Colorectal cancer (CRC) is a deadly form of cancer but treatable if caught in its early stages. Aware of this, we developed a biosensor that has (1) the capacity to detect CRC in early stages (2) doesn’t cause any fatal harm and (3) is easily removed from the body. As a team of students, we are very passionate about our project and wanted to make it attainable and clear at the start, so we needed help from experts to see what is possible and how to obtain our goals. Thus, we had thorough and insightful discussions with people in various fields: biologists, engineers, businessmen, patients and health workers. We also conducted a survey to understand how patients and healthcare workers think about CRC. The Integrated Human Practice happened in every phase of our project.
Understanding the problem
Since the beginning of our project, we worked with prof. Dr. Luc Colemont, founder of Stop Darmkanker vzw, who has dedicated his life to bringing awareness to colorectal cancer and focusing on early detection methods for this form of cancer. Prior to meeting with Dr. Luc Colemont, we had done our own research into colorectal cancer, the current detection and treatment methods available, and the statistics on this cancer. We had our first meeting with Dr. Luc Colemont on the 27th of July, 2022, where we explained to him the intentions of our project, which was a proof of concept of a bacterial biosensor for the detection of colorectal cancer. We also explained to him our design and the way we plan to execute our plan with labwork and modelling.
On our first meeting on July 27th, prof. Dr. Luc Colemont showed great enthusiasm towards our project, and he was very happy that a student team was working on a topic which he is very passionate about. In this meeting, he gave us a brief overview on colorectal cancer related deaths and the current early detection methods of CRC.
Figure 1: Stop Darmkanker logo (Figure obtained from Stop Darmkanker, 2022)
He explained that at this moment, colorectal cancer is one of the top 3 common cancers in Belgium but only 20% is inheritable, which is why screening is so important and can be the solution to track down early-stage polyps. He also encouraged us to look into the classification of the different cancers on CMS: consensus molecular subtypes, explaining that there are four subtypes that are divided on the basis of diagnostics (biomarkers), prognosis and therapy.
Design
By reading papers, we came up with the idea to develop a biosensor that can enter the microbiome in the gut and can leave it safely without losing its efficiency. Initially, integration of the sensor in the gut was considered for wet lab experiments, but not novel enough according to Professor Abram Aertsen in microbial technology, which caused us to combine the eat and shoot part and focus on this together with leave part. This in order to be able to innovate the SynBio field with our dose dependent response system.. Professor Aertsen advised us a lot in the shoot design of the project on how the dimerization and the equilibrium between NarX WT and NarX mutant could be implemented. Continuous progress was made when i.e. a primer wouldn’t work optimally, plasmids wouldn’t integrate properly or fluorescent results did not meet our expectations...
Prof. Dr. Vitor B. Pinheiro works in the Rega Institute for Medical Research and is our PI. We were able to work in his lab during the summer, where he took care of orders we placed, gave us necessary lab materials and gave feedback on our progress. He followed up on our wet lab planning and problems so he could interfere with his knowledge to form a solution.
Figure 2: Vitor B. Pinheiro our PI
To be able to separate our wet lab portions of the shoot and leave part, we chose to work in the lab of prof. Dr. Joleen Masschelein, professor in molecular biotechnology of plants and micro-organisms. She was very eager to have a student team working in her lab during the summer and provided all tools we needed.
Modelling
Figure 3: Modelling of our project
Prof. Dr. Vitor B. Pinheiro, our PI, also helped us immensely with our model. As the system that we were modelling was very complex and since there wasn’t much data available from what we found online, he sent us studies that could help shape our model and he guided us on how to start with our model. He recommended that we should start by dividing the complex system into smaller models in order to slowly build the interactions between different components. He also advised us to start modelling our model on Net Logo, to slowly start building a system and to fully understand the effects of adding new components to our system, and after we fully understand each interaction, he consulted us to move our model to SimBiology. The difference was that Net Logo was specifically for agent-based modelling, while SimBiology is an extension of Matlab that is specifically made for the purpose of computing differential equations and computing interactions between proteins.
While researching papers that modelled similar interactions to our system, we came across a paper by Dr. Brecht De Paepe, a researcher at the faculty of Bioscience Engineering and Biotechnology in Ghent University. In his study “Modularization and Response Curve Engineering of a Naringenin-
Responsive Transcriptional Biosensor” he modelled and tested a 2-component system with a naringenin responsive system. In order to start with our model before our wet lab team had generated data, we needed data as a baseline for our assumptions regarding the behaviour of our system with the presence of a mutant. Therefore, we contacted Dr. De Paepe to ask if we could use his data to help adjust our model. He was very enthusiastic to hear that our team found his study helpful. He was happy to send us his data and help us with any concerns we may have. Aside from that, he was interested in seeing the outcome of our model, as our system had extra components included such as the nitrate sensing two-component system.Dr. De Paepe guided us on how to proceed and also passed advice from his colleagues that would help us with our model. We met him a couple of times, first to discuss how his pSynSens2.5000 plasmid would fit in our design, then to pick up the sample, lastly on the 3rd of October 2022 to explain to us exactly how he modelled his hill function and the interactions between his molecules. Overall, Dr. Brecht De Paepe’s guidance and data helped us tremendously with our modelling and helped us improve our model to be as accurate as possible.
Biosafety and ethics
Figure 4: Presentation of Kris Dierickx on ethics (Figure obtained from Powerpoint sent by Kris dierickx on ‘Genetics and the idea of making better people.’)
Focusing on biosafety, we contacted Markus Schmidt, doctor and cofounder of the organization for international dialogue and conflict management. He raised questions regarding the risks of genetically engineered bacteria. He suggested us some papers about the standardization of biosafety in synthetic biology to flourish in the future. He pointed out biosafety goes beyond what we achieve and at every step in the project we should think about the containment system.
A discussion with Massimiliano Simons, an assistant Professor in Philosophy of Technology at Maastricht University, gave us an ethical point of view on our product. Massimiliano put science into a broader perspective i.e. cars are difficult to get rid of since our cities are built around them. If we want to detect cancer in the body with our biosensor, it’s still not fully prevented. If cancer is the consequence of an unhealthy lifestyle and poverty is related to malnourishment, the question could be asked whether a double bandage was added on top of a wound instead of sewing it. Cancer patients and governmental constitutions will have the most participation in the legalization and integration of the product into our lifestyle. Belgium is very strict on genetically engineered products. If the biosensor is ready to use, trust has to be won from the government on one side, since it is able to stop the project at any point, and the patients on the other side, who have to take in the product. In vivo testing would have to be implemented in further studies to search for possible repercussions that the biosensor might have within the gut. We debated if this would be ethically possible or there would be too much resistance for moral integrity.
Massimiliano has next to ethics, also a say in the implementation. According to him the construct could be used to act as a possible surveillance sensor. If an older patient becomes senile or gets Alzheimer’s disease, the sensor’s concentration dependency can be used to check up on patients and whether they’ve taken the proper medication. For this to happen however, the sensor’s construct and the recognition molecule would need to be altered with the concentration dependency.
Professor Kris Dierickx of biomedical ethics and rights opened the discussion on genetically engineered organisms and human health with an emphasis on ethics. He debated if it is better to prevent than to treat, which is an important persuasion of our project. Also, the line between treating and enhancing is something to keep in mind. We should focus on the well-being of a group and not individual happiness when designing something newly engineered. As a conclusion, dialogue among stakeholder groups is necessary to make little steps towards a better future in a safe way.
Implementation
Figure 5: Mathias Vissers in an online meeting
Product implementation and use were discussed with alumni iGEM KU Leuven member, Mathias Vissers of Netic Health, a biomedical start-up on 16th of August. Particularly, we wanted to have some aid for the pitching of our project on the Jamboree, as he already had some experience with it. He gave us suggestions on which parts to highlight and how to make our journey a story. After explaining our whole concept, he brainstormed with us and suggested a possible pill for continuous testing of patients and indicated how we could reach the 47% of the Flemish population who doesn’t do the screening for colorectal cancer every 10 years. This way, we would be able to increase the number of people doing the screening. Aside from this, he gave us insight into patenting the pill we designed. Since we want our proof of concept to service other researchers, we did not further research patenting our product.
Next, we had a discussion with Lien Lybaert of Persomed, who is developing a personalized vaccine against CRC. Although vaccines and biosensors are two different approaches, we learned from her how to finish up the product implementation and how our products could supplement or complete each other. Her research is based on the immune response against the mutanome and requires different signalling pathways, but in essence, it is both a product to boost human health regarding cancer. In the future, it might be useful to have an insight into how our biosensor would react in the body, when it is already injected with the vaccine.
Figure 6: Persomed logo (Figure obtained from Persomed, 2022)
Entrepreneurship
Ellen Demarsin is the head of education and students at the Economics faculty of KU Leuven, but next to this she is part of the executive committee of Technovation Hub. Technovation hub facilitates innovative, enterprising and high-tech student projects.
Our iGEM KU Leuven team is part of this umbrella organization to assist us with opening a bank account, insurance, finding a new location for our office… They aid many different student teams whom we met at the Technovation Networking event, where we had our own booth. We had monthly meetings with the board to discuss how being part of Technovation Hub could be more beneficial for us as an iGEM team and how they could facilitate the takeover of next year’s team and accelerate their start-up. Ellen Demarsin was our point of contact throughout this whole process.
To be more involved in STEM and research, we had an online meeting with the KICK, a collaboration of 4 cities for economics and the representative of the Hangar K concept. Hangar K helps start-ups grow and let scale-ups flourish into networking corporates. Some important partners are Universities in Kortrijk like KU Leuven, Vives and Howest, for collaborations with their students to guide their entrepreneurial ideas. When students finish school and do not know how to realize their plan, concept K interferes. Now, they want to elaborate their organization by expanding more to science-related projects like ours for research entrepreneurship. As a consequence, we brought them in contact with Technovation Hub as they share the same concept and they directed us to Luc Colemont of the Stop Darmkanker vzw. Next to this, they suggested some medical start-ups for our MedTech networking event in November.
Figure 8: Hangar K logo (Figure obtained from Hangar K, 2022)
Wim Devroye and Laurens van Keerbergen helped us with our bank account and finance-related problems. Laurens was a member of iGEM KU Leuven 2021, who helped us get started with the finance plan. He gave suggestions on how to contact companies and provided a template, told us about which grants we could acquire and referred us to key individuals like Ellen Demarsin to get our accounts set up. Wim is part of the electrical engineering department at KU Leuven and is responsible for our account at Technovation Hub, which means he is in charge of both incomes and expenses.
References
Hangar K. (2022). Onderneem in Kortrijk. Retrieved August 3, 2022, from https://www.kortrijk.be/onderneeminkortrijk/hangar-k
Persomed. (2022). Persomed. Retrieved August 12, 2022, from https://www.persomed.be/
Stop Darmkanker. (2022). Stop Darmkanker. Retrieved August 5, 2022, from https://www.stopdarmkanker.be/
Technovation Hub. (2022). Technovation Hub. Retrieved July 31, 2022, from https://technovationhub.be/
Powerpoint sent by Kris dierickx on ‘Genetics and the idea of making better people.’
