Proteomic profiling of cancer-opportunities, challenges, and context

Journal of Pathology

Volumn 222, Issue 1, 2010, Pages 16-20

  Arnott, David ^a   Emmert Buck, Michael R ^b  

^a GENENTECH INC   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Biomarker protein profiles; Field cancerization; HNSCC; Pharynx and oesophagus carcinoma; Proteomics; SELDI TOF MS

Indexed keywords

BIOLOGICAL MARKER; MICRORNA;

CANCER RECURRENCE; CANCER RESEARCH; CARCINOGENESIS; ENZYME LINKED IMMUNOSORBENT ASSAY; HEAD AND NECK CANCER; HEAD AND NECK SQUAMOUS CELL CANCER; HUMAN; MACHINE LEARNING; NOTE; PREDICTION; PRIORITY JOURNAL; PROTEIN MICROARRAY; PROTEOMICS; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TUMOR BIOPSY; TUMOR MICROENVIRONMENT; VALIDATION PROCESS;

CARCINOMA, SQUAMOUS CELL; HEAD AND NECK NEOPLASMS; HUMANS; NEOPLASM PROTEINS; NEOPLASMS; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 77955499961     PISSN: 00223417     EISSN: 10969896     Source Type: Journal    
DOI: 10.1002/path.2750     Document Type: Note

References (47)

1. Roesch-Ely M, Leipold A, Nees M, et al . Proteomic analysis of field cancerization in pharynx and oesophagus: a prospective pilot study. J Pathol 2010; 221: 462-470.
2. Hall PA, Reis-Filho JS, Tomlinson IP, et al . An introduction to genes, genomes and disease. J Pathol 2010; 220: 109-113.
3. Hood BL, Stewart NA, Conrads TP. Development of high-throughput mass spectrometry-based approaches for cancer biomarker discovery and implementation. Clin Lab Med 2009; 29: 115-138.
4. Schaaij-Visser TB, Brakenhoff RH, Leemans CR, et al . Protein biomarker discovery for head and neck cancer. J Proteomics 2010; Epub ahead of print.
5. Tainsky MA. Genomic and proteomic biomarkers for cancer: a multitude of opportunities. Biochim Biophys Acta 2009; 1796: 176-193.
6. VanMeter A, Signore M, Pierobon M, et al . Reverse-phase protein microarrays: application to biomarker discovery and translational medicine. Expert Rev Mol Diagn 2007; 7: 625-633. (Pubitemid 47547727)
7. Ye X, Blonder J, Veenstra TD. Targeted proteomics for validation of biomarkers in clinical samples. Brief Funct Genomic Proteomic 2009; 8: 126-135.
8. Ulrich-Merzenich G, Panek D, Zeitler H, et al . New perspectives for synergy research with the 'omic'-technologies. Phytomedicine 2009; 16: 495-508.
9. Wong SC, Chan CM, Ma BB, et al . Advanced proteomic technologies for cancer biomarker discovery. Expert Rev Proteomics 2009; 6: 123-134.
10. Findeisen P, Neumaier M. Mass spectrometry based proteomics profiling as diagnostic tool in oncology: current status and future perspective. Clin Chem Lab Med 2009; 47: 666-684.
11. Kelleher MT, Fruhwirth G, Patel G, et al . The potential of optical proteomic technologies to individualize prognosis and guide rational treatment for cancer patients. Target Oncol 2009; 4: 235-252.
12. Lescuyer P, Farina A, Hochstrasser DF. Proteomics in clinical chemistry: will it be long? Trends Biotechnol 2010; 28: 225-229.
13. Nagaraj NS. Evolving 'omics' technologies for diagnostics of head and neck cancer. Brief Funct Genomic Proteomic 2009; 8: 49-59.
14. Speer R, Wulfkuhle J, Espina V, et al . Molecular network analysis using reverse phase protein microarrays for patient tailored therapy. Adv Exp Med Biol 2008; 610: 177-186.
15. Tan DS, Thomas GV, Garrett MD, et al . Biomarker-driven early clinical trials in oncology: a paradigm shift in drug development. Cancer J 2009; 15: 406-420.
16. Fang B, Haura EB, Smalley KS, et al . Methods for investigation of targeted kinase inhibitor therapy using chemical proteomics and phosphorylation profiling. Biochem Pharmacol 2010; DOI 10.1016/j.bcp.2010.1003.1027.
17. Parikh K, Peppelenbosch MP. Kinome profiling of clinical cancer specimens. Cancer Res 2010; 70: 2575-2578.
18. Slaughter DP, Southwick HW, Smejkal W. Field cancerization in oral stratified squamous epithelium; clinical implications of multicentric origin. Cancer 1953; 6: 963-968.
19. Braakhuis BJ, Leemans CR, Brakenhoff RH. Expanding fields of genetically altered cells in head and neck squamous carcinogenesis. Semin Cancer Biol 2005; 15: 113-120.
20. Braakhuis BJ, Tabor MP, Kummer JA, et al . A genetic explanation of Slaughter's concept of field cancerization: evidence and clinical implications. Cancer Res 2003; 63: 1727-1730.
21. Tabor MP, Brakenhoff RH, Ruijter-Schippers HJ, et al . Multiple head and neck tumors frequently originate from a single preneoplastic lesion. Am J Pathol 2002; 161: 1051-1060.
22. Ostrowski J, Wyrwicz LS. Integrating genomics, proteomics and bioinformatics in translational studies of molecular medicine. Expert Rev Mol Diagn 2009; 9: 623-630.
23. Hanash SM, Pitteri SJ, Faca VM. Mining the plasma proteome for cancer biomarkers. Nature 2008; 452: 571-579.
24. Lancashire LJ, Lemetre C, Ball GR. An introduction to artificial neural networks in bioinformatics-application to complex microarray and mass spectrometry datasets in cancer studies. Brief Bioinform 2009; 10: 315-329.
25. Ransohoff DF. Proteomics research to discover markers: what can we learn from Netflix? Clin Chem 2010; 56: 172-176.
26. Wang P, Whiteaker JR, Paulovich AG. The evolving role of mass spectrometry in cancer biomarker discovery. Cancer Biol Ther 2009; 8: 1083-1094.
27. Mao L. Can molecular assessment improve classification of head and neck premalignancy? Clin Cancer Res 2000; 6: 321-322. (Pubitemid 30111445)
28. Partridge M, Pateromichelakis S, Phillips E, et al . A case-control study confirms that microsatellite assay can identify patients at risk of developing oral squamous cell carcinoma within a field of cancerization. Cancer Res 2000; 60: 3893-3898. (Pubitemid 32204583)
29. Rosin MP, Cheng X, Poh C, et al . Use of allelic loss to predict malignant risk for low-grade oral epithelial dysplasia. Clin Cancer Res 2000; 6: 357-362. (Pubitemid 30111451)
30. Voravud N, Shin DM, Ro JY, et al . Increased polysomies of chromosomes 7 and 17 during head and neck multistage tumorigenesis. Cancer Res 1993; 53: 2874-2883. (Pubitemid 23180530)
31. Wolf C, Flechtenmacher C, Dietz A, et al . p53-positive tumordistant squamous epithelia of the head and neck reveal selective loss of chromosome 17. Laryngoscope 2004; 114: 698-704. (Pubitemid 38548783)
32. Anderson L, Hunter CL. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics 2006; 5: 573-588.
33. Kitteringham NR, Jenkins RE, Lane CS, et al . Multiple reaction monitoring for quantitative biomarker analysis in proteomics and metabolomics. J Chromatogr B Anal Technol Biomed Life Sci 2009; 877: 1229-1239.
34. Poon TC. Opportunities and limitations of SELDI-TOF-MS in biomedical research: practical advices. Expert Rev Proteomics 2007; 4: 51-65.
35. Caldwell RL, Caprioli RM. Tissue profiling by mass spectrometry. Mol Cell Proteomics 2005; 4: 394-401.
36. Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 2002; 1: 845-867.
37. Petricoin EF, Ardekani AM, Hitt BA, et al . Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002; 359: 572-577.
38. Sorace JM, Zhan M. A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics 2003; 4: 24. (Pubitemid 38751246)
39. Gerszten RE, Accurso F, Bernard GR, et al . Challenges in translating plasma proteomics from bench to bedside: update from the NHLBI Clinical Proteomics Programs. Am J Physiol Lung Cell Mol Physiol 2008; 295: L16-L22.
40. Omenn GS, States DJ, Adamski M, et al . Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005; 5: 3226-3245.
41. Liao H, Wu J, Kuhn E, et al . Use of mass spectrometry to identify protein biomarkers of disease severity in the synovial fluid and serum of patients with rheumatoid arthritis. Arthritis Rheum 2004; 50: 3792-3803.
42. Carbone DP, Salmon JS, Billheimer D, et al . VeriStrat((R)) classifier for survival and time to progression in non-small cell lung cancer (NSCLC) patients treated with erlotinib and bevacizumab. Lung Cancer 2009; Epub ahead of print.
43. Cazares LH, Troyer D, Mendrinos S, et al . Imaging mass spectrometry of a specific fragment of mitogen-activated protein kinase/extracellular signal-regulated kinase kinase kinase 2 discriminates cancer from uninvolved prostate tissue. Clin Cancer Res 2009; 15: 5541-5551.
44. Anderson NL, Anderson NG, Haines LR, et al . Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J Proteome Res 2004; 3: 235-244.
45. Keshishian H, Addona T, Burgess M, et al . Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics 2007; 6: 2212-2229.
46. Rodriguez H, Tezak Z, Mesri M, et al . Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA interagency oncology task force on molecular diagnostics. Clin Chem 2010; 56: 237-243.
47. Anderson NL. The roles of multiple proteomic platforms in a pipeline for new diagnostics. Mol Cell Proteomics 2005; 4: 1441-1444.