Project: Development of unique platform for new type of disease biomarker discovery (Active peptide biomarker platform)
When biological samples are taken from its natural surroundings, rapid changes in protein integrity can be expected due to continued activity of proteases, a group of enzymes that conduct degradation of proteins. This degradation process starts immediately after sampling and is considered to be a large problem within life science research since a delay of stabilization of the sample leads to loss of important information about the sample. _x000D__x000D_There is a great need to be able to pose correct diagnosis of potential diseases and this creates the opportunity to turn the problem of post-sampling degradation into an advantage; the degradation is namely specific for different tissue types and also for specific diseases. This means that if the degradation profile of a disease is known, it can be used as a marker to determine the stage of a disease (a so called disease-marker). Studies of enzymatic activity are generally called Activity Based Protein Profiling (ABPP) or catalomics. When ABPP is used to investigate enzymatic degradation pathways for example in cancer, peptides containing enzyme cleavage motif can be added to samples and degradation of these peptides is monitored by purpose. Studying sample degradation profiles and enzyme kinetic is only feasible if it is possible to stop degradation at specific and reproducible time points which allows determination of specific degradation profile for a disease as a function of time. _x000D__x000D_The project aims to investigate this type of specific enzymatic activity and protein degradation in tissue – and biological fluid samples in combination with a library of synthetic peptides in order to allow for early detection of different cancer diseases. _x000D__x000D_Denator AB has developed and launched a system, Stabilizor, for stabilization and prevention of degradation of proteins in tissue samples, for instance biopsies, at the time of sampling. By using the Stabilizor system, the information of the sample at the time of sampling can be preserved for future analysis. Compared to existing methods on the market, such as chemical inhibitors, there is no need for addition of foreign substances when using the Stabilizor system. This has several advantages since these additives are often toxic, expensive, unfavorable for specific downstream analysis and staining techniques, and in many cases ineffective. A further development of this technique would allow stopping enzyme activity not just to inhibit degradation for sample stabilization, but also to stop protease activity after a controlled time under defined conditions to study the protease activity._x000D__x000D_Denator has initiated a collaboration with the research group of Theo Luider at Erasmus Medical Center in Rotterdam. This group has, in a previous study (Dekker, L. J. et al., Differential expression of protease activity in serum samples of prostate carcinoma patients with metastases, Proteomics 2010), observed that synthetic peptides can be used to monitor specific enzymatic activity in serum samples as a function of prostate carcinoma. Significant disease-related differences between cancerous and healthy samples could be observed. _x000D__x000D_The combination of a well-defined set of synthetic peptides and the Stabilizor system, would allow determination of degradation profiles at any time point without risking loss of sample information due to uncontrolled degradation further down in the analysis. This would thereby enable a new way of disease-marker discovery to be studied and applied in the clinic without today’s problem of sample degradation. _x000D_A number of clinically-relevant synthetic peptides must be selected and validated to identify cases where the Stabilizor technology can make a large impact in clinical diagnostics. The result would be a new technology platform consisting of an updated Stabilizor system with the capabilities of automated processing of multiple samples combined with a library of synthetic peptides with specific degradation profiles correlated with specific diseases. This would establish the technology as an alternative or even a golden standard for diagnosis of different cancer diseases and research fields as diverse as medical microbiology._x000D_
| Acronym | APB-platform (Reference Number: 6875) |
| Duration | 01/06/2012 - 31/12/2014 |
| Project Topic | The project aims to investigate specific enzymatic protease activity and protein/peptide degradation in biofluids and tissue sections using an array of synthetic peptides. This is a valuable tool since it would enable the development of_x000D_ completely new disease markers and allow for early diagnosis. |
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Project Results (after finalisation) |
We were able to collect Barrett specimens for the detection of natural occurring peptides and specific proteases that are specific for Barrett disease. This work was performed with the ErasmusMC who has sent information about these experiments. |
| Network | Eurostars |
| Call | Eurostars Cut-Off 7 |
Project partner
| Number | Name | Role | Country |
|---|---|---|---|
| 3 | Denator AB | Coordinator | Sweden |
| 3 | Dept of Gastroenterology Amsterdam Medical Center | Partner | Netherlands |
| 3 | The Department of Neurology, Erasmus Medical Center | Partner | Netherlands |