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Sensors 2012

Biomarker Discovery by Novel Sensors Based on Nanoproteomics Approaches

DOI: 10.3390/s120202284

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

Keywords: biomarker, cancer, nanosensor, high-throughput techniques, microarray, proteomics

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Abstract:

During the last years, proteomics has facilitated biomarker discovery by coupling high-throughput techniques with novel nanosensors. In the present review, we focus on the study of label-based and label-free detection systems, as well as nanotechnology approaches, indicating their advantages and applications in biomarker discovery. In addition, several disease biomarkers are shown in order to display the clinical importance of the improvement of sensitivity and selectivity by using nanoproteomics approaches as novel sensors.

References

[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.

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