Direct tissue proteomics in human diseases: Potential applications to melanoma research

Expert Review of Proteomics

Volumn 5, Issue 3, 2008, Pages 405-412

  Rezaul, Karim ^a   Wilson, Lori L ^a   Han, David K ^a  

^a UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

Author keywords

Biomarker; Direct tissue proteomics; DTP; FFPE; Formalin fixed paraffin embedded; Melanoma; Personalized medicine

Indexed keywords

BIOLOGICAL MARKER; FORMALDEHYDE; PARAFFIN;

CANCER DIAGNOSIS; CANCER SCREENING; GENE EXPRESSION; HUMAN; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MELANOMA; PROGNOSIS; PROTEOMICS; REVIEW; RISK ASSESSMENT; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

BIOLOGICAL MARKERS; HUMANS; MASS SPECTROMETRY; MELANOMA; PROTEOMICS; SKIN NEOPLASMS;

EID: 45749091807     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.5.3.405     Document Type: Review

References (55)

1. de Hoog CL, Mann M. Proteomics. Annu. Rev. Genomics Hum. Genet. 5, 267-293 (2004).
2. Anderson L, Seilhamer J. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18(3-4), 533-537 (1997).
3. Alaiya A, Roblick U, Egevad L et al. Polypeptide expression in prostate hyperplasia and prostate adenocarcinoma. Anal. Cell Pathol. 21(1), 1-9 (2000).
4. Chen G, Gharib TG, Wang H et al. Protein profiles associated with survival in lung adenocarcinoma. Proc. Natl Acad. Sci. USA 100(23), 13537-13542 (2003).
5. Nishizuka S, Charboneau L, Young L et al. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc. Natl Acad. Sci. USA 100(24), 14229-14234 (2003).
6. Izzotti A, Bagnasco M, Cartiglia C, Longobardi M, De Flora S. Proteomic analysis as related to transcriptome data in the lung of chromium (VI)-treated rats. Int. J. Oncol. 24(6), 1513-1522 (2004).
7. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 422(6928), 198-207 (2003). • Extensive discussion of different proteomic technologies and their applications.
8. Domon B, Aebersold R. Mass spectrometry and protein analysis. Science 312(5771), 212-217 (2006).
9. Azad NS, Rasool N, Annunziata CM et al. Proteomics in clinical trials and practice: present uses and future promise. Mol. Cell. Proteomics 5(10), 1819-1829 (2006). • Discusses functional and expression proteomics and their application in clinical trial and practice.
10. Cho WC. Contribution of oncoproteomics to cancer biomarker discovery. Mol. Cancer 6, 25 (2007).
11. Houghton JP, Roddy S, Carroll S, McCluggage WG. A simple method for the prevention of endometrial autolysis in hysterectomy specimens. J. Clin. Pathol. 57(3), 332-333 (2004).
12. Fox CH, Johnson FB, Whiting J, Roller PP. Formaldehyde fixation. J. Histochem. Cytochem. 33(8), 845-853 (1985).
13. Ikeda K, Monden T, Kanoh T et al. Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin-embedded tissue sections. J. Histochem. Cytochem. 46(3), 397-403 (1998).
14. Prieto DA, Hood BL, Darfler MM et al. Liquid tissue: proteomic profiling of formalin-fixed tissues. Biotechniques 38(Suppl.), 32-35 (2005).
15. Yamashita S, Okada Y. Mechanisms of heat-induced antigen retrieval: analyses in vitro employing SDS-PAGE and immunohistochemistry. J. Histochem. Cytochem. 53(1), 13-21 (2005).
16. Petricoin EF III, Ornstein DK, Paweletz CP et al. Serum proteomic patterns for detection of prostate cancer. J. Natl Cancer Inst. 94(20), 1576-1578 (2002).
17. Adam BL, Qu Y, Davis JW et al. Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res. 62(13), 3609-3614 (2002).
18. Mian S, Ball G, Hornbuckle J et al. A prototype methodology combining surface-enhanced laser desorption/ionization protein chip technology and artificial neural network algorithms to predict the chemoresponsiveness of breast cancer cell lines exposed to paclitaxel and doxorubicin under in vitro conditions. Proteomics 3(9), 1725-1737 (2003).
19. Yang SY, Xiao XY, Zhang WG et al. Application of serum SELDI proteomic patterns in diagnosis of lung cancer. BMC Cancer 5, 83 (2005).
20. Zhukov TA, Johanson RA, Cantor AB, Clark RA, Tockman MS. Discovery of distinct protein profiles specific for lung tumors and pre-malignant lung lesions by SELDI mass spectrometry. Lung Cancer 40(3), 267-279 (2003).
21. Petricoin EF, Liotta LA. Clinical applications of proteomics. J. Nutr. 133(7 Suppl.), 2476S-2484S (2003).
22. Emmert-Buck MR, Bonner RF, Smith PD et al. Laser capture microdissection. Science 274(5289), 998-1001 (1996).
23. Wasinger VC, Corthals GL. Proteomic tools for biomedicine. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 771(1-2), 33-48 (2002).
24. Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl Acad. Sci. USA 97(17), 9390-9395 (2000).
25. Gauss C, Kalkum M, Lowe M, Lehrach H, Klose J. Analysis of the mouse proteome (I) brain proteins: separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation. Electrophoresis 20(3), 575-600 (1999).
26. Hwang SI, Thumar J, Lundgren DH et al. Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene 26(1), 65-76 (2007).
27. Hood BL, Darfler MM, Guiel TG et al. Proteomic analysis of formalin-fixed prostate cancer tissue. Mol. Cell. Proteomics 4(11), 1741-1753 (2005).
28. Shi SR, Liu C, Balgley BM, Lee C, Taylor CR. Protein extraction from formalin-fixed, paraffin-embedded tissue sections: quality evaluation by mass spectrometry. J. Histochem. Cytochem. 54(6), 739-743 (2006).
29. Jiang X, Feng S, Tian R, Ye M, Zou H. Development of efficient protein extraction methods for shotgun proteome analysis of formalin-fixed tissues. J. Proteome Res. 6(3), 1038-1047 (2007).
30. Palmer-Toy DE, Krastins B, Sarracino DA, Nadol JB Jr, Merchant SN. Efficient method for the proteomic analysis of fixed and embedded tissues. J. Proteome Res. 4(6), 2404-2411 (2005).
31. Guo T, Wang W, Rudnick PA et al. Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. J. Histochem. Cytochem. 55(7), 763-772 (2007).
32. Fowler CB, Cunningham RE, O'Leary TJ, Mason JT. 'Tissue surrogates' as a model for archival formalin-fixed paraffin-embedded tissues. Lab. Invest. 87(8), 836-846 (2007).
33. Fowler CB, Cunningham RE, Waybright TJ et al. Elevated hydrostatic pressure promotes protein recovery from formalin-fixed, paraffin-embedded tissue surrogates. Lab. Invest. 88(2), 185-195 (2008). • Discusses an improved method to extract proteins from archival formalin-fixed paraffin-embedded tissues for the high-throughput proteomic analysis of disease.
34. Pedrioli PG, Raught B, Zhang XD et al. Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software. Nat. Methods 3(7), 533-539 (2006).
35. Espina V, Heiby M, Pierobon M, Liotta LA. Laser capture microdissection technology. Expert Rev. Mol. Diagn. 7(5), 647-657 (2007). • Provides a thorough description of laser-capture microdissection (LCM) techniques, with an emphasis on tips and troubleshooting advice derived from LCM users.
36. Bagnato C, Thumar J, Mayya V et al. Proteomics analysis of human coronary atherosclerotic plaque: a feasibility study of direct tissue proteomics by liquid chromatography and tandem mass spectrometry. Mol. Cell. Proteomics 6(6), 1088-1102 (2007).
37. Ishihama Y, Oda Y, Tabata T et al. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 4(9), 1265-1272 (2005).
38. Wang G, Wu WW, Zeng W, Chou CL, Shen RF. Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: reproducibility, linearity, and application with complex proteomes. J. Proteome Res. 5(5), 1214-1223 (2006).
39. Bondarenko PV, Chelius D, Shaler TA. Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal. Chem. 74(18), 4741-4749 (2002).
40. Chelius D, Bondarenko PV. Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J. Proteome Res. 1(4), 317-323 (2002).
41. Wang W, Zhou H, Lin H et al. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 75(18), 4818-4826 (2003).
42. Higgs RE, Knierman MD, Gelfanova V, Butler JP, Hale JE. Comprehensive label-free method for the relative quantification of proteins from biological samples. J. Proteome Res. 4(4), 1442-1450 (2005).
43. Li XJ, Yi EC, Kemp CJ, Zhang H, Aebersold R. A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol. Cell. Proteomics 4(9), 1328-1340 (2005).
44. Liu H, Sadygov RG, Yates JR III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76(14), 4193-4201 (2004).
45. Barr JR, Maggio VL, Patterson DG Jr et al. Isotope dilution - mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I. Clin. Chem. 42(10), 1676-1682 (1996).
46. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl Acad. Sci. USA 100(12), 6940-6945 (2003).
47. Zhang F, Bartels MJ, Stott WT. Quantitation of human glutathione S-transferases in complex matrices by liquid chromatography/tandem mass spectrometry with signature peptides. Rapid Commun. Mass Spectrom. 18(4), 491-498 (2004).
48. Pan S, Zhang H, Rush J et al. High throughput proteome screening for biomarker detection. Mol. Cell. Proteomics 4(2), 182-190 (2005).
49. Bertucci F, Finetti P, Cervera N et al. Gene expression profiling and clinical outcome in breast cancer. Omics 10(4), 429-443 (2006).
50. Eng JK, McCormack AL, Yates JR III. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in protein database. J. Am. Soc. Mass Spectrom. 5, 976-989 (1994).
51. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20(18), 3551-3567 (1999).
52. Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20(9), 1466-1467 (2004).
53. Tanner S, Shu H, Frank A et al. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 77(14), 4626-4639 (2005).
54. Craig R, Cortens JC, Fenyo D, Beavis RC. Using annotated peptide mass spectrum libraries for protein identification. J. Proteome Res. 5(8), 1843-1849 (2006).
55. Lam H, Deutsch EW, Eddes JS et al. Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7(5), 655-667 (2007).