Recent Advances in Capillary Electrophoresis-Based Proteomic Techniques for Biomarker Discovery

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 984)

Abstract

Due to the inherent disadvantage of biomarker dilution in complex biological fluids such as serum/plasma, urine, and saliva, investigative studies directed at tissues obtained from the primary site of pathology probably afford the best opportunity for the discovery of disease biomarkers. Still, the large variation of protein relative abundances with clinical specimens often exceeds the dynamic range of currently available proteomic techniques. Furthermore, since the sizes of human tissue biopsies are becoming significantly smaller due to the advent of minimally invasive methods and early detection and treatment of lesions, a more effective discovery-based proteomic technology is critically needed to enable comprehensive and comparative studies of protein profiles that will have diagnostic and therapeutic relevance.

This review therefore focuses on the most recent advances in capillary electrophoresis-based single and multidimensional separations coupled with mass spectrometry for performing comprehensive proteomic analysis of clinical specimens. In addition to protein identification, monitoring quantitative changes in protein expression is essential for the discovery of disease-associated biomarkers. Comparative proteomics involving measurements in changes of biological pathways or functional processes are further expected to provide relevant markers and networks, molecular relationships among different stages of disease, and molecular mechanisms that drive the progression of disease.

Key words

Biomarker discovery Capillary electrophoresis Mass spectrometry Reversed-phase liquid chromatography Tissue proteomics 

Notes

Acknowledgment

We thank the National Cancer Institute (CA143177), the National Center for Research Resources (RR032333), and the National Institute of General Medical Sciences (GM103536) for supporting portions of our research activities reviewed in this chapter.

References

  1. 1.
    Drube J, Zurbig P, Schiffer E, Lau E, Ure B, Gluer S, Kirschstein M, Pape L, Decramer S, Bascands J-L, Schanstra JP, Mischak H, Ehrich JHH (2010) Urinary proteome analysis identifies infants but not older children requiring pyeloplasty. Pediatr Nephrol 25:1673–1678PubMedCrossRefGoogle Scholar
  2. 2.
    Theodorescu D, Schiffer E, Bauer HW, Douwes F, Eichhorn F, Polley R, Schmidt T, Schofer W, Zurbig P, Good DM, Coon JJ, Mischak H (2008) Discovery and validation of urinary biomarkers for prostate cancer. Proteomics Clin Appl 2:556–570PubMedCrossRefGoogle Scholar
  3. 3.
    Schiffer E, Vlahou A, Petrolekas A, Stravodimos K, Tauber R, Geschwend JE, Neuhaus J, Stolzenburg J-U, Conaway MR, Mischak H, Theodorescu D (2009) Prediction of muscle-invasive bladder cancer using urinary proteomics. Clin Cancer Res 15:4935–4943PubMedCrossRefGoogle Scholar
  4. 4.
    Schiffer E, Bick C, Grizelj B, Pietzker S, Schofer W (2012) Urinary proteome analysis for prostate cancer diagnosis: cost-effective application in routine clinical practice in Germany. Int J Urol 19:118–125PubMedCrossRefGoogle Scholar
  5. 5.
    Haubitz M, Good DM, Woywodt A, Haller H, Rupprecht H, Theodorescu D, Dakna M, Coon JJ, Mischak H (2009) Identification and validation of urinary biomarkers for differential diagnosis and evaluation of therapeutic intervention in anti-neutrophil cytoplasmic antibody-associated vasculitis. Mol Cell Proteomics 8:2296–2307PubMedCrossRefGoogle Scholar
  6. 6.
    Zimmerli LU, Schiffer E, Zurbi P, Good DM, Kellmann M, Mouls L, Pitt AR, Coon JJ, Schmieder RE, Peter KH, Mischak H, Kolch W, Delles C, Dominiczak AF (2008) Urinary proteomic biomarkers in coronary artery disease. Mol Cell Proteomics 7:290–298PubMedGoogle Scholar
  7. 7.
    von Zur Muhlen C, Schiffer E, Zuerbig P, Kellmann M, Brasse M, Meert N, Vanholder RC, Dominiczak AF, Chen YC, Mischak H, Bode C, Peter K (2009) Evaluation of urine proteome pattern analysis for its potential to reflect coronary artery atherosclerosis in symptomatic patients. J Proteome Res 8:335–345CrossRefGoogle Scholar
  8. 8.
    Snell-Bergeon JK, Maahs DM, Ogden LG, Kinney GL, Hokanson JE, Schiffer E, Rewers M, Mischak H (2009) Evaluation of urinary biomarkers for coronary artery disease, diabetes, and diabetic kidney disease. Diabetes Technol Ther 11:1–9PubMedCrossRefGoogle Scholar
  9. 9.
    Jantos-Siwy J, Schiffer E, Brand K, Schumann G, Rossing K, Delles C, Mischak H, Metzger J (2009) Quantitative urinary proteome analysis for biomarker evaluation in chronic kidney disease. J Proteome Res 8:268–281PubMedCrossRefGoogle Scholar
  10. 10.
    Kistler AD, Mischak H, Poster D, Dakna M, Wuthrich RP, Serra AL (2009) Identification of a unique urinary biomarker profile in patients with autosomal dominant polycystic kidney disease. Kidney Int 76:89–96PubMedCrossRefGoogle Scholar
  11. 11.
    Good DM, Zurbig P, Argiles A, Bauer HW, Behrens G, Coon JJ, Dakna M, Decramer S, Delles C, Dominiczak AF, Ehrich JHH, Eitner F, Fliser D, Frommberger M, Ganser A, Girolami MA, Golovko I, Gwinner W, Haubitz M, Herget-Rosenthal S, Jankowski J, Jahn H, Jerums G, Julian BA, Kellmann M, Kliem V, Kolch W, Krolewski AS, Luppi M, Massy Z, Melter M, Neususs C, Novak J, Peter K, Rossing K, Rupprecht H, Schanstra JP, Schiffer E, Stolzenburg J-U, Tarnow L, Theodorescu D, Thongboonkerd V, Vanholder R, Weissinger EM, Mischak H, Schmitt-Kopplin P (2010) Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease. Mol Cell Proteomics 9:2424–2437PubMedCrossRefGoogle Scholar
  12. 12.
    Raedler TJ, Wittke S, Jahn H, Koessler A, Mischak H, Wiedemann K (2008) Capillary electrophoresis mass spectrometry as a potential tool to detect lithium-induced nephropathy: preliminary results. Prog Neuropsycho-pharmacol Biol Psychiatry 32:673–678PubMedCrossRefGoogle Scholar
  13. 13.
    Weissinger EM, Schiffer E, Hertenstein B, Ferrara JL, Holler E, Stadler M, Kolb H-J, Zander A, Zurbig P, Kellmann M, Ganser A (2007) Proteomic patterns predict acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation. Blood 109:5511–5519PubMedCrossRefGoogle Scholar
  14. 14.
    Haselberg R, de Jong GJ, Somsen GW (2011) Capillary electrophoresis-mass spectrometry for the analysis of intact proteins 2007–2010. Electrophoresis 32:66–82PubMedCrossRefGoogle Scholar
  15. 15.
    Albalat A, Mischak H, Mullen W (2011) Clinical application of urinary proteomics/peptidomics. Expert Rev Proteomics 8:615–629PubMedCrossRefGoogle Scholar
  16. 16.
    Mischak H, Schanstra JP (2011) CE-MS in biomarker discovery, validation, and clinical application. Proteomics Clin Appl 5:9–23PubMedCrossRefGoogle Scholar
  17. 17.
    Metzger J, Chatzikyrkou C, Broecker V, Schiffer E, Jaensch L, Iphoefer A, Mengel M, Mullen W, Mischak H, Haller H, Gwinner W (2011) Diagnosis of subclinical and clinical acute T-cell-mediated rejection in renal transplant patients by urinary proteome analysis. Proteomics Clin Appl 5:322–333PubMedCrossRefGoogle Scholar
  18. 18.
    Zuberovic A, Wetterhall M, Hanrieder J, Bergquist J (2009) CE MALDI-TOF/TOF MS for multiplexed quantification of proteins in human ventricular cerebrospinal fluid. Electrophoresis 30:1836–1843PubMedCrossRefGoogle Scholar
  19. 19.
    Wiese S, Reidegeld KA, Meyer HE, Warscheid B (2007) Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics 7:340–350PubMedCrossRefGoogle Scholar
  20. 20.
    Wang W, Guo T, Rudnick PA, Song T, Li J, Zhuang Z, Zheng W, Devoe DL, Le CS, Balgley BM (2007) Membrane proteome analysis of microdissected ovarian tumor tissues using capillary isoelectric focusing/reversed-phase liquid chromatography-tandem MS. Anal Chem 79:1002–1009PubMedCrossRefGoogle Scholar
  21. 21.
    Guo T, Wang W, Rudnick PA, Song T, Li J, Zhuang Z, Weil RJ, DeVoe DL, Lee CS, Balgley BM (2007) Proteome analysis of microdissected formalin-fixed and Paraffin-embedded tissue specimens. J Histochem Cytochem 55:763–772PubMedCrossRefGoogle Scholar
  22. 22.
    Liu H, Sadygov RG, Yates JR (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76:4193–4201PubMedCrossRefGoogle Scholar
  23. 23.
    Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M (2005) 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 4:1265–1272PubMedCrossRefGoogle Scholar
  24. 24.
    Balgley BM, Wang W, Song T, Fang X, Yang L, Lee CS (2008) Evaluation of confidence and reproducibility in quantitative proteomics performed by a capillary isoelectric focusing-based proteomic platform coupled with a spectral counting approach. Electrophoresis 29:3047–3054PubMedCrossRefGoogle Scholar
  25. 25.
    Dai L, Li C, Shedden KA, Misek DE, Lubman DM (2009) Comparative proteomic study of two closely related ovarian endometrioid adenocarcinoma cell lines using cIEF fractionation and pathway analysis. Electrophoresis 30:1119–1131PubMedCrossRefGoogle Scholar
  26. 26.
    Hanrieder J, Zuberovic A, Bergquist J (2009) Surface modified capillary electrophoresis combined with in solution isoelectric focusing and MALDI-TOF/TOF MS: a gel-free multidimensional electrophoresis approach for proteomic profiling–exemplified on human follicular fluid. J Chromatogr A 1216:3621–3628PubMedCrossRefGoogle Scholar
  27. 27.
    Hood L (2003) Systems biology: integrating technology, biology, and computation. Mech Ageing Dev 124:9–16PubMedCrossRefGoogle Scholar
  28. 28.
    Aebersold R, Cravatt BF (2002) Proteomics–advances, applications and the challenges that remain. Trends Biotechnol 20:1–2CrossRefGoogle Scholar
  29. 29.
    An Y, Cooper JW, Balgley BM, Lee CS (2006) Selective enrichment and ultrasensitive identification of trace peptides in proteome analysis using transient capillary isotachophoresis/zone electrophoresis coupled with nano-ESI-MS. Electrophoresis 27:3599–3608PubMedCrossRefGoogle Scholar
  30. 30.
    Fang X, Yang L, Wang W, Song T, Lee C, Devoe D, Balgley B (2007) Comparison of Electrokinetics-Based Multidimensional Separations Coupled with Electrospray Ionization-Tandem Mass Spectrometry for Characterization of Human Salivary Proteins. Anal Chem 79:5785–5792PubMedCrossRefGoogle Scholar
  31. 31.
    Fang X, Wang W, Yang L, Chandrasekaran K, Kristian T, Balgley BM, Lee CS (2008) Application of capillary isotachophoresis-based multidimensional separations coupled with electrospray ionization-tandem mass spectrometry for characterization of mouse brain mitochondrial proteome. Electrophoresis 29:2215–2223PubMedCrossRefGoogle Scholar
  32. 32.
    Fang X, Balgley BM, Wang W, Park DM, Lee CS (2009) Comparison of multidimensional shotgun technologies targeting tissue proteomics. Electrophoresis 30:4063–4070PubMedCrossRefGoogle Scholar
  33. 33.
    Wolters DA, Washburn MP, Yates JR (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 73:5683–5690PubMedCrossRefGoogle Scholar
  34. 34.
    Jinawath N, Vasoontara C, Jinawath A, Fang X, Zhao K, Yap K-L, Guo T, Lee CS, Wang W, Balgley BM, Davidson B, Wang T-L, Shih I-M (2010) Oncoproteomic analysis reveals co-upregulation of RELA and STAT5 in carboplatin resistant ovarian carcinoma. PLoS One 5:e11198PubMedCrossRefGoogle Scholar
  35. 35.
    Chen Z, Fadiel A, Xia Y (2006) Functional duality of merlin: a conundrum of proteome complexity. Med Hypotheses 67:1095–1098PubMedCrossRefGoogle Scholar
  36. 36.
    Huang K-C, Park DC, Ng S-K, Lee JY, Ni X, Ng W-C, Bandera CA, Welch WR, Berkowitz RS, Mok SC, Ng S-W (2006) Selenium binding protein 1 in ovarian cancer. Int J Cancer 118:2433–2440PubMedCrossRefGoogle Scholar
  37. 37.
    Chekhun VF, Lukyanova NY, Urchenko OV, Kulik GI (2005) The role of expression of the components of proteome in the formation of molecular profile of human ovarian carcinoma A2780 cells sensitive and resistant to cisplatin. Exp Oncol 27:191–195PubMedGoogle Scholar
  38. 38.
    Smith-Beckerman DM, Fung KW, Williams KE, Auersperg N, Godwin AK, Burlingame AL (2005) Proteome changes in ovarian epithelial cells derived from women with BRCA1 mutations and family histories of cancer. Mol Cell Proteomics 4:156–168PubMedGoogle Scholar
  39. 39.
    Duan Z, Foster R, Bell DA, Mahoney J, Wolak K, Vaidya A, Hampel C, Lee H, Seiden MV (2006) Signal transducers and activators of transcription 3 pathway activation in drug-resistant ovarian cancer. Clin Cancer Res 12:5055–5063PubMedCrossRefGoogle Scholar
  40. 40.
    Haura EB, Zheng Z, Song L, Cantor A, Bepler G (2005) Activated epidermal growth factor receptor-Stat-3 signaling promotes tumor survival in vivo in non-small cell lung cancer. Clin Cancer Res 11:8288–8294PubMedCrossRefGoogle Scholar
  41. 41.
    Chen L-F, Greene WC (2004) Shaping the nuclear action of NF-kappaB. Nat Rev Mol Cell Biol 5:392–401PubMedCrossRefGoogle Scholar
  42. 42.
    Xu H, Yang L, Wang W, Shi S-R, Liu C, Liu Y, Fang X, Taylor CR, Lee CS, Balgley BM (2008) Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues. J Proteome Res 7:1098–1108PubMedCrossRefGoogle Scholar
  43. 43.
    Balgley BM, Guo T, Zhao K, Fang X, Tavassoli FA, Lee CS (2009) Evaluation of Archival Time on Shotgun Proteomics of Formalin-Fixed and Paraffin-Embedded Tissues. J Proteome Res 8:917–925PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Department of Chemistry and BiochemistryUniversity of MarylandCollege ParkUSA
  2. 2.Calibrant BiosystemsRockvilleUSA

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