Strategies for Miniaturized Biomarker Detection Adler, Belinda

149 Pages·2017·11.72 MB·English

Strategies for Miniaturized Biomarker Detection
Adler, Belinda
2014
Link to publication
Citation for published version (APA):
Adler, B. (2014). Strategies for Miniaturized Biomarker Detection. [Doctoral Thesis (compilation), Department of
Biomedical Engineering]. Department of Biomedical Engineering, Lund university.
Total number of authors:
1
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LUND UNIVERSITY
PO Box 117
221 00 Lund
[phone]
Strategies for Miniaturized
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ISBN: 978-91-7473-945-9 (printed)
ISBN: 978-91-7473-946-6 (electronic) Department of Biomedical Engineering
ISRN: LUTEDX/TEEM – 1095 – SE
Faculty of Engineering
Report: 2/14
Lund University
Strategies for Miniaturized
Biomarker Detection
A tale of invisible things

Belinda Adler
Advisors
Prof. Thomas Laurell, Biomedical Engineering, LTH, Lund University, Lund
Assistant Advisors
Dr. Simon Ekström, Biomedical Engineering, LTH, Lund University, Lund
Prof. Sophia Hober, Biotechnology, KTH, Stockholm
Faculty Opponent
Prof. Richard Oleschuk, Chemistry, Queens University, Kingston, Canada
Board of Examination
Prof. Åsa Emmer, Applied Physical Chemistry, KTH, Stockholm
Associate Prof. Martin Johansson, Laboratory Medicine, Pathology, Lund Univ, Malmö
Associate Prof. Ann Brinkmalm, Neuroscience and Physiology, Sahlgrenska Academy,
University of Gothenburg, Gothenburg
Deputy
Associate Prof. Patrik Önnerfjord, Molecular Skeletal Biology, Lund University, Lund
Public Defense
Doctoral thesis by due permission of the Faculty of Engineering, Lund University, Sweden,
will be publicly defended on Wednesday 28 May, 2014, at 9.30 a.m. in E:1406, Ole
Römers väg 3, Lund.

Copyright © Belinda Adler 2014
Department of Biomedical Engineering
Faculty of Engineering, Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
www.bme.lth.se

ISBN: 978-91-7473-945-9 (printed version)
ISBN: 978-91-7473-946-6 (electronic version)
ISRN: LUTEDX/TEEM – 1095 – SE
Report: 2/14

Printed in Sweden by Tryckeriet E-huset, Lund University
Till Anders, Mamma, Pappa och Pontus
Contents
List of Publications .................................................................................................. 1 
Abbreviations ........................................................................................................... 2 
Introduction ............................................................................................................ 3 
Background ............................................................................................................. 4 
Biomarkers .............................................................................................................. 5 
Sensitivity and Specificity .............................................................................. 7 
Prostate Specific Antigen ............................................................................... 8 
Proteomics ............................................................................................................. 10 
Sample Preparation ..................................................................................... 11 
Solid Phase Extraction ........................................................................ 12 
Protein Digestion ........................................................................................ 13 
Affinity Purification ..................................................................................... 14 
Immunoaffinity .................................................................................. 15 
Aptamer Affinity ................................................................................. 15 
Metal Ion Affinity ............................................................................... 16 
Miniaturization ...................................................................................................... 17 
Scaling Effects in Microfluidics .................................................................... 19 
Micro Fabrication ........................................................................................ 21 
Porous Silicon ..................................................................................... 21 
Antibody Microarrays ............................................................................................ 23 
Mass Spectrometry ................................................................................................. 25 
MALDI ....................................................................................................... 25 
PMF and MS/MS........................................................................................ 27 
Sample Preparation Platforms ...................................................................... 27 
Mass Tags .................................................................................................... 28 
ISET Platform ....................................................................................................... 29
Applications ................................................................................................ 32 
Summary of the Manuscripts ................................................................................. 33 
Paper I ........................................................................................................ 33 
Paper II ....................................................................................................... 34 
Paper III ...................................................................................................... 35 
Paper IV ...................................................................................................... 36 
Paper V ....................................................................................................... 37 
Paper VI ...................................................................................................... 38 
Outlook ................................................................................................................ 39 
Populärvetenskaplig sammanfattning ..................................................................... 40 
Acknowledgement ................................................................................................. 42 
References ............................................................................................................. 44 
Appendix: Paper I-IV ............................................................................................ 58

List of Publications
This thesis is based on the following papers, which will be referred to in the text by
their Roman numerals (I-VI). The papers are appended at the end of the thesis.
I. Porous Silicon Antibody Microarrays for Quantitative Analysis:
Measurement of Free and Total PSA in Clinical Plasma Samples
Järås, K.*, Adler, B.*, Tojo, A., Malm, J., Marko-Varga, G., Lilja, H.
and Laurell, T. Clinica Chimica Acta, 414, 76-84 (2012)

II. Optimizing Nanovial Outlet Designs for Improved Solid-Phase
Extraction in the Integrated Selective Enrichment Target–ISET
Adler, B., Laurell, T. and Ekström, S. Electrophoresis, 33, 3143-3150
(2012). Cover illustration.

III. MALDI-Target Integrated Platform for Affinity-Captured Protein
Digestion
Ahmad-Tajudin, A., Adler, B., Ekström, S., Marko-Varga, G., Malm, J.,
Lilja, H. and Laurell, T. Analytica Chimica Acta, 807, 1-8 (2014). Cover
illustration.

IV. Miniaturized and Automated High-Throughput Verification of
Proteins in the ISET Platform with MALDI MS
Adler, B.*, Boström, T.*, Ekström, S., Hober, S. and Laurell, T.
Analytical Chemistry, 84, 8663-8669 (2012)

V. Mass Tag Enhanced Immuno-MALDI Mass Spectrometry for
Diagnostic Biomarker Assays
Lorey, M., Adler, B., Yan, H., Soliymani, R., Ekström, S., Yli-
Kauhaluoma, J., Laurell, T. and Baumann, M. Submitted

VI. Aptamer/ISET-MS: A New Affinity Based MALDI Technique for
Improved Detection of Biomarkers
Lee, S., Adler, B., Ekström, S., Rezeli, M., Vegvari, A., Park, J., Malm,
J., and Laurell, T. Submitted

* Authors contributed equally. Printed with permission.
1
Abbreviations
BCA bicinchoninic acid assay LOC lab-on-a-chip
BPH benign prostatic hyperplasia MALDI matrix assisted laser
desorption/ionization
CHCA α-cyano-4-hydroxycinnamic
acid MS mass spectrometry
CRP c-reactive protein PCR polymerase chain reaction
DHB 2,5-dihydroxybenzoic acid PDMS polydimethylsiloxane
DNA deoxyribonucleic acid PEEK polyetheretherketone
DRIE deep reactive-ion etching pI isoelectric point
DTT dithiothreitol PMF peptide mass fingerprint
EGF epidermal growth factor PrEST protein epitope signature
tags
ELISA enzyme-linked
immunosorbent assay PSA prostate specific antigen
ESI electrospray ionization PTM posttranslational
modification
FDA U.S. food and drug
administration RNA ribonucleic acid
His histidine RP reverse phase
hk2 human kallikrein 2 SAX strong anion exchange
HPA Human proteome atlas SCX strong cation exchange
HUPO Human proteome SELEX systematic evolution of
organization ligands by exponential
enrichment
IMAC immobilized metal ion
affinity chromatography SPE solid phase extraction
IMER immobilized enzyme reactor TOF time of flight
ISET integrated selective μTAS micro total analysis systems
enrichment target

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