Abstract
Advances in genome scale analysis provide an alternative tool to combine large-scale screening of chemicals with detailed mechanistic studies, in which expression signatures for specific factors can be used as predictors of response or serve as new therapeutic targets in vitro and in vivo. Recently, the possibility of analyzing the effects of nanomaterials on a large number of genes has led to toxicogenomic studies in nanotechnology. Furthermore, expression signatures are providing potential targets for the design of ligand-mediated tumor targeting. In this respect, the integration of phage display technique with nanotechnology has been explored as a new approach to generate cancer-targeted nanomedicines. In this chapter we outline advances in microarray technology and in the selection of peptides and antibodies by display techniques. Furthermore, we add insights into their application in the field of toxicogenomics and in the development of targeted nanomedicines.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Allen TM (2002) Ligand-targeted therapeutics in anticancer therapy. Nat Rev Cancer 2(10):750–763
Allison DB, Cui X, Page GP, Sabripour M (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7(1):55–65
Amorim MJ, Novais SC, Van Der Ven K et al (2011) Development of a microarray for Enchytraeus albidus (Oligochaeta): preliminary tool with diverse applications. Environ Toxicol Chem 30(6):1395–1402
Bar H, Yacoby I, Benhar I (2008) Killing cancer cells by targeted drug-carrying phage nanomedicines. BMC Biotechnol 8:37
Baugh LR, Hill AA, Brown EL et al (2001) Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res 29(5):E29
Benucci M, Saviola G, Manfredi M et al (2012) Tumor necrosis factors blocking agents: analogies and differences. Acta Biomed 83(1):72–80
Bertschinger J, Neri D (2004) Covalent DNA display as a novel tool for directed evolution of proteins in vitro. Protein Eng Des Sel 17(9):699–707
Bezalel S, Asher I, Elbirt D et al (2012) Novel biological treatments for systemic lupus erythematosus: current and future modalities. Isr Med Assoc J 14(8):508–514
Bowers PM, Horlick RA, Neben TY et al (2011) Coupling mammalian cell surface display with somatic hypermutation for the discovery and maturation of human antibodies. Proc Natl Acad Sci U S A 108(51):20455–20460
Chen L, Zurita AJ, Ardelt PU et al (2004) Design and validation of a bifunctional ligand display system for receptor targeting. Chem Biol 11(8):1081–1091
Clementi N, Mancini N, Solforosi L et al (2012) Phage display-based strategies for cloning and optimization of monoclonal antibodies directed against human pathogens. Int J Mol Sci 13(7):8273–8292
Cui Y, Liu H, Ze Y et al (2012) Gene expression in liver injury caused by long-term exposure to titanium dioxide nanoparticles in mice. Toxicol Sci 128(1):171–185
Damoiseaux R, George S, Li M et al (2011) No time to lose—high throughput screening to assess nanomaterial safety. Nanoscale 3(4):1345–1360
Dantas-Barbosa C, de Macedo Brigido M, Maranhao AQ (2012) Antibody phage display libraries: contributions to oncology. Int J Mol Sci 13(5):5420–5440
Deramchia K, Jacobin-Valat MJ, Vallet A et al (2012) In vivo phage display to identify new human antibody fragments homing to atherosclerotic endothelial and subendothelial tissues [corrected]. Am J Pathol 180(6):2576–2589
Ferreira C, Sartori-da-Silva M, Justo G (2011) Zebrafish as a suitable model for evaluating nanocosmetics and nanomedicines. In: Beck R, Guterres S, Pohlmann A (eds) Nanocosmetics and nanomedicines. Springer, Berlin, pp 239–251
Fischer HC, Chan WC (2007) Nanotoxicity: the growing need for in vivo study. Curr Opin Biotechnol 18(6):565–571
Fisichella M, Berenguer F, Steinmetz G et al (2012) Intestinal toxicity evaluation of TiO2 degraded surface-treated nanoparticles: a combined physico-chemical and toxicogenomics approach in caco-2 cells. Part Fibre Toxicol 9:18
FitzGerald K (2000) In vitro display technologies—new tools for drug discovery. Drug Discov Today 5(6):253–258
Foldbjerg R, Irving ES, Hayashi Y et al (2012) Global gene expression profiling of human lung epithelial cells after exposure to nanosilver. Toxicol Sci 130:145–157
Froehlicher M, Liedtke A, Groh KJ et al (2009) Zebrafish (Danio rerio) neuromast: promising biological endpoint linking developmental and toxicological studies. Aquat Toxicol 95(4):307–319
Fujita K, Morimoto Y, Endoh S et al (2010) Identification of potential biomarkers from gene expression profiles in rat lungs intratracheally instilled with C(60) fullerenes. Toxicology 274:34–41
Gagne F, Andre C, Skirrow R et al (2012) Toxicity of silver nanoparticles to rainbow trout: a toxicogenomic approach. Chemosphere 89(5):615–622
Gesteira TF, Coulson-Thomas VJ, Taunay-Rodrigues A et al (2011) Inhibitory peptides of the sulfotransferase domain of the heparan sulfate enzyme, N-deacetylase-N-sulfotransferase-1. J Biol Chem 286(7):5338–5346
Giordano RJ, Cardo-Vila M, Lahdenranta J et al (2001) Biopanning and rapid analysis of selective interactive ligands. Nat Med 7(11):1249–1253
Gomes SI, Novais SC, Scott-Fordsmand JJ et al (2012) Effect of Cu-nanoparticles versus Cu-salt in Enchytraeus albidus (Oligochaeta): differential gene expression through microarray analysis. Comp Biochem Physiol C Toxicol Pharmacol 155(2):219–227
Gomes SI, Soares AM, Scott-Fordsmand JJ et al (2013) Mechanisms of response to silver nanoparticles on Enchytraeus albidus (Oligochaeta): survival, reproduction and gene expression profile. J Hazard Mater 254–255:336–344
Griffitt RJ, Hyndman K, Denslow ND et al (2009) Comparison of molecular and histological changes in zebrafish gills exposed to metallic nanoparticles. Toxicol Sci 107(2):404–415
Griffitt RJ, Feswick A, Weil R et al (2011) Investigation of acute nanoparticulate aluminum toxicity in zebrafish. Environ Toxicol 26(5):541–551
Groves M, Lane S, Douthwaite J et al (2006) Affinity maturation of phage display antibody populations using ribosome display. J Immunol Methods 313(1–2):129–139
Gu J, Liu X, Li Y et al (2012) A method for generation phage cocktail with great therapeutic potential. PLoS One 7(3):e31698
Gui S, Zhang Z, Zheng L et al (2011) Molecular mechanism of kidney injury of mice caused by exposure to titanium dioxide nanoparticles. J Hazard Mater 195:365–370
Gui S, Sang X, Zheng L et al (2013) Intragastric exposure to titanium dioxide nanoparticles induced nephrotoxicity in mice, assessed by physiological and gene expression modifications. Part Fibre Toxicol 10:4
Haas BJ, Zody MC (2010) Advancing RNA-Seq analysis. Nat Biotechnol 28(5):421–423
Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144(5):646–674
Hanes J, Pluckthun A (1997) In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl Acad Sci U S A 94(10):4937–4942
Haq IU, Chaudhry WN, Akhtar MN et al (2012) Bacteriophages and their implications on future biotechnology: a review. Virol J 9:9. doi:10.1186/1743-422X-9-9
Hashemi H, Pouyanfard S, Bandehpour M et al (2012) Immunization with M2e-displaying T7 bacteriophage nanoparticles protects against influenza A virus challenge. PLoS One 7(9):e45765
Jayanna PK, Bedi D, Gillespie JW et al (2010) Landscape phage fusion protein-mediated targeting of nanomedicines enhances their prostate tumor cell association and cytotoxic efficiency. Nanomedicine 6(4):538–546
Jones CF, Grainger DW (2009) In vitro assessments of nanomaterial toxicity. Adv Drug Deliv Rev 61(6):438–456
Kalive M, Zhang W, Chen Y, Capco DG (2012) Human intestinal epithelial cells exhibit a cellular response indicating a potential toxicity upon exposure to hematite nanoparticles. Cell Biol Toxicol 28:343–368
Lammers T, Hennink WE, Storm G (2008) Tumour-targeted nanomedicines: principles and practice. Br J Cancer 99(3):392–397
Lee TL, Raitano JM, Rennert OM et al (2012) Accessing the genomic effects of naked nanoceria in murine neuronal cells. Nanomedicine 8:599–608
Lettieri T (2006) Recent applications of DNA microarray technology to toxicology and ecotoxicology. Environ Health Perspect 114(1):4–9
Lewinski N, Colvin V, Drezek R (2008) Cytotoxicity of nanoparticles. Small 4(1):26–49
Liao M, Liu H (2012) Gene expression profiling of nephrotoxicity from copper nanoparticles in rats after repeated oral administration. Environ Toxicol Pharmacol 34:67–80
Lipovsek D, Pluckthun A (2004) In-vitro protein evolution by ribosome display and mRNA display. J Immunol Methods 290(1–2):51–67
Mattheakis LC, Bhatt RR, Dower WJ (1994) An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc Natl Acad Sci U S A 91(19):9022–9026
Mazumdar S (2009) Raxibacumab. MAbs 1(6):531–538
Miller AV, Ranatunga SK (2012) Immunotherapies in rheumatologic disorders. Med Clin North Am 96(3):475–496
Niazi JH, Sang BI, Kim YS et al (2011) Global gene response in Saccharomyces cerevisiae exposed to silver nanoparticles. Appl Biochem Biotechnol 164(8):1278–1291
Noble CO, Kirpotin DB, Hayes ME et al (2004) Development of ligand-targeted liposomes for cancer therapy. Expert Opin Ther Targets 8(4):335–353
Odegrip R, Coomber D, Eldridge B et al (2004) CIS display: in vitro selection of peptides from libraries of protein-DNA complexes. Proc Natl Acad Sci U S A 101(9):2806–2810
Peano C, Severgnini M, Cifola I et al (2006) Transcriptome amplification methods in gene expression profiling. Expert Rev Mol Diagn 6(3):465–480
Petrenko V (2008) Evolution of phage display: from bioactive peptides to bioselective nanomaterials. Expert Opin Drug Deliv 5(8):825–836
Porto G, Giordano RJ, Marti LC et al (2011) Identification of novel immunoregulatory molecules in human thymic regulatory CD4+ CD25+ T cells by phage display. PLoS One 6(8):e21702
Poynton HC, Vulpe CD (2009) Ecotoxicogenomics: emerging technologies for emerging contaminants. J Am Water Resour Assoc 45(1):83–96
Poynton HC, Lazorchak JM, Impellitteri CA et al (2011) Differential gene expression in Daphnia magna suggests distinct modes of action and bioavailability for ZnO nanoparticles and Zn ions. Environ Sci Technol 45(2):762–768
Poynton HC, Lazorchak JM, Impellitteri CA et al (2012) Toxicogenomic responses of nanotoxicity in Daphnia magna exposed to silver nitrate and coated silver nanoparticles. Environ Sci Technol 46(11):6288–6296
Prisco A, De Berardinis P (2012) Filamentous bacteriophage fd as an antigen delivery system in vaccination. Int J Mol Sci 13(4):5179–5194
Pritchard L, Corne D, Kell D et al (2005) A general model of error-prone PCR. J Theor Biol 234(4):497–509
Rothe A, Hosse RJ, Power BE (2006) In vitro display technologies reveal novel biopharmaceutics. FASEB J 20(10):1599–1610
Sergeeva A, Kolonin MG, Molldrem JJ et al (2006) Display technologies: application for the discovery of drug and gene delivery agents. Adv Drug Deliv Rev 58(15):1622–1654
Shim W, Paik MJ, Nguyen DT et al (2012) Analysis of changes in gene expression and metabolic profiles induced by silica-coated magnetic nanoparticles. ACS Nano 6:7665–7680
Shimizu Y, Kanamori T, Ueda T (2005) Protein synthesis by pure translation systems. Methods 36(3):299–304
Simon DF, Domingos RF, Hauser C et al (2013) RNA-Seq analysis of the effects of metal nanoparticle exposure on the transcriptome of Chlamydomonas reinhardtii. Appl Environ Microbiol 79(16):4774–4785
Singh S, Nalwa HS (2007) Nanotechnology and health safety—toxicity and risk assessments of nanostructured materials on human health. J Nanosci Nanotechnol 7(9):3048–3070
Smith GP (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228(4705):1315–1317
Staquicini FI, Ozawa MG, Moya CA et al (2011) Systemic combinatorial peptide selection yields a non-canonical iron-mimicry mechanism for targeting tumors in a mouse model of human glioblastoma. J Clin Invest 121(1):161–173
Tabata N, Sakuma Y, Honda Y et al (2009) Rapid antibody selection by mRNA display on a microfluidic chip. Nucleic Acids Res 37(8):e64
Tonelli RR, Colli W, Alves MJ (2013) Selection of binding targets in parasites using phage-display and aptamer libraries in vivo and in vitro. Front Immunol 3:419. doi:10.3389/fimmu.2012.00419
Torchilin VP (2010) Passive and active drug targeting: drug delivery to tumors as an example. Handb Exp Pharmacol 197:3–53
Tuteja R, Tuteja N (2004) Serial analysis of gene expression (SAGE): application in cancer research. Med Sci Monit 10(6):RA132–RA140
Van Den Hondel CA, Schoenmakers JG (1976) Cleavage maps of the filamentous bacteriophages M13, fd, fl, and ZJ/2. J Virol 18:1024–1039
Wang Z, Gerstein M, Snyder M (2009) RNA-seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63
Wang T, Kulkarni N, Bedi D et al (2011a) In vitro optimization of liposomal nanocarriers prepared from breast tumor cell specific phage fusion protein. J Drug Target 19(8):597–605
Wang T, Kulkarni N, D’Souza GG et al (2011b) On the mechanism of targeting of phage fusion protein-modified nanocarriers: only the binding peptide sequence matters. Mol Pharm 8(5):1720–1728
Wei Z, Maeda Y, Matsui H (2011) Discovery of catalytic peptides for inorganic nanocrystal synthesis by a combinatorial phage display approach. Angew Chem Int Ed Engl 50(45):10585–10588
Xu L, Li X, Takemura T et al (2012) Genotoxicity and molecular response of silver nanoparticle (NP)-based hydrogel. J Nanobiotechnol 10:16
Yabe R, Suzuki R, Kuno A et al (2007) Tailoring a novel sialic acid-binding lectin from a ricin-B chain-like galactose-binding protein by natural evolution-mimicry. J Biochem 141(3):389–399
Yamamoto M, Wakatsuki T, Hada A et al (2001) Use of serial analysis of gene expression (SAGE) technology. J Immunol Methods 250(1–2):45–66
Yauk CL, Berndt ML (2007) Review of the literature examining the correlation among DNA microarray technologies. Environ Mol Mutagen 48(5):380–394
Zawada JF (2012) Preparation and testing of E. coli S30 in vitro transcription translation extracts. Methods Mol Biol 805:31–41
Ze Y, Hu R, Wang X et al (2013) Neurotoxicity and gene-expressed profile in brain-injured mice caused by exposure to titanium dioxide nanoparticles. J Biomed Mater Res A. doi:10.1002/jbm.a.34705 [Epub ahead of print]
Zhou C, Jacobsen FW, Cai L et al (2010) Development of a novel mammalian cell surface antibody display platform. MAbs 2(5):508–518
Acknowledgments
Our research in this field is supported by the government agencies Fundação de Amparo à pesquisa do Estado de São Paulo (FAPESP), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and Brazilian Network on Nanotoxicology (MCTI/CNPq).
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media New York
About this chapter
Cite this chapter
Justo, G.Z., Suarez, E.R., Melo, C., Lima, M.A., Nader, H.B., Pinhal, M.A.S. (2014). From Combinatorial Display Techniques to Microarray Technology: New Approaches to the Development and Toxicological Profiling of Targeted Nanomedicines. In: Durán, N., Guterres, S., Alves, O. (eds) Nanotoxicology. Nanomedicine and Nanotoxicology. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8993-1_7
Download citation
DOI: https://doi.org/10.1007/978-1-4614-8993-1_7
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4614-8992-4
Online ISBN: 978-1-4614-8993-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)