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Peptide microarrays as diagnostic tool for cancer associated protease profiling

Dyrcz, Eric

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Abstract

In the human organism more than 500 proteases have been described so far. Many of them are essential in the regulation of physiological processes, as inflammation, immune response, coagulation or growth. A dysregulation in protease activity corresponds to severe malfunctions and causes numerous pathophysiological diseases, as neurodegenerative disorders, cardiovascular diseases and cancer. When it comes to cancer, proteases play an important role in progression and metastasis. Some are secreted from the tumor and can be found in the extracellular matrix of the tumor microenvironment and also in the bloodstream. Functional protease profiling aims at discovering tumor associated protease activity in clinical specimens (serum, plasma and tissue), which could be used for diagnostic and prognostic purposes. Therefore, it is necessary to find substrates, which are specifically cleaved by cancer-associated proteases. Various approaches using antibody based antigen detection or MS-based techniques, are limited in the number of samples, which can be screened in parallel. To overcome these problems, peptide microarrays were used. Compared to Ronald Frank´s SPOT-synthesis, micro-particle solid phase peptide synthesis (mpSPPS) allows much higher peptide densities with up to 1000 different peptides per cm2, dependent on the layout. This PhD thesis dealt with the development of a high-throughput screening assay platform based on in-situ synthesized peptide microarrays. As first step a model system, using known proteases (trypsin, thrombin, proteinase k etc.), was developed. To check for general applicability of the PEGMA/MMA surface, on which the peptide synthesis takes place, the manufactured peptide microarrays, containing N-terminal antibody recognition sequences (FLAG- & HA-tags), were used without further chemical modification. After proteases incubation, the respective fluorescently labeled anti-FLAG- & anti-HA antibodies will only bind to peptides, bearing the intact tag-sequence, leading to a decrease in fluorescence intensity, where the enzymes were active. After demonstrating on-chip proteolysis, using indirect antibody labeling, the biotin-streptavidin system was introduced to minimize the peptide label to a smaller tag. This allowed greater sequence variability and avoided false positive cleavage, as when using a proteinogenic tag sequence. Together with the PEPperPRINT Company, a biotin toner was developed, to integrate this labeling reagent into the in-situ synthesis process, which turned out to be advantageous compared to in-solution modification of the peptide content. To further overcome limitations on the part of the solid support, the polymer film was optimized, by introducing a new dextran surface. Preliminary experiments in lab-scale showed good proteolytic cleavages with model proteases and spotted peptides. The transfer to production scale however, showed the requirement of optimization, regarding polymer composition and peptide density, which is an ongoing process.

Item Type: Dissertation
Supervisor: Dahint, Prof. (apl.) Dr. Reiner
Date of thesis defense: 29 January 2016
Date Deposited: 16 Feb 2016 14:47
Date: 2016
Faculties / Institutes: Fakultät für Chemie und Geowissenschaften > Institute of Physical Chemistry
Subjects: 540 Chemistry and allied sciences
570 Life sciences
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