Mass spectrometry-based membrane proteomics in cancer biomarker discovery

Expert Review of Molecular Diagnostics

Volumn 14, Issue 5, 2014, Pages 549-563

  Mermelekas, George ^a   Zoidakis, Jerome ^a  

^a BIOMEDICAL RESEARCH FOUNDATION   (Greece)

Author keywords

Biomarkers; Cancer; Mass spectrometry; Membrane proteins; Proteomics

Indexed keywords

ACTIVATED LEUKOCYTE CELL ADHESION MOLECULE; BIOLOGICAL MARKER; CARCINOEMBRYONIC ANTIGEN RELATED CELL ADHESION MOLECULE 1; CARCINOEMBRYONIC ANTIGEN RELATED CELL ADHESION MOLECULE 6; CARCINOEMBRYONIC ANTIGEN RELATED CELL ADHESION MOLECULE 7; CARCINOEMBRYONIC ANTIGEN RELATED CELL ADHESION MOLECULE 8; CELL MEMBRANE PROTEIN; CELL SURFACE PROTEIN; GALECTIN 3; HLA ANTIGEN CLASS 1; HLA ANTIGEN CLASS 2; HLA DR ANTIGEN; JUNCTIONAL ADHESION MOLECULE C; LYSOSOME ASSOCIATED MEMBRANE PROTEIN; MULTIDRUG RESISTANCE ASSOCIATED PROTEIN 1; NERVE CELL ADHESION MOLECULE; NEUTROPHIL GELATINASE ASSOCIATED LIPOCALIN; REDUCED FOLATE CARRIER; UNCLASSIFIED DRUG; MEMBRANE PROTEIN; PROTEOME; TUMOR MARKER;

BREAST CANCER; CELL INTERACTION; CHEMICAL LABELING; COLORECTAL CANCER; DOWN REGULATION; GLIOBLASTOMA; HUMAN; ION EXCHANGE CHROMATOGRAPHY; MASS SPECTROMETRY; METASTASIS; NEOPLASM; PAPILLARY CARCINOMA; PLEURA MESOTHELIOMA; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN ISOLATION; PROTEIN METABOLISM; PROTEOMICS; REVIEW; SOLUBILIZATION; STOMACH CANCER; TRANSLATION REGULATION; TRIPLE NEGATIVE BREAST CANCER; UPREGULATION; CHEMISTRY; GENETICS; METABOLISM; NEOPLASMS; PROCEDURES;

BIOMARKERS, TUMOR; HUMANS; MASS SPECTROMETRY; MEMBRANE PROTEINS; NEOPLASMS; PROTEOME; PROTEOMICS;

EID: 84901280454     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/14737159.2014.917965     Document Type: Review

References (71)

1. Rhea JM, Molinaro RJ. Cancer biomarkers: Surviving the journey from. bench to bedside. MLO Med Lab Obs 2011;43(3): 10-12, 16, 18.quiz 20, 22
2. Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: The long and uncertain path to clinical utility. Nat Biotechnol 2006;24(8):971-83 (Pubitemid 44215392
3. Stevens TJ, Arkin IT. Do more complex organisms have a greater proportion of membrane proteins in their genomes?. Proteins 2000;39(4):417-20
4. Kabbani N. Proteomics of membrane receptors and signaling. Proteomics 2008; 8(19):4146-55
5. Shukla HD, Vaitiekunas P, Cotter RJ. Advances in membrane proteomics and cancer biomarker discovery: Current status and future perspective. Proteomics 2012; 12(19-20):3085-104
6. Leth-Larsen R, Lund RR, Ditzel HJ. Plasma membrane proteomics and its application in clinical cancer biomarker discovery. Mol Cell Proteomics 2010;9(7):1369-82
7. Bantscheff M, Lemeer S, Savitski MM, Kuster B. Quantitative mass spectrometry in proteomics: Critical review update from 2007 to the present. Anal Bioanal Chem 2012;404(4):939-65
8. Van Riper SK, De Jong EP, Carlis JV, Griffin TJ. Mass spectrometry-based proteomics: Basic principles and emerging technologies and directions. Adv Exp Med Biol 2013;990:1-35
9. Sandin M, Teleman J, Malmstrom J, Levander F. Data processing methods and quality control strategies for label-free LCMS protein quantification. Biochim Biophys Acta 2014;1844(1 Pt A):29-41
10. Choi H, Fermin D, Nesvizhskii AI. Significance analysis of spectral count data in label-free shotgun proteomics. Mol Cell Proteomics 2008;7(12):2373-85
11. Nahnsen S, Bielow C, Reinert K, Kohlbacher O. Tools for label-free peptide quantification. Mol Cell Proteomics 2013; 12(3):549-56
12. Clough T, Thaminy S, Ragg S, et al. Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs. BMC Bioinformatics 2012;13(Suppl 16): S6
13. Ong SE, Mann M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc 2006;1(6): 2650-60
14. Rodriguez H, Rivers R, Kinsinger C, et al. Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: An NCI-CPTC initiative perspective. Proteomics Clin Appl 2010; 4(12):904-14
15. Liebler DC, Zimmerman LJ. Targeted quantitation of proteins by mass spectrometry. Biochemistry 2013;52(22): 3797-806
16. Nagaraj N, Wisniewski JR, Geiger T, et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 2011;7:548
17. Lund R, Leth-Larsen R, Jensen ON, Ditzel HJ. Efficient isolation and quantitative proteomic analysis of cancer cell plasma membrane proteins for identification of metastasis-Associated cell surface markers. J Proteome Res 2009;8(6):3078-90
18. Nielsen PA, Olsen JV, Podtelejnikov AV, et al. Proteomic mapping of brain plasma membrane proteins. Mol Cell Proteomics 2005;4(4):402-8 (Pubitemid 40590560
19. Dormeyer W, Van Hoof D, Mummery CL, et al. A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cells. Proteomics 2008;8(19):4036-53
20. Elschenbroich S, Kim Y, Medin JA, Kislinger T. Isolation of cell surface proteins for mass spectrometry-based proteomics. Expert Rev Proteomics 2010;7(1):141-54
21. Cao R, Li X, Liu Z, et al. Integration of a two-phase partition method into proteomics research on rat liver plasma membrane proteins. J Proteome Res 2006;5(3):634-42 (Pubitemid 43364104
22. Xiong X, Huang S, Zhang H, et al. Enrichment and proteomic analysis of plasma membrane from rat dorsal root ganglions. Proteome Sci 2009;7:41
23. Weekes MP, Antrobus R, Lill JR, et al. Comparative analysis of techniques to purify plasma membrane proteins. J Biomol Tech 2010;21(3):108-15
24. Elia G. Biotinylation reagents for the study of cell surface proteins. Proteomics 2008; 8(19):4012-24
25. Karhemo PR, Ravela S, Laakso M, et al. An optimized isolation of biotinylated cell surface proteins reveals novel players in cancer metastasis. J Proteomics 2012;77: 87-100
26. Schnitzer JE, Mcintosh DP, Dvorak AM, et al. Separation of caveolae from associated microdomains of GPI-Anchored proteins. Science 1995;269(5229):1435-9
27. Durr E, Yu J, Krasinska KM, et al. Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat Biotechnol 2004; 22(8):985-92 (Pubitemid 39014475
28. Timpe LC, Yen R, Haste NV, et al. Systemic alteration of cell-surface and secreted glycoprotein expression in malignant breast cancer cell lines. Glycobiology 2013;23(11):1240-9
29. Zhang H, Li XJ, Martin DB, Aebersold R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol 2003;21(6): 660-6 (Pubitemid 36638093
30. Wollscheid B, Bausch-Fluck D, Henderson C, et al. Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat Biotechnol 2009;27(4):378-86
31. Yen TY, Haste N, Timpe LC, et al. Using a cell line breast cancer progression system to identify biomarker candidates. J Proteomics 2014;96:173-83
32. Cordwell SJ, Thingholm TE. Technologies for plasma membrane proteomics. Proteomics 2010;10(4):611-27
33. Vuckovic D, Dagley LF, Purcell AW, Emili A. Membrane proteomics by high performance liquid chromatography-Tandem mass spectrometry: Analytical approaches and challenges. Proteomics 2013;13(3-4): 404-23
34. Speers AE, Wu CC. Proteomics of integral membrane proteins-Theory and application. Chem Rev 2007;107(8): 3687-714 (Pubitemid 47322748
35. Ruth MC, Old WM, Emrick MA, et al. Analysis of membrane proteins from human chronic myelogenous leukemia cells: Comparison of extraction methods for multidimensional LC-MS/MS. J Proteome Res 2006;5(3):709-19 (Pubitemid 43364111
36. Macher BA, Yen TY. Proteins at membrane surfaces-A review of approaches. Mol Biosyst 2007;3(10):705-13 (Pubitemid 47449625
37. Masuda T, Tomita M, Ishihama Y. Phase transfer surfactant-Aided trypsin digestion for membrane proteome analysis. J Proteome Res 2008;7(2):731-40 (Pubitemid 351294035
38. Shevchenko G, Musunuri S, Wetterhall M, Bergquist J. Comparison of extraction methods for the comprehensive analysis of mouse brain proteome using shotgun-based mass spectrometry. J Proteome Res 2012; 11(4):2441-51
39. Griffiths LG, Choe L, Lee KH, et al. Protein extraction and 2-DE of waterand lipid-soluble proteins from bovine pericardium, a low-cellularity tissue. Electrophoresis 2008;29(22): 4508-15
40. Bunai K, Nozaki M, Hamano M, et al. Proteomic analysis of acrylamide gel separated proteins immobilized on polyvinylidene difluoride membranes following proteolytic digestion in the presence of 80% acetonitrile. Proteomics 2003;3(9):1738-49 (Pubitemid 37129821
41. Bunai K, Nozaki M, Kakeshita H, et al. Quantitation of de novo localized (15)Nlabeled lipoproteins and membrane proteins having one and two transmembrane segments in a Bacillus subtilis secA temperature-sensitive mutant using 2D-PAGE and MALDI-TOF MS. J Proteome Res 2005;4(3):826-36
42. Wisniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods 2009;6(5):359-62
43. Shevchenko A, Tomas H, Havlis J, et al. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 2006;1(6):2856-60
44. Lu X, Zhu H. Tube-gel digestion: A novel proteomic approach for high throughput analysis of membrane proteins. Mol Cell Proteomics 2005;4(12):1948
45. Choksawangkarn W, Edwards N, Wang Y, et al. Comparative study of workflows optimized for in-gel, in-solution, and on-filter proteolysis in the analysis of plasma membrane proteins. J Proteome Res 2012; 11(5):3030-4
46. Lu M, Whitelegge JP, Whelan SA, et al. Hydrophobic Fractionation Enhances Novel Protein Detection by Mass Spectrometry in Triple Negative Breast Cancer. J Proteomics Bioinform 2010;3(2):1-10
47. Lu M, Whelan SA, He J, et al. Hydrophobic Proteome Analysis of Triple Negative and Hormone-Receptor-Positive-Her2-Negative Breast Cancer by Mass Spectrometer. Clin Proteomics 2010;6(3): 93-103
48. Lin Y, Liu H, Liu Z, et al. Development and evaluation of an entirely solution-based combinative sample preparation method for membrane proteomics. Anal Biochem 2013; 432(1):41-8
49. Blonder J, Chan KC, Issaq HJ, Veenstra TD. Identification of membrane proteins from mammalian cell/tissue using methanol-facilitated solubilization and tryptic digestion coupled with 2D-LC-MS/MS. Nat Protoc 2006;1(6):2784-90
50. Cox B, Emili A. Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics. Nat Protoc 2006;1(4):1872-8 (Pubitemid 46778056
51. Zhang N, Chen R, Young N, et al. Comparison of SDS-And methanol-Assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS. Proteomics 2007;7(4):484-93 (Pubitemid 46362611
52. Obuchi W, Ohtsuki S, Uchida Y, et al. Identification of transporters associated with Etoposide sensitivity of stomach cancer cell lines and methotrexate sensitivity of breast cancer cell lines by quantitative targeted absolute proteomics. Mol Pharmacol 2013; 83(2):490-500
53. Han CL, Chen JS, Chan EC, et al. An informatics-Assisted label-free approach for personalized tissue membrane proteomics: Case study on colorectal cancer. Mol Cell Proteomics 2011;10(4):M110 003087
54. Conn EM, Madsen MA, Cravatt BF, et al. Cell surface proteomics identifies molecules functionally linked to tumor cell intravasation. J Biol Chem 2008;283(39): 26518-27
55. Roesli C, Borgia B, Schliemann C, et al. Comparative analysis of the membrane proteome of closely related metastatic and nonmetastatic tumor cells. Cancer Res 2009;69(13):5406-14
56. Dumont B, Castronovo V, Peulen O, et al. Differential proteomic analysis of a human breast tumor and its matched bone metastasis identifies cell membrane and extracellular proteins associated with bone metastasis. J Proteome Res 2012;11(4): 2247-60
57. Turtoi A, Dumont B, Greffe Y, et al. Novel comprehensive approach for accessible biomarker identification and absolute quantification from precious human tissues. J Proteome Res 2011;10(7):3160-82
58. Whelan SA, Lu M, He J, et al. Mass spectrometry (LC-MS/MS) site-mapping of N-glycosylated membrane proteins for breast cancer biomarkers. J Proteome Res 2009;8(8):4151-60
59. Arcinas A, Yen TY, Kebebew E, Macher BA. Cell surface and secreted protein profiles of human thyroid cancer cell lines reveal distinct glycoprotein patterns. J Proteome Res 2009; 8(8):3958-68
60. Bock T, Moest H, Omasits U, et al. Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines. J Proteome Res 2012;11(10):4885-93
61. SILAC. Available from: www.silac.org
62. Leth-Larsen R, Lund R, Hansen HV, et al. Metastasis-related plasma membrane proteins of human breast cancer cells identified by comparative quantitative mass spectrometry. Mol Cell Proteomics 2009; 8(6):1436-49
63. Liang X, Zhao J, Hajivandi M, et al. Quantification of membrane and membrane-bound proteins in normal and malignant breast cancer cells isolated from the same patient with primary breast carcinoma. J Proteome Res 2006;5(10): 2632-41 (Pubitemid 44595165
64. Aggelis V, Craven RA, Peng J, et al. Proteomic identification of differentially expressed plasma membrane proteins in renal cell carcinoma by stable isotope labelling of a von Hippel-Lindau transfectant cell line model. Proteomics 2009;9(8):2118-30
65. Ziegler A, Cerciello F, Bigosch C, et al. Proteomic surfaceome analysis of mesothelioma. Lung cancer 2012;75(2): 189-96
66. Polisetty RV, Gautam P, Sharma R, et al. LC-MS/MS analysis of differentially expressed glioblastoma membrane proteome reveals altered calcium signaling and other protein groups of regulatory functions. Mol Cell Proteomics 2012;11(6):M111013565
67. Muraoka S, Kume H, Watanabe S, et al. Strategy for SRM-based verification of biomarker candidates discovered by iTRAQ method in limited breast cancer tissue samples. J Proteome Res 2012;11(8): 4201-10
68. Chen JS, Chen KT, Fan CW, et al. Comparison of membrane fraction proteomic profiles of normal and cancerous human colorectal tissues with gel-Assisted digestion and iTRAQ labeling mass spectrometry. FEBS J 2010;277(14): 3028-38
69. Yang Y, Toy W, Choong LY, et al. Discovery of SLC3A2 cell membrane protein as a potential gastric cancer biomarker: Implications in molecular imaging. J Proteome Res 2012;11(12): 5736-47
70. Zhang Z, Zhang L, Hua Y, et al. Comparative proteomic analysis of plasma membrane proteins between human osteosarcoma and normal osteoblastic cell lines. BMC Cancer 2010;10:206
71. Yokoyama T, Enomoto T, Serada S, et al. Plasma membrane proteomics identifies bone marrow stromal antigen 2 as a potential therapeutic target in endometrial cancer. Int J Cancer 2013;132(2):472-84