brentnall TA, Pan S, Cooke K, Moves KW, et al. (2007) Quantitative proteomics analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer. Mol Cell Proteomics 6: 1331-1342.
60. Gronborg M, Kristiansen TZ, Iwahori A, Chang R, Reddy R, et al. (2006) Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol Cell Proteomics 5: 157-171.
61. Crnogorac-Jurcevic T, Gangeswaran R, Bhakta V, Capurso G, Lattimore S, et al. (2005) Proteomic analysis of chronic pancreatitis and pancreatic adenocarcinoma. Gastroenterology 129: 1454-1463.
62. Bloomston M, Shafii A, Zervos EE, Rosemurgy AS (2002) TIMP-1 over-expression in pancreatic cancer attenuates tumor growth, decreases implantation and metastasis, and inhibits angiogenesis. J Surg Res 102: 39-44.
63. van Grevenstein WM, Hofland LJ, Jeekel J, van Eijck CH (2006) The expression of adhesion molecules and the influence of inflammatory cytokines on the adhesion of human pancreatic carcinoma cells to mesothelial monolayers. Pancreas 32: 396-402.
64. Jonas L, Kruger B, Tessenow W (1993) Immunohistochemical detection of lactoferrin in different human glandular tissues with special reference to the exocrine pancreas. Acta Histochem 95: 53-59.
65. Kim JH, Ho SB, Montgomery CK, Kim YS (1990) Cell lineage markers in human pancreatic cancer. Cancer 66: 2134-2143.
66. Aust G, Steinert M, Schutz A, Boltze C, Wahlbuhl M, et al. (2002) CD97, but not its closely related EGF-TM7 family member EMR2, is expressed on gastric, pancreatic, and esophageal carcinomas. Am J Clin Pathol 118: 699-707.
67. Shi SQ, Cai JT, Yang JM (2006) Expression of trefoil factors 1 and 2 in precancerous condition and gastric cancer. World J Gastroenterol 12: 3119-3122.
68. Tobita K, Kijima H, Dowaki S, Oida Y, Kashiwagi H, et al. (2002) Thrombospondin-1 expression as a prognostic predictor of pancreatic ductal carcinoma. Int J Oncol 21: 1189-1195.