Biomarker discovery by novel sensors based on nanoproteomics approaches

Sensors

Volumn 12, Issue 2, 2012, Pages 2284-2308

  Dasilva, Noelia ^a   Díez, Paula ^a   Matarraz, Sergio ^a   González González, María ^a   Paradinas, Sara ^a   Orfao, Alberto ^a   Fuentes, Manuel ^a  

^a UNIVERSITY OF SALAMANCA   (Spain)

Author keywords

Biomarker; Cancer; High throughput techniques; Microarray; Nanosensor; Proteomics

Indexed keywords

BIOLOGICAL MARKER;

EQUIPMENT; EQUIPMENT DESIGN; GENETIC PROCEDURES; INSTRUMENTATION; NANOTECHNOLOGY; PROTEIN MICROARRAY; PROTEOMICS; REVIEW; TRANSDUCER;

BIOLOGICAL MARKERS; BIOSENSING TECHNIQUES; EQUIPMENT DESIGN; EQUIPMENT FAILURE ANALYSIS; NANOTECHNOLOGY; PROTEIN ARRAY ANALYSIS; PROTEOMICS; TRANSDUCERS;

EID: 84857536353     PISSN: 14248220     EISSN: None     Source Type: Journal    
DOI: 10.3390/s120202284     Document Type: Review

References (79)

1. Wong, S.C.; Chan, C.M.; Ma, B.B.; Lam, M.Y.; Choi, G.C.; Au, T.C.; Chan, A.S.; Chan, A.T. Advanced proteomic technologies for cancer biomarker discovery. Expert Rev. Proteomics 2009, 6, 123-134.
2. Madu, C.O.; Lu, Y. Novel diagnostic biomarkers for prostate cancer. J. Cancer 2010, 1, 150-177.
3. Rakowska, P.D.; Ryadnov, M.G. Nano-enabled biomarker discovery and detection. Biomark. Med. 2011, 5, 387-396.
4. Gonzalez-Gonzalez, M.; Jara-Acevedo, R.; Matarraz, S.; Jara-Acevedo, M.; Paradinas, S.; Sayagues, J.M.; Orfao, A.; Fuentes, M. Nanotechniques in proteomics: Protein microarrays and novel detection platforms. Eur. J. Pharm. Sci. 2011, 45, 499-506.
5. Matarraz, S.; Gonzalez-Gonzalez, M.; Jara, M.; Orfao, A.; Fuentes, M. New Technologies in cancer. Protein microarrays for biomarker discovery. Clin. Transl. Oncol. 2011, 13, 156-161.
6. Xia, H.; Murray, K.; Soper, S.; Feng, J. Ultra sensitive affinity chromatography on avidin-functionalized PMMA microchip for low abundant post-translational modified protein enrichment. Biomed. Microdevices 2011, doi: 10.1007/s10544-011-9586-7.
7. Chandra, H.; Reddy, P.J.; Srivastava, S. Protein microarrays and novel detection platforms. Expert Rev. Proteomics 2011, 8, 61-79.
8. Ray, S.; Reddy, P.J.; Choudhary, S.; Raghu, D.; Srivastava, S. Emerging nanoproteomics approaches for disease biomarker detection: A current perspective. J. Proteomics 2011, 74, 2660-2681.
9. Tomizaki, K.Y.; Usui, K.; Mihara, H. Protein-protein interactions and selection: Array-based techniques for screening disease-associated biomarkers in predictive/early diagnosis. FEBS J. 2010, 277, 1996-2005.
10. LaBaer, J.; Ramachandran, N. Protein microarrays as tools for functional proteomics. Curr. Opin. Chem. Biol. 2005, 9, 14-19.
11. Hu, Y.; Uttamchandani, M.; Yao, S.Q. Microarray: A versatile platform for high-throughput functional proteomics. Comb. Chem. High Throughput Screen. 2006, 9, 203-212.
12. Grasso, V.; Lambertini, V.; Ghisellini, P.; Valerio, F.; Stura, E.; Perlo, P.; Nicolini, N. Nanostructuring of a porous alumina matrix for a biomolecular microarray. Nanotechnology 2006, 17, 795-798.
13. Collings, F.B.; Vaidya, V.S. Novel technologies for the discovery and quantitation of biomarkers of toxicity. Toxicology 2008, 245, 167-174.
14. Meany, D.L.; Zhang, Z.; Sokoll, L.J.; Zhang, H.; Chan, D.W. Glycoproteomics for prostate cancer detection: Changes in serum PSA glycosylation patterns. J. Proteome Res. 2009, 8, 613-619.
15. Srivastava, M.; Eidelman, O.; Jozwik, C.; Paweletz, C.; Huang, W.; Zeitlin, P.L.; Pollard, H.B. Serum proteomic signature for cystic fibrosis using an antibody microarray platform. Mol. Genet. Metab. 2006, 87, 303-310.
16. Zhou, H.; Bouwman, K.; Schotanus, M.; Verweij, C.; Marrero, J.A.; Dillon, D.; Costa, J.; Lizardi, P.; Haab, B.B. Two-color, rolling-circle amplification on antibody microarrays for sensitive, multiplexed serum-protein measurements. Genome Biol. 2004, 5, R28.
17. Wu, W.; Slastad, H.; de la Rosa Carrillo, D.; Frey, T.; Tjonnfjord, G.; Boretti, E.; Aasheim, H.C.; Horejsi, V.; Lund-Johansen, F. Antibody array analysis with label-based detection and resolution of protein size. Mol. Cell. Proteomics 2009, 8, 245-257.
18. Blazer, L.L.; Roman, D.L.; Muxlow, M.R.; Neubig, R.R. Use of flow cytometric methods to quantify protein-protein interactions. Curr. Protoc. Cytom 2010, doi: 10.1002/0471142956.cy1311s51.
19. Harsha, H.C.; Molina, H.; Pandey, A. Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nat. Protoc. 2008, 3, 505-516.
20. Everley, P.A.; Krijgsveld, J.; Zetter, B.R.; Gygi, S.P. Quantitative cancer proteomics: Stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Mol. Cell. Proteomics 2004, 3, 729-735.
21. Waanders, L.F.; Hanke, S.; Mann, M. Top-down quantitation and characterization of SILAC-labeled proteins. J. Am. Soc. Mass Spectrom. 2007, 18, 2058-2064.
22. Zhu, W.; Smith, J.W.; Huang, C.M. Mass spectrometry-based label-free quantitative proteomics. J. Biomed. Biotechnol. 2010, doi: 10.1155/2010/840518.
23. Kodoyianni, V. Label-free analysis of biomolecular interactions using SPR imaging. BioTechniques 2011, 50, 32-40.
24. Stern, E.; Vacic, A.; Rajan, N.K.; Criscione, J.M.; Park, J.; Ilic, B.R.; Mooney, D.J.; Reed, M.A.; Fahmy, T.M. Label-free biomarker detection from whole blood. Nat. Nanotechnol. 2010, 5, 138-142.
25. Umehara, S.; Karhanek, M.; Davis, R.W.; Pourmand, N. Label-free biosensing with functionalized nanopipette probes. Proc. Natl. Acad. Sci. USA 2009, 106, 4611-4616.
26. Lin, J.; Wei, Z.; Mao, C. A label-free immunosensor based on modified mesoporous silica for simultaneous determination of tumor markers. Biosens. Bioelectron. 2011, 29, 40-45.
27. Chikkaveeraiah, B.V.; Mani, V.; Patel, V.; Gutkind, J.S.; Rusling, J.F. Microfluidic electrochemical immunoarray for ultrasensitive detection of two cancer biomarker proteins in serum. Biosens. Bioelectron. 2011, 26, 4477-4483.
28. Nicolini, C.; Pechkova, E. Nanoproteomics for nanomedicine. Nanomedicine (Lond.) 2010, 5, 677-682.
29. Nicolini, C.; Sivozhelezov, V.; Bavastrello, V.; Bezzerra, T.; Scudieri, D.; Spera, R.; Pechkova, E. Matrices for sensors from inorganic, organic, and biological nanocomposites. Materials 2011, 4, 1483-1518.
30. Maccioni, E.; Radicchi, G.; Erokhin, V.; Paddeu, S.; Facci, P.; Nicolini, C. Bacteriorhodopsin thin film as a sensitive layer for an anaesthetic sensor. Thin Solid Films 1996, 284-285, 898-900.
31. Paternolli, C.; Ghisellini, P.; Nicolini, C. Nanostructuring of heme-proteins for biodevice applications. IET Nanobiotechnol. 2007, 1, 22-26.
32. Paternolli, C.; Neebe, M.; Stura, E.; Barbieri, F.; Ghisellini, P.; Hampp, N.; Nicolini, C. Photoreversibility and photostability in films of octopus rhodopsin isolated from octopus photoreceptor membranes. J. Biomed. Mater. Res. A 2009, 88, 947-951.
33. Nicolini, C.; Pechkova, E. An overview of nanotechnology-based functional proteomics for cancer and cell cycle progression. Anticancer Res. 2010, 30, 2073-2080.
34. Nicolini, C.; LaBaer, J. Functional Proteomics & Nanotechnology-Based Microarrays; Pan Stanford Series on Nanobiotechnology: Singapore, 2010; Volume 2, Chapters 1-12, pp. 1-347.
35. Ramachandran, N.; Larson, D.N.; Stark, P.R.; Hainsworth, E.; LaBaer, J. Emerging tools for real-time label-free detection of interactions on functional protein microarrays. FEBS J. 2005, 272, 5412-5425.
36. Torreri, P.; Ceccarini, M.; Macioce, P.; Petrucci, T.C. Biomolecular interactions by surface plasmon resonance technology. Ann. Ist. Super. Sanita 2005, 41, 437-441.
37. Ladd, J.; Taylor, A.D.; Piliarik, M.; Homola, J.; Jiang, S. Label-free detection of cancer biomarker candidates using surface plasmon resonance imaging. Anal. Bioanal. Chem. 2009, 393, 1157-1163.
38. Zhang, X.; Guo, Q.; Cui, D. Recent advances in nanotechnology applied to biosensors. Sensors 2009, 9, 1033-1053.
39. Zahavy, E.; Whitesell, J.K.; Fox, M.A. Surface effects in water-soluble shell-core hybrid gold nanoparticles in oligonucleotide single strand recognition for sequence-specific bioactivation. Langmuir 2010, 26, 16442-16446.
40. Bao, Y.P.; Wei, T.F.; Lefebvre, P.A.; An, H.; He, L.; Kunkel, G.T.; Muller, U.R. Detection of protein analytes via nanoparticle-based bio bar code technology. Anal. Chem. 2006, 78, 2055-2059.
41. Wagner, M.K.; Li, F.; Li, J.; Li, X.F.; Le, X.C. Use of quantum dots in the development of assays for cancer biomarkers. Anal. Bioanal Chem. 2010, 397, 3213-3224.
42. Yezhelyev, M.V. In situ molecular profiling of breast cancer biomarkers with multicolor quantum dots. Adv. Mater. 2007, 19, 3146-3151.
43. Sinha, N.; Yeow, J.T.-W. Carbon nanotubes for biomedical applications. IEE Trans. Nanobiosci. 2005, 4, 180-195.
44. Malhotra, R.; Patel, V.; Vaque, J.P.; Gutkind, J.S.; Rusling, J.F. Ultrasensitive electrochemical immunosensor for oral cancer biomarker IL-6 using carbon nanotube forest electrodes and multilabel amplification. Anal. Chem. 2010, 82, 3118-3123.
45. Wang, J. Carbon-nanotube based electrochemical biosensors: A review. Electroanalysis 2005, 17, 7-14.
46. Cerasoli, E.; Rakowska, P.D.; Horgan, A.; Ravi, J.; Bradley, M.; Vincent, B.; Ryadnov, M.G. MiS-MALDI: Microgel-selected detection of protein biomarkers by MALDI-ToF mass spectrometry. Mol. Biosyst. 2010, 6, 2214-2217.
47. Luchini, A.; Geho, D.H.; Bishop, B.; Tran, D.; Xia, C.; Dufour, R.L.; Jones, C.D.; Espina, V.; Patanarut, A.; Zhou, W., et al. Smart hydrogel particles: Biomarker harvesting: One-step affinity purification, size exclusion, and protection against degradation. Nano Lett. 2008, 8, 350-361.
48. Stura, E.; Bruzzese, D.; Valerio, F.; Grasso, V.; Perlo, P.; Nicolini, C. Anodic porous alumina as mechanical stability enhancer for LDL-cholesterol sensitive electrodes. Biosens. Bioelectron. 2007, 23, 655-660.
49. Bavastrello, V.; Stura, E.; Carrara, S.; Erokhin, V.; Nicolini, C. Poly(2,5-dimethylaniline)-MWNTs nanocomposite: A new material for conductometric acid vapours sensor. Sens. Actuat. B Chem. 2004, 98, 247-253.
50. Jokerst, J.V.; Raamanathan, A.; Christodoulides, N.; Floriano, P.N.; Pollard, A.A.; Simmons, G.W.; Wong, J.; Gage, C.; Furmaga, W.B.; Redding, S.W., et al. Nano-bio-chips for high performance multiplexed protein detection: determinations of cancer biomarkers in serum and saliva using quantum dot bioconjugate labels. Biosens. Bioelectron. 2009, 24, 3622-3629.
51. Makridakis, M.; Vlahou, A. Secretome proteomics for discovery of cancer biomarkers. J. Proteomics 2010, 73, 2291-2305.
52. Goo, Y.A.; Goodlett, D.R. Advances in proteomic prostate cancer biomarker discovery. J. Proteomics 2010, 73, 1839-1850.
53. Misek, D.E.; Kim, E.H. Protein biomarkers for the early detection of breast cancer. Int. J. Proteomics 2011, doi: 10.1155/2011/343582.
54. Zhang, H.; Kong, B.; Qu, X.; Jia, L.; Deng, B.; Yang, Q. Biomarker discovery for ovarian cancer using SELDI-TOF-MS. Gynecol. Oncol. 2006, 102, 61-66.
55. Gold, D.V.; Modrak, D.E.; Ying, Z.; Cardillo, T.M.; Sharkey, R.M.; Goldenberg, D.M. New MUC1 serum immunoassay differentiates pancreatic cancer from pancreatitis. J. Clin. Oncol. 2006, 24, 252-258.
56. Buxbaum, J.L.; Eloubeidi, M.A. Molecular and clinical markers of pancreas cancer. JOP 2010, 11, 536-544.
57. Hueber, W.; Robinson, W.H. Proteomic biomarkers for autoimmune disease. Proteomics 2006, 6, 4100-4105.
58. Krenn, V.; Petersen, I.; Haupl, T.; Koepenik, A.; Blind, C.; Dietel, M.; Konthur, Z.; Skriner, K. Array technology and proteomics in autoimmune diseases. Pathol. Res. Pract. 2004, 200, 95-103.
59. Pinto, J.A.; Rego, I.; Rodriguez-Gomez, M.; Canete, J.D.; Fernandez-Lopez, C.; Freire, M.; Fernandez-Sueiro, J.L.; Sanmarti, R.; Blanco, F.J. Polymorphisms in genes encoding tumor necrosis factor-alpha and HLA-DRB1 are not associated with response to infliximab in patients with rheumatoid arthritis. J. Rheumatol. 2008, 35, 177-178.
60. Lee, S.; Serada, S.; Fujimoto, M.; Naka, T. Application of Novel Quantitative Proteomic Technologies to Identify New Serological Biomarkers in Autoimmune Diseases. Available online: http://www.intechopen.com/source/pdfs/20669/InTechApplication_of_novel_quantitative_proteomic_technologies_to_identify_new_serological_biomarkers_in_autoimmune_diseases.pdf (accessed on 1 December 2011).
61. Li, Q.Z.; Xie, C.; Wu, T.; Mackay, M.; Aranow, C.; Putterman, C.; Mohan, C. Identification of autoantibody clusters that best predict lupus disease activity using glomerular proteome arrays. J. Clin. Invest. 2005, 115, 3428-3439.
62. Drouvalakis, K.A.; Bangsaruntip, S.; Hueber, W.; Kozar, L.G.; Utz, P.J.; Dai, H. Peptide-coated nanotube-based biosensor for the detection of disease-specific autoantibodies in human serum. Biosens. Bioelectron. 2008, 23, 1413-1421.
63. Chen, Z.; Tabakman, S.M.; Goodwin, A.P.; Kattah, M.G.; Daranciang, D.; Wang, X.; Zhang, G.; Li, X.; Liu, Z.; Utz, P.J., et al. Protein microarrays with carbon nanotubes as multicolor raman labels. Nat. Biotechnol. 2008, 26, 1285-1292.
64. Carlsson, A.; Wuttge, D.M.; Ingvarsson, J.; Bengtsson, A.A.; Sturfelt, G.; Borrebaeck, C.A.; Wingren, C. Serum protein profiling of systemic lupus erythematosus and systemic sclerosis using recombinant antibody microarrays. Mol. Cell. Proteomics 2011, doi: 10.1074/mcp.M110.005033.
65. Bell, C.; Smith, G.T.; Sweredoski, M.J.; Hess, S. Characterization of the mycobacterium tuberculosis proteome by liquid chromatography mass spectrometry-based proteomics techniques: A comprehensive resource for tuberculosis research. J. Proteome Res. 2012, 11, 119-130.
66. Liu, T.; Xue, R.; Huang, X.; Zhang, D.; Dong, L.; Wu, H.; Shen, X. Proteomic profiling of hepatitis B virus-related hepatocellular carcinoma with magnetic bead-based matrix-assisted Laser desorption/ionization time-of-flight mass spectrometry. Acta Biochim. Biophys. Sin. (Shanghai) 2011, 43, 542-550.
67. Gaudieri, S. Biomarkers that reflect immune activation or dysfunction will be important in the management of infectious diseases. Biomark. Med. 2011, 5, 109-112.
68. Hauck, T.S.; Giri, S.; Gao, Y.; Chan, W.C. Nanotechnology diagnostics for infectious diseases prevalent in developing countries. Adv. Drug Deliv. Rev. 2010, 62, 438-448.
69. Agranoff, D.; Fernandez-Reyes, D.; Papadopoulos, M.C.; Rojas, S.A.; Herbster, M.; Loosemore, A.; Tarelli, E.; Sheldon, J.; Schwenk, A.; Pollok, R., et al. Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum. Lancet 2006, 368, 1012-1021.
70. Gupta, N.; Shankernarayan, N.P.; Dharmalingam, K. Alpha1-acid glycoprotein as a putative biomarker for monitoring the development of the type II reactional stage of leprosy. J. Med. Microbiol. 2010, 59, 400-407.
71. Tang, S.; Moayeri, M.; Chen, Z.; Harma, H.; Zhao, J.; Hu, H.; Purcell, R.H.; Leppla, S.H.; Hewlett, I.K. Detection of anthrax toxin by an ultrasensitive immunoassay using europium nanoparticles. Clin. Vaccine Immunol. 2009, 16, 408-413.
72. Lee, Y.F.; Lien, K.Y.; Lei, H.Y.; Lee, G.B. An integrated microfluidic system for rapid diagnosis of dengue virus infection. Biosens. Bioelectron. 2009, 25, 745-752.
73. Oliver, B.G.; Price, P. The search for biomarkers of immune restoration disease associated with mycobacterium tuberculosis in HIV patients beginning antiretroviral therapy. Biomark. Med. 2011, 5, 149-154.
74. Sanchez, J.C.; Guillaume, E.; Lescuyer, P.; Allard, L.; Carrette, O.; Scherl, A.; Burgess, J.; Corthals, G.L.; Burkhard, P.R.; Hochstrasser, D.F. Cystatin C as a potential cerebrospinal fluid marker for the diagnosis of creutzfeldt-jakob disease. Proteomics 2004, 4, 2229-2233.
75. Mabbott, N.A.; Mackay, F.; Minns, F.; Bruce, M.E. Temporary inactivation of follicular dendritic cells delays neuroinvasion of scrapie. Nat. Med. 2000, 6, 719-720.
76. Ray, S.; Reddy, P.J.; Jain, R.; Gollapalli, K.; Moiyadi, A.; Srivastava, S. Proteomic technologies for the identification of disease biomarkers in serum: Advances and challenges ahead. Proteomics 2011, 11, 2139-2161.
77. Kim, H.J.; Cho, E.H.; Yoo, J.H.; Kim, P.K.; Shin, J.S.; Kim, M.R.; Kim, C.W. Proteome analysis of serum from type 2 diabetics with nephropathy. J. Proteome Res. 2007, 6, 735-743.
78. Pickup, J.C.; Zhi, Z.L.; Khan, F.; Saxl, T.; Birch, D.J. Nanomedicine and its potential in diabetes research and practice. Diabetes Metab. Res. Rev. 2008, 24, 604-610.
79. Cash, K.J.; Clark, H.A. Nanosensors and nanomaterials for monitoring glucose in diabetes. Trends Mol. Med. 2010, 16, 584-593.