Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-f554764f5-fr72s Total loading time: 0 Render date: 2025-04-20T20:09:44.277Z Has data issue: false hasContentIssue false

Chapter 5 - Bioassay development

Published online by Cambridge University Press:  05 April 2013

By
Hugo Fernandes ,
Roderick Beijersbergen ,
Lino Ferreira ,
Koen Dechering ,
Prabhas Moghe  and
Katharina Maniura-Weber
Edited by
Jan de Boer  and
Clemens A. van Blitterswijk
Jan de Boer
Affiliation:
University of Twente, Enschede, The Netherlands
Clemens A. van Blitterswijk
Affiliation:
University of Twente, Enschede, The Netherlands
Get access

Summary

Scope

Combinatorial chemistry and high-throughput synthesis of novel materials warrant a paradigm shift in current methods to analyse biological responses. This chapter will provide an overview on bioassay development and how novel assays amenable to high-throughput screening platforms can be adapted to more complex systems. Special emphasis will be devoted to the development of assays that can be used in platforms that closely mimic the in vivo complexity of tissues and organs. In that respect, assays that can cope with co-culture systems as well as 3D environments will be discussed. Moreover, modifications or development of new assays and techniques will be described as well as their respective advantages and disadvantages.

Basic principles of assay development

The ability to measure the speed of light changed the field of physics and the world. Chemical reactions led to the Big Bang and the creation of the Universe, but the ability to measure and control those reactions changed the face of the Earth. We can surely say that the need to see more, and in more detail, led to the development of technologies that made that possible and ultimately contributed to the advance of science and society.

Type
Chapter
Information
Materiomics
High-Throughput Screening of Biomaterial Properties
 , pp. 67 - 84
Publisher: Cambridge University Press
Print publication year: 2013

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Book purchase

Temporarily unavailable

References

Mei, Y, Saha, K, Bogatyrey, SR et al. Combinatorial development of biomaterials for clonal growth of human pluripotent stem cells. Nat Mater. 2010; 9:768–78.CrossRefGoogle Scholar
Rigbolt, KT, Prokhorova, TA, Akimov, V et al. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. Sci Signal. 2011;4, rs3.Google Scholar
Rugg-Gunn, PJ, Cox, BJ, Lanner, F et al. Cell-surface proteomics identifies lineage-specific markers of embryo-derived stem cells. Devel Cell. 2012;1–15.Google Scholar
Lee, MJ, Ye, AS, Gardino, AK, Heijink, AM et al. Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell. 2012 May 11;149(4):780–94.Google Scholar
Sachlos, E, Risueño, RM, Laronde, S et al. Identification of drugs including a dopamine receptor antagonist that selectively target cancer stem cells. Cell. 2012 Jun. 8;149(6):1284–97.Google Scholar
Kshitiz, , Hubbi, ME, Ahn, EH et al. Matrix rigidity controls endothelial differentiation and morphogenesis of cardiac precursors. Sci Signal. 2012;5(227):ra41–1.Google Scholar
Trappmann, B, Gautrot, JE, Connelly, JT et al. Extracellular-matrix tethering regulates stem-cell fate. Nat Mater. 2012;11(7):1–8.Google Scholar
Kohler, G, Milstein, C. Continuous cultures of fused cells secreting antibody of predefined specificity. Nature. 1975;256(5517):495–7.CrossRefGoogle Scholar
Riechmann, L, Clark, M, Waldmann, H, Winter, G. Reshaping human antibodies for therapy. Nature. 1988;332(6162):323–7.CrossRefGoogle Scholar
Johnson, K, Zhu, S, Tremblay, MS, Payette, JN et al. A stem cell-based approach to cartilage repair. Science. 2012;336(6082):717–21.CrossRefGoogle Scholar
Flaim, CJ, Chien, S, Bhatia, SN. An extracellular matrix microarray for probing cellular differentiation. Nat Methods. 2005;2(2):119–25.CrossRefGoogle Scholar
Yliperttula, M, Chung, BG, Navaladi, A, Manbachi, A, Urtti, A. High-throughput screening of cell responses to biomaterials. Eur J Pharmaceut Sci. 2008;35(3):151–60.CrossRefGoogle Scholar
Miraoui, H, Marie, PJ. Fibroblast growth factor receptor signaling crosstalk in skeletogenesis. Sci Signal. 2010;3(146):re9-re.Google Scholar
Siddappa, R, Fernandes, H, Liu, J, van Blitterswijk, C, de Boer, J. The response of human mesenchymal stem cells to osteogenic signals and its impact on bone tissue engineering. Curr Stem Cell Res Therapy. 2007;2(3):209–20. Epub 2008/01/29.Google Scholar
Macarron, R, Banks, MN, Bojanic, D et al. Impact of high-throughput screening in biomedical research. Nat Rev Drug Discovery. 2011;10(3):188–95.CrossRefGoogle Scholar
Wan, C, Gilbert, SR, Wang, Y et al. Activation of the hypoxia-inducible factor-1alpha pathway accelerates bone regeneration. Proc Natl Acad Sci. 2008;105(2):686–91.CrossRefGoogle Scholar
Hubbell, J. Synthetic biomaterials as instructive extracellular microenvironments for morphogenesis in tissue engineering. Nat Biotechnol. 2005;23:47–55.CrossRefGoogle Scholar
Langer, R, Vacanti, JP. Tissue engineering. Science. 1993;260(5110):920–6.CrossRefGoogle Scholar
Anderson, DG, Levenberg, S, Langer, R. Nanolitre-scale synthesis of arrayed biomaterials and application to human embryonic stem cells. Nat Biotechnol. 2004;22(7):863–6.CrossRefGoogle Scholar
Dalby, MJ, Gadegaard, N, Tare, R et al. The control of human mesenchymal cell differentiation using nanoscale symmetry and disorder. Nat Mater. 2007;6(12):997–1003.CrossRefGoogle Scholar
Khan, F, Tare, RS, Kanczler, JM, Oreffo, ROC, Bradley, M. Strategies for cell manipulation and skeletal tissue engineering using high-throughput polymer blend formulation and microarray techniques. Biomaterials. 2010;31(8):2216–28.CrossRefGoogle Scholar
Lovmand, J, Justesen, J, Foss, M et al. The use of combinatorial topographical libraries for the screening of enhanced osteogenic expression and mineralization. Biomaterials. 2009;30(11):2015–22.CrossRefGoogle Scholar
McMurray, RJ, Gadegaard, N, Tsimbouri, PM et al. Nanoscale surfaces for the long-term maintenance of mesenchymal stem cell phenotype and multipotency. Nat Mater. 2011;10(8):637–44.CrossRefGoogle Scholar
Unadkat, HV, Hulsman, M, Cornelissen, K et al. An algorithm-based topographical biomaterials library to instruct cell fate. Proc Natl Acad Sci. 2011;108(40):16565–70.CrossRefGoogle Scholar
Caplan, AI. Adult mesenchymal stem cells for tissue engineering versus regenerative medicine. J Cell Physiol. 2007;213(2):341–7.CrossRefGoogle Scholar
Doorn, J, Moll, G, Le Blanc, K, van Blitterswijk, C, de Boer, J. Therapeutic applications of mesenchymal stromal cells; paracrine effects and potential improvements. Tissue Eng B: Rev. 2011.
Birmingham, A, Selfors, LM, Forster, T et al. Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods. 2009;6(8):569–75. Epub 2009/08/01.Google Scholar
Clark, NR, Ma’ayan, A. Introduction to statistical methods for analyzing large data sets: gene-set enrichment analysis. Sci Signal. 2011;4(190):tr4-tr.Google Scholar
Malo, N, Hanley, JA, Cerquozzi, S, Pelletier, J, Nadon, R. Statistical practice in high-throughput screening data analysis. Nat Biotechnol. 2006;24(2):167–75.CrossRefGoogle Scholar
Vaux, DL, Fidler, F, Cumming, G. Replicates and repeats – what is the difference and is it significant?EMBO Rep. 2012;13(4):291–6.CrossRefGoogle Scholar
Mei, Y, Saha, K, Bogatyrev, SR et al. Combinatorial development of biomaterials for clonal growth of human pluripotent stem cells. Nat Mater. 2010;9(9):768–78.CrossRefGoogle Scholar
Saha, K, Mei, Y, Reisterer, CM et al. Surface-engineered substrates for improved human pluripotent stem cell culture under fully defined conditions. Proc Natl Acad Sci USA. 2011;108(46):18714–19.CrossRefGoogle Scholar
Barradas, AMC, Lachmann, K, Hlawacek, G et al. Surface modifications by gas plasma control osteogenic differentiation of MC3T3-E1 cells. Acta Biomater. 2012:8:1–9.Google Scholar
Rigbolt, KT, Prokhorova, TA, Akimov, V et al. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. Sci Signal. 2011;4(164):rs3. Epub 2011/03/17.Google Scholar
Rugg-Gunn, PJ, Cox, BJ, Lanner, F et al. Cell-surface proteomics identifies lineage-specific markers of embryo-derived stem cells. Devel Cell. 2012:1–15.
Schirle, M, Bantscheff, M, Kuster, B. Mass spectrometry-based proteomics in preclinical drug discovery. Chem Biol. 2012;19(1):72–84.CrossRefGoogle Scholar
Steinhauser, ML, Bailey, AP, Senyo, SE et al. Multi-isotope imaging mass spectrometry quantifies stem cell division and metabolism. Nature. 2012:481;1–5.Google Scholar
Kumar, G, Tison, CK, Chatterjee, K et al. The determination of stem cell fate by 3D scaffold structures through the control of cell shape. Biomaterials. 2011;32(35):9188–96.CrossRefGoogle Scholar
Liu, E, Treiser, MD, Patel, H et al. High-content profiling of cell responsiveness to graded substrates based on combinatorially variant polymers. Comb Chem High Throughput Screen. 2009;12(7):646–55. Epub 2009/06/18.Google Scholar
Treiser, MD, Yang, EH, Gordonov, S et al. Cytoskeleton-based forecasting of stem cell lineage fates. Proc Natl Acad Sci. 2010;107(2):610–5.CrossRefGoogle Scholar
Riedl, J, Crevenna, AH, Kessenbrock, K et al. Lifeact: a versatile marker to visualize F-actin. Nat Methods. 2008;5(7):605–7.CrossRefGoogle Scholar
Longo, D, Hasty, J. Dynamics of single-cell gene expression. Mol Syst Biol. 2006;22: .Google Scholar
White, AK, VanInsberghe, M, Petriv, OI, Hamidi, M, Sikorski, D, Marra, MA, et al. High-throughput microfluidic single-cell RT-qPCR. Proc Natl Acad Sci. 2011;108(34):13999–4004.CrossRefGoogle Scholar
de Boer, J, van Blitterswijk, C, Löwik, C. Bioluminescent imaging: Emerging technology for non-invasive imaging of bone tissue engineering. Biomaterials. 2006;27(9):1851–8.CrossRefGoogle Scholar
Dower, SK, Qwarnstrom, EE, Kiss-Toth, E. Fluorescent protein reporter systems for single-cell measurements. Methods Mol Biol. 2007;411:111–9.CrossRefGoogle Scholar
Liu, J, Barradas, A, Fernandes, H, Janssen, F et al. In vitro and in vivo bioluminescent imaging of hypoxia in tissue-engineered grafts. Tissue Eng C Methods. 2010;16(3):479–85. Epub 2009/08/19.Google Scholar
Conrad, C, Wunsche, A, Tan, TH et al. Micropilot: automation of fluorescence microscopy-based imaging for systems biology. Nat Methods. 2011;8(3):246–9.CrossRefGoogle Scholar
Hirsch, JD, Haugland, RP. Conjugation of antibodies to biotin. Methods Mol Biol. 2005;295:135–54.Google Scholar
Steinberg, TH, Agnew, BJ, Gee, KR et al. Global quantitative phosphoprotein analysis using Multiplexed Proteomics technology. Proteomics. 2003;3(7):1128–44.CrossRefGoogle Scholar
Demarco, IA, Periasamy, A, Booker, CF, Day, RN. Monitoring dynamic protein interactions with photoquenching FRET. Nat Methods. 2006;3(7):519–24.CrossRefGoogle Scholar
Sun, Y, Day, RN, Periasamy, A. Investigating protein–protein interactions in living cells using fluorescence lifetime imaging microscopy. Nat Protocols. 2011;6(9):1324–40.CrossRefGoogle Scholar
Sun, Y, Wallrabe, H, Booker, CF, Day, RN, Periasamy, A. Three-Color spectral FRET microscopy localizes three interacting proteins in living cells. Biophys J. 2010;99(4):1274–83.CrossRefGoogle Scholar
Mendell, JT, Olson, EN. MicroRNAs in stress signaling and human disease. Cell. 2012;148(6):1172–87.CrossRefGoogle Scholar
Pasquinelli, AE. MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nature Rev Genet. 2012;13(4):271–82.CrossRefGoogle Scholar
Orvedahl, A, Sumpter, R, Xiao, G et al. Image-based genome-wide siRNA screen identifies selective autophagy factors. Nature. 2011;480(7375):113–7.CrossRefGoogle Scholar
Paul, P, van den Hoorn, T, Jongsma, MLM et al. A genome-wide multidimensional RNAi screen reveals pathways controlling MHC Class II antigen presentation. Cell. 2011;145(2):268–83.CrossRefGoogle Scholar
Bernards, R, Brummelkamp, TR, Beijersbergen, RL. shRNA libraries and their use in cancer genetics. Nat Methods. 2006;3(9):701–6.CrossRefGoogle Scholar
Mullenders, J, Fabius, AW, Madiredjo, M, Bernards, R, Beijersbergen, RL. A large scale shRNA barcode screen identifies the circadian clock component ARNTL as putative regulator of the p53 tumor suppressor pathway. PLoS ONE. 2009;4(3):e4798. Epub 2009/03/12.Google Scholar
Jain, A, Liu, R, Ramani, B et al. Probing cellular protein complexes using single-molecule pull-down. Nature. 2011;473(7348):484–8.CrossRefGoogle Scholar
Schwalb, NK, Temps, F. Base sequence and higher-order structure induce the complex excited-state dynamics in DNA. Science. 2008;322(5899):243–5.CrossRefGoogle Scholar
Downes, A, Mouras, R, Bagnaninchi, P, Elfick, A. Raman spectroscopy and CARS microscopy of stem cells and their derivatives. J Raman Spectrosc. 2011;42(10):1864–70.CrossRefGoogle Scholar

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×