Proteomics in cancer research: Are we ready for clinical practice?

Critical Reviews in Oncology/Hematology

Volumn 96, Issue 3, 2015, Pages 437-448

  Maes, Evelyne ^a,b   Mertens, Inge ^a,b   Valkenborg, Dirk ^a,b   Pauwels, Patrick ^c   Rolfo, Christian ^c   Baggerman, Geert ^a,b  

^a FLEMISH INSTITUTE FOR TECHNOLOGICAL RESEARCH VITO   (Belgium)

^b UNIVERSITY OF ANTWERP   (Belgium)

^c ANTWERP UNIVERSITY HOSPITAL   (Belgium)

Author keywords

Biomarkers; Clinical proteomics; Complexity; Sample quality; Study design; Translation to clinic

Indexed keywords

ALPHA FETOPROTEIN; CA 125 ANTIGEN; CA 15-3 ANTIGEN; CA 19-9 ANTIGEN; CA 27-29 ANTIGEN; CARCINOEMBRYONIC ANTIGEN; CHORIONIC GONADOTROPIN BETA SUBUNIT; CYTOKERATIN; EPIDERMAL GROWTH FACTOR RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; FIBRIN; HUMAN EPIDIDYMIS PROTEIN 4; NUCLEAR MATRIX PROTEIN 22; PROGESTERONE RECEPTOR; PROSTATE SPECIFIC ANTIGEN; PROTEIN P63; PROTEOME; THYROGLOBULIN; TUMOR MARKER;

BLADDER CANCER; BLOOD; BREAST CANCER; CANCER PATIENT; CANCER PROGNOSIS; CANCER RECURRENCE; CANCER RESEARCH; CANCER STAGING; CANCER TISSUE; CLINICAL DECISION MAKING; CLINICAL PRACTICE; COLON CANCER; COLORECTAL CANCER; EARLY DIAGNOSIS; ENZYME LINKED IMMUNOSORBENT ASSAY; GASTROINTESTINAL TUMOR; GENOMICS; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; ONCOLOGY; OVARY CANCER; PANCREAS CANCER; PATIENT CARE; PATIENT MONITORING; PATIENT SELECTION; PLASMA; PRACTICE GUIDELINE; PROSTATE CANCER; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEOMICS; REVIEW; SERUM; SIGNAL TRANSDUCTION; TESTIS CANCER; THYROID CANCER; URINE; METABOLISM; NEOPLASMS; PROCEDURES; PROGNOSIS;

BIOMARKERS, TUMOR; HUMANS; NEOPLASMS; PROGNOSIS; PROTEOMICS;

EID: 84961291054     PISSN: 10408428     EISSN: 18790461     Source Type: Journal    
DOI: 10.1016/j.critrevonc.2015.07.006     Document Type: Review

References (105)

1. Addona T.A., Abbatiello S.E., Schilling B., et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 2009, 27:633-641.
2. Alban A., David S.O., Bjorkesten L., et al. A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 2003, 3:36-44.
3. Altelaar A.F., Munoz J., Heck A.J. Next-generation proteomics: towards an integrative view of proteome dynamics. Nat. Rev. Genet. 2013, 14:35-48.
4. Anon Is clinical proteomics heading towards to "bench to bedside"?. Transl. Proteomics 2013, 1:53-56.
5. Baker E.S., Liu T., Petyuk V.A., et al. Mass spectrometry for translational proteomics: progress and clinical implications. Genome Med. 2012, 4:63.
6. Bell A.W., Deutsch E.W., Au C.E., et al. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat. Methods 2009, 6:423-430.
7. Blagoev B., Ong S.E., Kratchmarova I., Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol. 2004, 22:1139-1145.
8. Boja E.S., Rodriguez H. The path to clinical proteomics research: integration of proteomics, genomics, clinical laboratory and regulatory science. Korean J. Lab. Med. 2011, 31:61-71.
9. Boja E.S., Rodriguez H. Proteogenomic convergence for understanding cancer pathways and networks. Clin. Proteomics 2014, 11:22.
10. Byers L.A., Wang J., Nilsson M.B., et al. Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. Cancer Discov. 2012, 2:798-811.
11. Cairns D.A. Statistical issues in quality control of proteomic analyses: good experimental design and planning. Proteomics 2011, 11:1037-1048.
12. Cho W.C. Contribution of oncoproteomics to cancer biomarker discovery. Mol. Cancer 2007, 6:25.
13. Diamandis, Eleftherios, Letter to the Editor about Differential exoprotease activities confer tumor-specific serum peptidome. Journal of Clinical Investigation. 21-2-2006. Ref Type: Generic.
14. Dayon L.C., Kussmann M. Proteomics of human plasma: A critical comparison of analytical workflows in terms of effort, throughput and outcome. EuPA Open Proteomics 2013, 1:8-16.
15. Dayon L., Hainard A., Licker V., et al. Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal. Chem. 2008, 80:2921-2931.
16. Diamandis E.P. The failure of protein cancer biomarkers to reach the clinic: why, and what can be done to address the problem. BMC Med. 2012, 10:87.
17. Diamandis E.P. The failure of protein cancer biomarkers to reach the clinic: why, and what can be done to address the problem. BMC Med. 2012, 10:87.
18. Diamandis E.P. Present and future of cancer biomarkers. Clin. Chem. Lab. Med. 2014, 52:791-794.
19. Diamandis E.P. Towards identification of true cancer biomarkers. BMC Med. 2014, 12:156.
20. Diaz J.A., Slomka T. State of the art review: colorectal cancer screening. Am. J. Lifestyle Med. 2012, 6:196-203.
21. Domon B., Gallien S. Recent advances in targeted proteomics for clinical applications. Proteomics Clin. Appl. 2015, 9:423-431.
22. Dove A. Proteomics translating genomics into products?. Nat. Biotechnol. 1999, 17:233-236.
23. Earle C.C., Schrag D., Neville B.A., et al. Effect of surgeon specialty on processes of care and outcomes for ovarian cancer patients. J. Natl. Cancer Inst. 2006, 98:172-180.
24. Edwards N.J., Oberti M., Thangudu R.R., et al. The CPTAC Data Portal: A Resource for Cancer Proteomics Research. J. Proteome Res. 2015.
25. Ezkurdia I., Juan D., Rodriguez J.M., et al. The shrinking human protein coding complement: are there fewer than 20,000 genes?. BioRxiv 2014.
26. Frantzi M., Bhat A., Latosinska A. Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development. Clin. Transl. Med. 2014, 3:7.
27. Fuzery A.K., Levin J., Chan M.M., Chan D.W. Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges. Clin. Proteomics 2013, 10:13.
28. Gallien S., Bourmaud A., Kim S.Y., Domon B. Technical considerations for large-scale parallel reaction monitoring analysis. J. Proteomics 2014, 100:147-159.
29. Garcia A. Clinical proteomics in platelet research: challenges ahead. J. Thromb. Haemost. 2010, 8:1784-1785.
30. Garraway L.A. Genomics-driven oncology: framework for an emerging paradigm. J. Clin. Oncol. 2013, 31:1806-1814.
31. Gregorc V., Novello S., Lazzari C., et al. Predictive value of a proteomic signature in patients with non-small-cell lung cancer treated with second-line erlotinib or chemotherapy (PROSE): a biomarker-stratified, randomised phase 3 trial. Lancet Oncol. 2014, 15:713-721.
32. Gupta S., Venkatesh A., Ray S., Srivastava S. Challenges and prospects for biomarker research: a current perspective from the developing world. Biochim. Biophys. Acta 2014, 1844:899-908.
33. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17:994-999.
34. Hanash S. Disease proteomics. Nature 2003, 422:226-232.
35. Hanash S.M. Why have protein biomarkers not reached the clinic. Genome Med. 2011, 3:66.
36. Hanash S.M., Baik C.S., Kallioniemi O. Emerging molecular biomarkers-blood-based strategies to detect and monitor cancer. Nat. Rev. Clin. Oncol. 2011, 8:142-150.
37. Henry N.L., Hayes D.F. Cancer biomarkers. Mol. Oncol. 2012, 6:140-146.
38. Hu J., Coombes K.R., Morris J.S., Baggerly K.A. The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. Brief Funct. Genomic Proteomic 2005, 3:322-331.
39. Jain K.K. Innovations, challenges and future prospects of oncoproteomics. Mol. Oncol. 2008, 2:153-160.
40. Jiang Y., Wang X. Comparative mitochondrial proteomics: perspective in human diseases. J. Hematol. Oncol. 2012, 5:11.
41. Jones R.P., Sutton P., Greensmith R.M., et al. Hepatic activation of irinotecan predicts tumour response in patients with colorectal liver metastases treated with DEBIRI: exploratory findings from a phase II study. Cancer Chemother. Pharmacol. 2013, 72:359-368.
42. Kang B., Park J., Cho S., et al. Current status, challenges, policies, and bioethics of biobanks. Genomics Inf. 2013, 11:211-217.
43. Kim M.S., Pinto S.M., Getnet D., et al. A draft map of the human proteome. Nature 2014, 509:575-581.
44. Kolch W., Pitt A. Functional proteomics to dissect tyrosine kinase signalling pathways in cancer. Nat. Rev. Cancer 2010, 10:618-629.
45. Krueger K.E., Srivastava S. Posttranslational protein modifications: current implications for cancer detection, prevention, and therapeutics. Mol. Cell Proteomics 2006, 5:1799-1810.
46. Lee R.S., Monigatti F., Briscoe A.C., Waldon Z., Freeman M.R., Steen H. Optimizing sample handling for urinary proteomics. J. Proteome Res. 2008, 7:4022-4030.
47. Leitner A., Sturm M., Lindner W. Tools for analyzing the phosphoproteome and other phosphorylated biomolecules: a review. Anal. Chim. Acta 2011, 703:19-30.
48. Leung F., Musrap N., Diamandis E.P., Kulasingam V. Advances in mass spectrometry-based technologies to direct personalized medicine in ovarian cancer. Transl. Proteomics 2013, 1:74-86.
49. Li Z., Adams R.M., Chourey K., Hurst G.B., Hettich R.L., Pan C. Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos. J. Proteome Res. 2012, 11:1582-1590.
50. Li X., Wang W., Chen J. From pathways to networks: connecting dots by establishing interaction networks in signaling pathways using affinity purification and mass spectrometry. Proteomics 2015, 15:188-202.
51. Liang B., Peng P., Chen S., et al. Characterization and proteomic analysis of ovarian cancer-derived exosomes. J. Proteomics 2013, 80:171-182.
52. Lilley K.S., Friedman D.B. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev. Proteomics 2004, 1:401-409.
53. Maes E., Broeckx V., Mertens I., et al. Analysis of the formalin-fixed paraffin-embedded tissue proteome: pitfalls, challenges, and future prospectives. Amino Acids 2013, 45:205-218.
54. Maes E., Landuyt B., Mertens I., Schoofs L. Interindividual variation in the proteome of human peripheral blood mononuclear cells. PLoS One 2013, 8:e61933.
55. Maes E., Valkenborg D., Baggerman G., et al. Determination of variation parameters as a crucial step in designing TMT-based clinical proteomics experiments. PLoS One 2015, 10:e0120115.
56. Mann M., Jensen O.N. Proteomic analysis of post-translational modifications. Nat. Biotechnol. 2003, 21:255-261.
57. Markiv A., Rambaruth N.D., Dwek M.V. Beyond the genome and proteome: targeting protein modifications in cancer. Curr. Opin. Pharmacol. 2012, 12:408-413.
58. Martens L. Bringing proteomics into the clinic: the need for the field to finally take itself seriously. Proteomics Clin. Appl. 2013, 7:388-391.
59. Mayer G., Montecchi-Palazzi L., Ovelleiro D., et al. The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford) 2013, 2013:bat009.
60. McIntosh M., Anderson G., Drescher C., et al. Ovarian cancer early detection claims are biased. Clin. Cancer Res. 2008, 14:7574-7579.
61. Megger D.A., Bracht T., Meyer H.E., Sitek B. Label-free quantification in clinical proteomics. Biochim. Biophys. Acta 2013, 1834:1581-1590.
62. Mermelekas G., Zoidakis J. Mass spectrometry-based membrane proteomics in cancer biomarker discovery. Expert Rev. Mol. Diagn. 2014, 14:549-563.
63. Millioni R., Tolin S., Puricelli L., et al. High abundance proteins depletion vs low abundance proteins enrichment: comparison of methods to reduce the plasma proteome complexity. PLoS One 2011, 6:e19603.
64. Minerva L., Ceulemans A., Baggerman G., Arckens L. MALDI MS imaging as a tool for biomarker discovery: methodological challenges in a clinical setting. Proteomics Clin. Appl. 2012, 6:581-595.
65. Mischak H. How to get proteomics to the clinic? Issues in clinical proteomics, exemplified by CE-MS. Proteomics Clin. Appl. 2012, 6:437-442.
66. Mischak H., Ioannidis J.P., Argiles A., et al. Implementation of proteomic biomarkers: making it work. Eur. J. Clin. Invest. 2012, 42:1027-1036.
67. Montagnana M., Danese E., Giudici S., et al. HE4 in ovarian cancer: from discovery to clinical application. Adv. Clin. Chem. 2011, 55:1-20.
68. Nanjundan M., Byers L.A., Carey M.S., et al. Proteomic profiling identifies pathways dysregulated in non-small cell lung cancer and an inverse association of AMPK and adhesion pathways with recurrence. J. Thorac. Oncol. 2010, 5:1894-1904.
69. Nilsson C.L. Advances in quantitative phosphoproteomics. Anal. Chem. 2012, 84:735-746.
70. Nixon A.B., Pang H., Starr M.D., et al. Prognostic and predictive blood-based biomarkers in patients with advanced pancreatic cancer: results from CALGB80303 (alliance). Clin. Cancer Res. 2013, 19:6957-6966.
71. Nolen B., Velikokhatnaya L., Marrangoni A., et al. Serum biomarker panels for the discrimination of benign from malignant cases in patients with an adnexal mass. Gynecol. Oncol. 2010, 117:440-445.
72. Noordzij M., Tripepi G., Dekker F.W., Zoccali C., Tanck M.W., Jager K.J. Sample size calculations: basic principles and common pitfalls. Nephrol. Dial. Transplant. 2010, 25:1388-1393.
73. Paradela A., Albar J.P. Advances in the analysis of protein phosphorylation. J. Proteome Res. 2008, 7:1809-1818.
74. Parker C.E., Borchers C.H. Mass spectrometry based biomarker discovery, verification, and validation-quality assurance and control of protein biomarker assays. Mol. Oncol. 2014, 8:840-858.
75. Parker C.E., Borchers C.H. Mass spectrometry based biomarker discovery, verification, and validation-quality assurance and control of protein biomarker assays. Mol. Oncol. 2014, 8:840-858.
76. Paulovich A.G., Whiteaker J.R., Hoofnagle A.N., Wang P. The interface between biomarker discovery and clinical validation: the tar pit of the protein biomarker pipeline. Proteomics Clin. Appl. 2008, 2:1386-1402.
77. Percy A.J., Chambers A.G., Parker C.E., Borchers C.H. Absolute quantitation of proteins in human blood by multiplexed multiple reaction monitoring mass spectrometry. Methods Mol. Biol. 2013, 1000:167-189.
78. Pierobon M., Wulfkuhle J., Liotta L., Petricoin E. Application of molecular technologies for phosphoproteomic analysis of clinical samples. Oncogene 2015, 34:805-814.
79. Rai A.J., Vitzthum F. Effects of preanalytical variables on peptide and protein measurements in human serum and plasma: implications for clinical proteomics. Expert Rev. Proteomics 2006, 3:409-426.
80. Ransohoff D.F. Bias as a threat to the validity of cancer molecular-marker research. Nat. Rev. Cancer 2005, 5:142-149.
81. Ransohoff D.F., Gourlay M.L. Sources of bias in specimens for research about molecular markers for cancer. J. Clin. Oncol. 2010, 28:698-704.
82. Rodriguez-Suarez E., Whetton A.D. The application of quantification techniques in proteomics for biomedical research. Mass Spectrom. Rev. 2013, 32(1):1-26.
83. Stoeckli M., Chaurand P., Hallahan D.E., Caprioli R.M. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nat. Med. 2001, 7:493-496.
84. Tabb D.L. Quality assessment for clinical proteomics. Clin. Biochem. 2013, 46:411-420.
85. Tan H.T., Lee Y.H., Chung M.C. Cancer proteomics. Mass Spectrom. Rev. 2012, 31:583-605.
86. Thompson A., Schafer J., Kuhn K., et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 2003, 75:1895-1904.
87. Tomlinson I.P., Whyman A., Barrett J.A., Kremer J.K. Tumour marker CA15-3: possible uses in the routine management of breast cancer. Eur. J. Cancer 1995, 31A:899-902.
88. Tuck M.K., Chan D.W., Chia D., et al. Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group. J. Proteome Res. 2009, 8:113-117.
89. Tong J., Taylor P., Moran M.F. Proteomic analysis of the epidermal growth factor receptor (EGFR) interactome and post-translational modifications associated with receptor endocytosis in response to EGF and stress. Mol. Cell Proteomics 2014, 13:1644-1658.
90. Unlu M., Morgan M.E., Minden J.S. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 1997, 18:2071-2077.
91. Van C.E., Oliveira J. Advanced colorectal cancer: ESMO clinical recommendations for diagnosis, treatment and follow-up. Ann. Oncol. 2009, 20(suppl. 4):61-63.
92. van Kempen L.C., Spatz A. From biomarker development towards implementation of multidimensional biomarker panels in a clinical setting. Mol. Oncol. 2014, 8:781-782.
93. Velez P., Izquierdo I., Rosa I., Garcia A. A 2D-DIGE-based proteomic analysis reveals differences in the platelet releasate composition when comparing thrombin and collagen stimulations. Sci. Rep. 2015, 5:8198.
94. Villanueva J., Shaffer D.R., Philip J., et al. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J. Clin. Invest. 2006, 116:271-284.
95. Visintin I., Feng Z., Longton G., et al. Diagnostic markers for early detection of ovarian cancer. Clin. Cancer Res. 2008, 14:1065-1072.
96. Vogel C., Marcotte E.M. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet. 2012, 13:227-232.
97. Wang X., Zhao H., Andersson R. Proteomics and leukocytes: an approach to understanding potential molecular mechanisms of inflammatory responses. J. Proteome Res. 2004, 3:921-929.
98. Wilhelm M., Schlegl J., Hahne H., et al. Mass-spectrometry-based draft of the human proteome. Nature 2014, 509:582-587.
99. Witkowska H.E., Hall S.C., Fisher S.J. Breaking the bottleneck in the protein biomarker pipeline. Clin. Chem. 2012, 58:321-323.
100. Whiteaker J.R., Lin C., Kennedy J., et al. A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat. Biotechnol. 2011, 29:625-634.
101. Yamashita K., Watanabe M. Clinical significance of tumor markers and an emerging perspective on colorectal cancer. Cancer Sci. 2009, 100:195-199.
102. Zhang Y., Fonslow B.R., Shan B., Baek M.C., Yates J.R.I.I.I. Protein analysis by shotgun/bottom-up proteomics. Chem. Rev. 2013, 113:2343-2394.
103. Zhao Y., Jensen O.N. Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques. Proteomics 2009, 9:4632-4641.
104. Zhu W., Smith J.W., Huang C.M. Mass spectrometry-based label-free quantitative proteomics. J. Biomed. Biotechnol. 2010, 2010:518-840.
105. Zubarev R.A. The challenge of the proteome dynamic range and its implications for in-depth proteomics. Proteomics 2013, 13:723-726.