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Microfluidic Methods for Protein Microarrays

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Microfluidic Methods for Protein Microarrays Microfluidic Methods for Protein Microarrays Michael Hartmann Doctoral Thesis School of Chemical Science and Engineering Department of Chemistry Division of Analytical Chemistry KTH, Royal Institute of Technology Stockholm, Sweden, 2010 AKADEMISK AVHANDLING som med tillstånd av Kungliga Tekniska Högskolan i Stockholm framlägges till offentlig granskning för avläggande av teknologie doktorsexamen 2010-11-19 i sal F3, Lindstedtsvägen 26, KTH, Stockholm. Avhandlingen presenteras på engelska. ii Microfluidic Methods for Protein Microarrays Michael Hartmann Thesis for the degree of PhD of Technology in Chemistry KTH, Royal Institute of Technology School of Chemical Science and Engineering Department of Chemistry Division of Analytical Chemistry SE-10044-Stockholm, Sweden. ISBN 978-91-7415-761-1 TRITA-CHE Report 2010:45 ISSN 1654-1081 Copyright © Michael Hartmann, 2010 All rights reserved for the summary part of this thesis, including all pictures and figures. No part of this publication may be reproduced or transmitted in any form or by any means, without prior permission in writing from the copyright holder. The copyright for the appended journal papers as well as some figures in the thesis belongs to the publishing houses of the journals concerned, and permission has been granted to reproduce this material in the thesis. Printed by E-Print iii Abstract Protein microarray technology has an enormous potential for in vitro diagnostics (IVD) 1. Miniaturized and parallelized immunoassays are powerful tools to measure dozens of parameters from minute amounts of sample, whilst only requiring small amounts of reagent. Protein microarrays have become well-established research tools in basic and applied research and the first diagnostic products are already released on the market. However, in order for protein microarrays to become broadly accepted tools in IVD, a number of criteria have to be fulfilled concerning robustness and automation. Robustness and automation are key demands to improve assay performance and reliability of multiplexed assays, and to minimize the time of analysis. These key demands are addressed in this thesis and novel methods and techniques concerning assay automation, array fabrication as well as performance and detection strategies related to protein microarrays are presented and discussed. In the first paper an automated assay format, based on planar protein microarrays is described and evaluated by the detection of several auto-antibodies from human serum and by quantification of matrix metalloproteases present in plasma. Diffusion-rate limited solid phase reactions were enhanced by microagitation, using the surface acoustic wave technology, resulting in a slightly increased signal-to-noise ratio. In the second paper of the thesis, a novel multiplexed immunoassay system was developed by combining a direct immunoassay with a competitive system. This set-up allows quantification of analytes present in widely varying concentrations within a single multiplex assay. In the third paper, a new concept for sample deposition is introduced, addressing contemporary problems of contact or non-contact microarrayers in protein microarray fabrication. In the fourth paper, a magnetic bead-based detection method for protein microarrays is described as a cost-effective alternative approach to the commonly used fluorescence-based confocal scanning systems. The magnetic bead-based detection could easily be performed by using an ordinary flatbed scanner. In addition, applying magnetic force to the magnetic bead-based detection approach enables to run the detection step more rapidly. Finally, in paper five, a microfluidic bead-based immunoassay for multiplexed detection of receptor tyrosine kinases in breast cancer tissue is presented. Since the assay is performed inside a capillary, the amounts of sample and reagent material could be reduced by a factor of 30 or more when compared with the current standard protein microarray assay. Stockholm, 2010 - Michael Hartmann iv Keywords: automation, microfluidic, microagitation, miniaturization, parallelization, protein microarray, bead-based microarray, magnetic beads, immunoassay, auto-antibodies, receptor tyrosine kinase Copyright © Michael Hartmann, 2010 ISBN 978-91-7415-761-1 v Contents Introduction ..........................................................................................................................1 1 Miniaturized multiplex immunoassays ....................................................................1 1.1 Historical review ..........................................................................................................1 1.2 From genomics to proteomics .....................................................................................2 1.3 Tame the proteins .......................................................................................................3 1.4 Binder Molecules.........................................................................................................4 1.5 Diffusion related limitation of solid phase assays.........................................................4 1.6 “Ambient analyte” theory .............................................................................................6 1.7 Multiplex detection.......................................................................................................8 2 Protein Microarrays.................................................................................................10 2.1 Planar microarrays ....................................................................................................10 2.2 Bead-based micro- assays ........................................................................................11 2.3 Assay formats............................................................................................................12 2.4 Global and focused approaches ................................................................................14 2.5 Detection strategies...................................................................................................15 2.6 Antigen microarrays for detection of auto-antibodies .................................................16 Present Investigations .......................................................................................................17 3 Objectives ................................................................................................................17 4 Semi-contact arraying (paper III) ............................................................................19 5 Microagitation and automation for planar protein microarrays (paper I) ............24 6 Expanding assay dynamics by combining a direct and a competitive assay (paper II)...................................................................................................................28 7 Microfluidic assisted assay system .......................................................................33 7.1 Magnetic bead-based detection for planar protein microarrays (paper IV) .................33 7.2 Microfluidic bead-based immunoassay (µFBI) with minimum amounts of sample (paper V).......................................................................................................36 Future Developments.........................................................................................................41 Acknowledgements............................................................................................................43 References..........................................................................................................................44 vi Publications I. Increasing Robustness and Sensitivity of Protein Microarrays through Microagitation and Automation M. Hartmann, A. Toegl, R. Kirchner, M.F. Templin and T.O. Joos Analytica Chimica Acta , 564 (2006) 66-73 II. Expanding Assay Dynamics: A Combined Competitive and Direct Assay System for the Quantification of Proteins in Multiplexed Immunoassays M. Hartmann, M. Schrenk, A. Döttinger, S. Nagel, J. Roeraade, T.O. Joos and M.F. Templin Clinical Chemistry , 54 (2008) 956-963 III. Non-contact Protein Microarray Fabrication Using a Procedure Based on Liquid Bridge Formation M. Hartmann, J. Sjödahl, M. Stjernström, J. Redeby, T.O. Joos and J. Roeraade Analytical and Bioanalytical Chemistry , 393 (2009) 591-598 IV. Magnetic Bead-Based Detection of Autoimmune Responses Using Protein Microarrays J. Gantelius, M. Hartmann, J.M. Schwenk, J. Roeraade, H. Andersson-Svahn and T.O. Joos New Biotechnology , 31 (2009) 269-276 V. µFBI – A Microfluidic Bead-based Immunoassay for Multiplexed Detection of Proteins from a µl-Sample Volume X. Yu, M. Hartmann, Q. Wang, O. Poetz, N. Schneiderhan, D. Stoll, C. Kazmaier, T.O. Joos PLoS ONE , 5 (2010) e13125 Reprints are published with kind permission of the journals. The contributions of the author of this thesis to these papers are: I. All experiments and major part of the writing II. All experiments and writing III. Part of the experiments and major part of the writing IV. Half of the experiments and writing V. Minor part of the experiments and writing vii Parts of the work presented in this thesis have also been presented at conferences: o Expanding assay dynamics: a combination of competitive and direct immunoassays for the quantification of proteins in microarray - based systems M. Hartmann, M. Schrenk, A. Döttinger, J. Roeraade, T.O. Joos, M.F. Templin. Poster presented at Status Seminar Chip Technologies 2007,
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