Purpose

Every year a new iGEM team is formed at Eindhoven University of Technology (TU/e). There are three Principal Investigators (PIs) at the TU/e who are deeply involved during an iGEM journey. Their expertise lies in the field of chemical biology, protein engineering and synthetic biology. After the team was formed officially on 7 February 2024, we started brainstorming about project ideas and we came up with some that we wanted to present to our PIs. Next to that, we thought it would be good to have a general introduction to each other and to the iGEM competition.

Contribution

In our first meeting we talked about the iGEM competition in general and about everyone’s motivation to join this year’s team. Due to this, we were all on the same page before continuing forward. Moreover, we discussed some project ideas. They saw potential in most of our ideas but needed more in-depth information about the execution of our ideas in order to be able to give us clear advice on which way to go. For that, they advised us to perform more literature research on different topics and suggested to talk to other researchers within the university. Not only to discuss existing ideas, but also to potentially come up with new project ideas.

Implementation

After our first meeting with the PIs we decided to do more literature research on the existing ideas. Since it was quite a lot, we decided to divide the work and have weekly update sessions with our team to discuss the progress and possible uncertainties of the project. Furthermore, we decided to plan multiple meetings with different researchers at our university to discuss the potential of the generated ideas.

Outlook

The next steps involved to do more in-depth research to create better defined projects and to talk to multiple researchers to validate our concepts or to maybe come up with new potential project ideas.

Purpose

We wanted to explore one of our ideas, which was about developing a project on rapid antibiotic resistance testing. Since antibiotics must be used cautiously to avoid the risk of multi-resistance, current testing methods, which takes several days, often result in patients receiving antibiotics through trial and error. This highlighted the need for new methods that could quickly determine bacterial resistance and identify the most effective antibiotics. We decided to reach out to Harm, since he has expertise in this field.

Contribution

Harm explained the research he had conducted thus far and noted that he had not yet developed a potential new test. He proposed an idea for how it might work, but we concluded that the solution lacked sufficient synthetic biology elements to be a suitable iGEM project

Implementation

Based on this conversation, and the lack of enthusiasm about this topic, we were almost certain not to continue researching on this topic. We aimed to draw a final conclusion after the PI meeting.

Outlook

The next steps were to continue researching the other ideas and engaging with different professors or researchers to discuss our other potential projects.

Purpose

In this meeting we wanted to present three project ideas to Willem and Roy, experts in precision medicine and synthetic biology.

The first idea was a point-of-care test for antimicrobial susceptibility. Current methods are slow and not suitable for point-of-care settings. The proposed solution involved reducing the testing time by culturing bacteria with antibiotics for a few hours and then measuring DNA levels to compare growth rates with and without antibiotics.

The second project was to create an intracellular protein delivery platform. Existing drug targeting methods are limited to membrane proteins or small molecules. This project aimed to develop a platform that could deliver therapeutic proteins directly into cells, thereby expanding the range of intracellular proteins that could be targeted.

The third idea focused on using bacterial membrane vesicles (BMVs) for cancer therapy. BMVs were being explored for their potential in targeted drug delivery for cancer treatment, benefiting from their tumor affinity, small size for better penetration, and potential for genetic engineering.

We aimed to gain insights into current research in these areas and wanted to receive feedback on the feasibility and potential of our proposed projects.

Contribution

The discussion provided valuable insights into the potential applications of BMVs in cancer (immuno)therapy. Willem and Roy's expertise shaped our understanding of the project's scope and potential, especially considering recent research findings discussed during the meeting.

Implementation

At the exploration phase, we had yet to finalize our decision on which project to pursue. We planned on gathering more information by consulting other professors and diving deeper into the BMV project to assess its feasibility and potential impact within the given timeframe and resourses.

Outlook

Moving forward, our next steps involved reaching out to various professors for additional insights and feedback. We also planned to conduct further research on the BMV project and the intracellular protein platform in order to better understand the potential and feasibility. Additionally, we needed to consider factors such as resources, timeline, and project scope to be able to make an informed decision on which project to pursue. Aside from that, we also thought it would be important to leave some room for possible new ideas.

Purpose

After the meetings with other researchers and doing more in-depth research, we had three main potential projects we wanted to discuss these with our PIs. These included the bacterial membrane vesicles (BMV) and the platform for intracellular protein delivery, which were based on the meeting with Roy van der Meel and Willem Mulder and the idea of antibiotic resistance testing discussed with Harm van der Veer, which we actually already gave up on. We wanted to present all ideas with their pros and cons to be able to make an informed decision about the project to persue.

Contribution

After discussing our ideas, the PIs expressed the most enthusiasm for using bacterial membrane vesicles for tumor therapy, while they showed the least interest in antibiotic resistance testing. However, they stated that all ideas were feasible as long as a clear synthetic biology component was included. We were again advised to conduct more in-depth research and carefully consider the synthetic biology elements for each project. Additionally, we were instructed to verify the feasibility of the projects with the resources available at the university, including ensuring that the bacteria we intended to use were allowed in our laboratories. For that, they suggested reaching out to the biosafety officer of the university. They advised us to weigh the pros and cons in order to make a final decision once we confirmed the feasibility of the projects. Next to that, we were also encouraged to continue consulting with other researchers at the university and to consider recruiting new team members for some extra support.

Implementation

We decided to delve deeper into the potential projects, paying special attention to the synthetic biology aspects. As a result, we confidently chose to discard the idea of antibiotic resistance testing. We planned to seek further input from additional researchers and professors and made a final call on recruitment of new team members, as we believed we indeed could use some extra support.

Outlook

The next step was to do more in-depth research to see whether projects were feasible at the university and in general talking to multiple researchers to validate our concepts. Also, we wanted to look for researchers or PhD-candidates that might be interested in helping us during the entire project next to the PIs. Furthermore, we wanted to draw a final conclusion on the project as soon as possible and try to recruit team members one last time.

Purpose

The purpose of this meeting was to receive feedback from an expert on infectious diseases and bio-organic chemistry regarding the use of bacterial components as immunotherapy to stimulate both the innate and adaptive immune responses. This was driven by the team's interest in using bacterial membrane vesicles (BMVs). Additionally, the team sought practical advice on how to approach this work in the laboratory.

Contribution

Jan van Hest responded positively to our explanation of how we developed the idea and was enthusiastic about the project's originality and relevance. He primarily advised us on how to functionalize our bacterial components with tumor antigens. One method involved introducing azide sugars into bacteria, allowing the outer bacterial layer to be functionalized for conjugation via click chemistry. Another approach was using SpyCatcher and SpyTag, two proteins that recognize each other through noncovalent affinity and then form a specific covalent bond. A key advantage of SpyCatcher and SpyTag was that they could be co-expressed. Additionally, he informed us that ovalbumin, or SINFEKL, was the most commonly used tumor antigen in research. He reminded us that the project must have a distinct new aspect and cautioned against making it overly complicated with too many novel elements. He also recommended contacting Joen Luirink from VU Amsterdam, who runs a company specializing in the bacterial components we aim to use.

Implementation

Based on this conversation, we concluded that we are on the right track with our project and should continue to explore the topic further. Jan’s guidance confirmed the potential of our approach, but also highlighted the importance of keeping the project focused and manageable by concentrating on one key innovation.

Outlook

The next steps were to continue researching and developing the idea into a viable iGEM project, considering feasibility, originality, and lab safety requirements. We needed to further explore and compare the functionalization strategies Jan suggested to determine which was most suitable for our project. Although we believed reaching out to Joen Luirink could be valuable, we were unable to proceed that until our ethical review was approved by the university. So we decided to keep his name in the back of our mind for the future and would reach out to him when necessary.

Project decision

Decription

After the new team was formed, we immediately began conducting wide-ranging literature research. Each week, we updated one another, brainstormed together, and divided tasks among the team. Moreover, we met with various professors and researchers to validate our ideas and gain new input for the project, all of which was shared with our PIs. Most of the time, the conclusion was to do more in-depth research to expand our understanding of the different potential topics and assess whether our ideas were innovative, original, feasible, and realistic. Additionally, we had to ensure that our ideas incorporated a synthetic biology component.

Feelings

All team members were enthusiastic about our potential project topics, which made everyone eager to dive deeper into the technical details and aspects of each. On one hand, we wanted to make a decision as soon as possible to narrow our focus and eliminate the uncertainties surrounding the project's direction. On the other hand, we were somewhat hesitant to make a final decision, knowing it would set the foundation for the entire project.

Evaluation & Analysis

To be able to make an informed final decision on our project, we spoke multiple times to our PIs and other professors. Moreover, as said before, we divided research tasks among our team and presented the results to each other in our team meetings. This helped us gain a lot of (technical) information in a relatively short period of time. Eventually, everyone ranked the ideas on preference and we discussed pros and cons with our PIs. Feasibility was one of the main aspects to take into consideration, as we thought would be very important that we would able to conduct most of our research here at Eindhoven University of Technology.

Conclusion

The preferences of the team members made it clear that the project would focus on engineering bacterial membrane vesicles to develop a novel cancer treatment through dual stimulation of the immune system. We divided the research areas among the team and prepared a pitch, along with a PowerPoint presentation, to present to our PIs in the upcoming meeting.

Action Plan

Our next step was to schedule a meeting with our PIs to validate our decisions and conduct more in-depth research into the technical aspects of the project, including the selection of the bacterium and methods for isolating and characterizing the bacterial membrane vesicles. We also aimed to involve some lab supervisors in our project and hoped to obtain ethical approval for engaging external parties as soon as possible.

Purpose

Since we decided to go for the idea of using bacterial membrane vesicles (BMVs) as a novel treatment for cancer, we wanted to discuss the theoretical and practical details that are necessary to improve the project with Roy and Willem. We thought this would be relevant since we discussed this particular idea with them before. Next to that, we hoped they could provide someone who was able to closely guide us in the laboratory throughout the project.

Contribution

During the discussion, we received valuable advice on various aspects of the project: we had a brainstorming session on how to produce, functionalize, and characterize different components with accessible equipment. Moreover, we explored modeling possibilities to refine project strategies. Also, we were lucky that they already found someone who could provide guidance and support during the project and called her in to introduce us to each other.

Implementation

Following the conversation, we concluded that further literature research was necessary to better shape the project. This included refining strategies for BMV production, functionalization and characterization, as well as exploring modeling approaches to optimize project outcomes. Next to that, we aimed to plan weekly meetings with our laboratory supervisor.

Outlook

Our next steps included engaging with (more) supervisors, reviewing feedback to enhance project design and execution, defining experimental and modeling designs, and documenting project progress.

Purpose

Our purpose in speaking with Joost Schoeber and Ronald ten Berge from The Gate, an initiative supporting tech startups, was to explore potential collaboration between iGEM and The Gate. We aimed to gather feedback on our project from Ronald ten Berge, a pharmacologist, and discuss the possibility of applying for a patent with insights from Nataša Maršić, an expert in intellectual property who was also present.

Contribution

They encouraged us to strengthen our argumentation on the relevance of our project, specifically addressing why our immunotherapy would hold more promise than existing treatments. Ronald ten Berge offered to engage in further discussions to help us developing this aspect. Additionally, they recommended us to attend an IP workshop offered by The Gate for further guidance.

Implementation

We took on the task of exploring the possibility of applying for a patent and therefore wanted to have regular contact with Nataša Maršić. Next to that, we also wanted to schedule a follow-up meeting with Ronald ten Berge to further develop the argumentation for the relevance of the project.

Outlook

The next steps included conducting further research on securing intellectual property and considering how to make our project more market-relevant. This was also a key focus for the TU contest. Additional details can be found on the Communication page. under events.

Purpose

After finalizing our project on using bacterial membrane vesicles (BMVs) for cancer treatment, we sought feedback from our PIs. To do so, we prepared a slide deck outlining our progress, key decisions, and potential challenges. Additionally, we wanted to inform them that three new supervisors had joined our team to assist with lab work and actively contribute to our iGEM journey.

Contribution

The PIs were pleased that we had found supervisors to guide us in the lab and support our iGEM journey, and they were impressed with our project's progress. However, they emphasized the need to improve how we present the project to ensure clarity from the outset. After sharing more details and having a brief discussion, they acknowledged the ambition and potential of our project. We also addressed unresolved aspects, such as the choice of bacteria and the functionalization of the BMVs. They cautioned us against tackling too much at once, advising us to focus on achieving concrete lab results before expanding further. Additionally, they recommended inviting Roy van der Meel and Willem Mulder from the Precision Medicine group to our next PI meeting, as their expertise would enhance the discussions.

Implementation

We scheduled weekly meetings with our three lab supervisors and invited Roy van der Meel and Willem Mulder to the next PI meeting. Furthermore, we worked on improving how we present our project and delved deeper into details.

Outlook

The next steps included making lab protocols and conducting more in-depth research to discuss with our supervisors, which prepared us to start working in the lab. Additionally, we planned to take the SMT (Safe Microbiological Techniques) course offered by the university to ensure safe lab practices and allowed more team members to work in the laboratory. Next to that, we arranged an introduction to the laboratory where we would be conducting our experiments.

Bacterium decision

Decription

Since we selected our project topic, we had been conducting extensive research to further develop it, including choosing the appropriate model bacterium and writing protocols for characterizing and isolating vesicles from it.

We initially considered Mycobacterium Bovis (M. BCG) due to its confirmed ability to stimulate the innate immune system, which aligned with our goal of dual stimulation of the immune system. However, we quickly discovered that M. BCG is unsafe to handle outside of a BSL-3 laboratory, which is neither available to us nor permitted by the iGEM community. Consequently, we sought an alternative and identified Mycobacterium smegmatis (M. smegmatis), a gram-positive bacterium with similar membrane proteins to M. BCG but safe to work within a BSL-1 environment. We decided to use M. smegmatis as a proof of concept with the potential to switch to M. BCG in the future.

Further research on M. smegmatis focused on its ability to secrete vesicles and incorporate proteins into its membrane, which is essential for stimulating the adaptive immune system and achieving our goal of dual stimulation of the immune system. Given the limited existing protocols and research for M. smegmatis, we developed our own library of proteins to fuse with the vesicle membranes. This library and our findings have been regularly discussed in our weekly meetings with our lab supervisors.

Feelings

We were excited to discover M. smegmatis, as it seemed like the ideal choice for our project. Unlike Escherichia coli (E. Coli) which is a commonly used model bacteria, M. smegmatis is a Gram-positive bacterium, making it a closer match to m. BCG, which we ultimately aim to use for vesicle secretion due to its ability to stimulate the innate immune system. We believed M. smegmatis could serve as an excellent proof of concept for our cancer treatment approach.

Evaluation & Analysis

In order to make a well-informed decision about our choice of bacterium, we consulted with our supervisors multiple times and conducted extensive research to determine the feasibility of our project. We divided research tasks among the team and utilized tools like AlphaFold and SnapGene. Ultimately, we developed a library of potential fusion proteins and planned a meeting with our biosafety officer to assess their safety in a BSL-1 environment (which is yet to come on this timeline). Although some proteins were deemed unsuitable, we kept a library of around ten proteins for which we planned to seek approval to test in the laboratory.

Conclusion

There were no further doubts about using M. smegmatis as our model bacterium. Therefore, we aimed to order all necessary materials as soon as possible to begin our lab work, after the biosafety officer gave green light. In the meantime, we focused on finalizing our protocols so that we could start our experiments immediately after receiving the products.

Action Plan

We scheduled a meeting with our PIs and supervisors to review the entire project thusfar, ensuring we had not overlooked any details, and gathered their feedback. Additionally, we needed to continue updating our protocols to make sure we could start lab work as soon as possible.

Purpose

We aimed to explore the possibilities of protecting our idea. Therefore, the primary purpose of the conversation was to seek expert advice regarding the benefits of patents, the patentability of our project idea and to understand the necessary steps for protecting our intellectual property (IP).

Contribution

Nataša's input significantly contributed to our project by providing clarity on the patent filing process, emphasizing the need for experimental data to support our idea's patentability, and highlighting the importance of confidentiality in safeguarding our IP. Her insights helped us understand the potential costs involved in patent filing and the potential avenues for funding the patent application.

Implementation

Based on Nataša's advice, we concluded that the only possibility to protect our ideas would be to file a provisional patent before entering the competition. To do so, we needed to prioritize gathering experimental data to support our idea's patentability. Additionally, we planned to engage with the Gate to explore strategies for protecting our IP and obtaining funding for patent application. We also considered drafting an NDA with the university's legal desk to ensure confidentiality when discussing the project with other stakeholders. We had not made a decision about pursuing a patent yet due to timing challenges and the need for further discussions with others involved.

Outlook

We initiated the gathering of experimental data to support our patent application, reviewed the privacy of public information, and engaged with The Gate to strategize IP protection and funding. We also considered drafting an NDA for discussions with external parties and exercised caution in sharing technical details with companies, being mindful of legal complexities.

Purpose

The goal of the follow-up meeting with both Nataša and Bart was to discuss the steps necessary for filing a provisional patent application. This involved gathering data and ensuring continuity, considering the year-long timeline until market entry after the provisional patent. Although we had not yet decided whether to pursue a patent, we recognized the importance of considering this early on.

Contribution

Nataša and Bart were both very enthusiastic about our idea and expressed their willingness to invest time in exploring opportunities for filing a provisional patent. To move forward, we needed to ensure that we were well-prepared and fully committed to pursuing this idea for the long term. We recognized the importance of thorough preparation and long-term commitment, focusing initially on assessing intellectual property (IP) readiness, team readiness, and funding readiness. Nataša agreed to facilitate the completion of an Invention Disclosure Form (IDF) and wanted to assist with patent searches. Additionally, discussions with the team and supervisors were crucial to clarify aspects of cooperation, inventorship, and patent ownership, particularly regarding the costs associated with a provisional patent and strategies for funding the application.

Implementation

Encouraged by Bart and Nataša's insights, we decided to consider pursuing a provisional patent. Consequently, we continued our data gathering efforts and engaged in discussions with team members and others involved to develop a plan for a provisional patent application before the competition.

Outlook

The next steps were to complete and submit the IDF from. Furthermore, we needed to review the findings from the patent search and integrate additional information provided by Bart on the spinning-out process into our planning. We were aware that we needed to schedule a team discussion to clarify ownership and roles within the project, as well as develop strategies for sharing technical details, particularly in preparation for the final competition. Moreover, we aimed to connect with former biotech business developers to gain their valuable insights.

The project was ethically approved

Decription

In addition to refining the project and exploring patent possibilities, we needed to submit an application for ethical approval from the university to engage with external parties. We had to carefully consider privacy and potential risks for participants, which required us to create an informed consent form that every external participant would need to sign. We asked whether this also holded for the Gate, but we were told not to worry, since The Gate already collaborated with the university. The form included details on how we would process and use data for publication and had a lot of focus on maintaining privacy. Participants could agree or disagree to several terms after reviewing the form, including whether we could take notes during interviews, use information on the wiki, display profile pictures on the timeline, record videos, mention their real names, and retain data for future research or educational purposes. Naturally, we were obligated to honor their decisions.

Feelings

We were excited to receive official approval from the university to engage with external parties and incorporate their feedback into our project. Although we had to wait a bit before reaching out to stakeholders, getting the green light was a tremendous relief. This approval, along with the informed consent form, would help us avoid potential disputes or dissatisfaction after publishing the wiki, providing us with peace of mind and assurance that we were managing personal data responsibly.

Evaluation and Analysis

Looking back, we feel that we might have submitted the file a bit late, as we had to wait before contacting stakeholders. We could have initiated this process earlier, but we were at least pleased to have it submitted by May 7th.

Conclusion

Once we received approval, we reached out to numerous new stakeholders and were glad that we could do so in an ethical and responsible manner. The delay did not diminish our satisfaction with the approval, as it allowed us to engage with stakeholders properly and ensured we handled their feedback, input and data with the utmost care, which was more important than reaching out sooner.

Action Plan

Our action plan included reaching out to a diverse range of new stakeholders to further refine our project. Additionally, we were aware that we needed to consult the Ethical Review Board when ethical concerns would arise in the future. Next to that, we planned to continue working the project and exploring possibilities for intellectual property (IP).

Purpose

The purpose of the meeting with Liesbeth Varion-Verhagen, the university's biosafety officer, and Peggy de Graaf, the lab manager of the BSL-I lab we would be working in, was to assess the feasibility of conducting our experiments with Mycobacterium smegmatis (M. smegmatis) within the BSL-I setting. Specifically, we needed to determine if the model bacterium, along with the vectors and inserts we planned to use, met the lab's biosafety standards.

A key objective was to ensure that all aspects of our experimental design, including the genetic modifications, would be safe and compliant with the regulations for BSL-I laboratories. We also sought to clarify the safety measures required for handling M. smegmatis, such as containment procedures, waste disposal, and personal protective equipment.

By addressing these concerns, we aimed to verify that our project could be safely carried out in the BSL-I environment and to determine any additional precautions or modifications required before initiating our lab work.

Contribution

We selected a number of inserts that were suitable for use in Mycobacterium smegmatis under BSL-I conditions according to literature research. During our meeting, we discussed the necessary safety precautions that must be followed when working with M. smegmatis. Specifically, it was advised that individuals should avoid handling M. smegmatis if they have any open wounds on their hands, as a preventive measure against potential infection. Additionally, separate glassware and equipment should be used exclusively for experiments involving M. smegmatis to prevent cross-contamination with other ongoing research in the laboratory.

Based on our project information, they recommended conducting an assay to test the immune response by using bacterial membrane vesicles (BMVs) derived from M. smegmatis in conjunction with T-cells. This would provide valuable insights into how the vesicles interact with the immune system, potentially informing further steps in our project.

Implementation

We integrated the recommended safety measures into our lab protocols and ensured that all team members were well-informed. This included precautions such as avoiding work with open wounds and using separate glassware to prevent cross-contamination with other experiments. Regarding the assay, we would need to evaluate in the future whether we could undertake something of that nature, as our immediate focus was to create and and isolate the vesicles.

Outlook

Our next steps was to coordinate with the lab manager to arrange separate glassware, ensuring that experiments involving M. smegmatis were conducted in isolation. This measure was crucial for preventing any cross-contamination with other ongoing research in the lab and maintaining strict biosafety protocols.

Purpose

We sought another perspective on modeling because we were struggling to integrate it effectively into our project. Specifically, we had difficulty understanding how modeling could both support and be informed by our lab work. The modeling team lacked detailed knowledge of the lab processes, while the lab group had limited experience with modeling techniques. Given Luke's background as a former iGEM participant and his experience with AI in a biomedical context, we believed he would be well-positioned to help us bridge this gap and facilitate better integration between our modeling and experimental efforts.

Contribution

We provided a comprehensive overview of our project and the various aspects we considered for modeling. Luke noted that modeling every step of the process was too ambitious, as each step could be a separate project. He advised focusing on specific areas rather than attempting to model everything at once.

Luke also expressed concerns about the feasibility of selecting tumor antigens based on DNA and suggested that a protein assay might be more practical. He recommended starting by examining our data to ensure our questions were relevant. Nevertheless, he identified that modeling the expression of bacterial membrane vesicles (BMVs) using ordinary differential equations, such as Michaelis-Menten equations, could be feasible. This approach would require lab data and could inform the lab, creating an effective engineering cycle.

Lastly, he warned about the potential unreliability of AI and directed us to experts who could assist with specific challenges, including accessing restricted datasets and modeling ordinary differential equations.

Implementation

We shifted our focus from AI-based antigen identification to a more classical modeling approach, at least initially. We also planned to collaborate more closely with the lab to better integrate our approach. One key realization was the need to avoid over-optimizing, as it was neither practical nor time-efficient for our project. We also acknowledged that we could not rely solely on AI predictions; instead, we needed to validate our results through experimental work. While AI and machine learning excel at managing large datasets where manual analysis is impractical, it was essential to corroborate key findings with experimental data.

Outlook

We planned to consult with our PI Tom, an expert on Ordinary Differential Equation (ODE) modeling, to gain deeper insights and to refine our approach. Additionally, we scheduled more meetings with both the lab team and the modeling group to foster better collaboration and ensure that our strategies were well-integrated. These steps aimed to bridge the gap between theoretical modeling and practical lab work, enhancing our project's overall coherence and effectiveness.

Purpose

We scheduled another meeting with the PIs to update them on the progress we had made with our project and the decisions we reached with our laboratory supervisors. We also wanted to take this opportunity to practice our pitch for the European meetup in Bielefeld, where we would present our project. Following prior recommendations, we also invited Willem Mulder and Roy van der Meel to the meeting.

Contribution

We started the meeting with a brief recap of our project and then presented some new information, including the choice of M. smegmatis as model bacterium and the protocols for characterizing and isolating the vesicles it secretes. We decided to initially use a number of fusion proteins with GFP, which we wanted to replace with Spy-catcher for future modularity of our treatment.

They were enthusiastic about our progress but advised us to also work with E. Coli to validate our proof of concept, as there are numerous protocols available for using E. Coli to secrete vesicles and load them with Spy-tag Spy-catcher. They recommended exploring micelle mixing as an alternative to fusion and advised implementing multiple strategies in parallel to enhance our chances of success, particularly since working with M. smegmatis was new for our university and existing protocols were limited. By working in parallel, we could validate our approach and ensure that any issues encountered with M. smegmatis were not attributable to errors in our own laboratory practices.

We also reviewed our protocols for isolating bacterial membrane vesicles (BMVs) and identified a challenge with our centrifuge, which did not meet the required specifications. Willem agreed to reach out to colleagues in Nijmegen to see if we could utilize their suitable equipment.

At the end of the meeting, we briefly discussed our current ideas and challenges related to modeling, particularly the integration of lab work with modeling and the data limitations. Willem and Roy would work on acquiring the necessary data for training our model, and the modeling subgroup was advised to schedule a meeting with Tom de Greef, one of the PIs with expertise in biochemical systems modeling and ordinary differential equations.

Implementation

We continued refining our protocols and exploring various strategies to ensure we had a comprehensive overview of all necessary laboratory steps. We developed protocols for both E. coli and M. smegmatis, aiming to work with both bacteria to enhance our chances of success. Additionally, we kept brainstorming about ideas to address the challenges in modeling.

Outlook

Our next steps were to order the DNA and bacteria needed for our project as soon as we have secured approval from the biosafety officer and supervisors. We had all the necessary materials for E. Coli already in the lab, so we planned on working with that immediately after finalizing the protocols. For M. smegmatis, we awaited the arrival of the materials and hoped for fast delivery. Additionally, we scheduled meetings with Tom de Greef, recognizing that his expertise would be essential for refining our modeling approach and ensuring its effective integration with our laboratory work.

Purpose

Yosta de Stigter is a doctoral candidate in the Protein Engineering group at the Technical University of Eindhoven. She has experience in plasmid design and vector choice. We reached out to her to ask her for advise on the plasmid design for E.coli and sought advice on vector choice for M. smegmatis.

Contribution

She was able to provide us with some clear advice on our plasmid design. For example, she told us there should be no extra distance between the TATA-box and the starting-codon in the E.coli plasmid. Furthermore, she noticed that the insert for M. smegmatis was not positioned correctly and therefore she advised us to read the corresponding research paper more thoroughly.

Implementation

We followed her advice and redesigned the E. Coli plasmids by eliminating the unnecessary gap between the TATA-box and the start codon, ensuring a more precise and efficient transcription initiation. In addition, we revisited the research paper on the M. smegmatis vector, this time with a greater focus on detail. Upon deeper review, we identified a significant issue: the vector was incompatible with our intended application due to its reliance on the Gateway Cloning system. This cloning technique, while widely used for its efficiency in DNA recombination, was not appropriate for our experimental needs, leading us to reconsider the use of this vector altogether. As a result, we began searching for alternative systems that better suited our project requirements.

Outlook

We needed to more research in order to be able to find another vector for expression in M. smegmatis. Furthermore, we were aware that we would need to keep working on the designs and try them out in the laboratory as soon as possible.

Purpose

The meeting had two purposes. On one hand, we wanted to explain the concept of our project to Till Mathan, a medical affairs professional with expertise on the realization of a medical concept, so that he could provide us with valuable feedback. On the other hand, we wanted discuss sponsoring possibilities with his company, Johnson and Johnson.

Contribution

Till provided us with multiple tips:

He explained that we should clearly explain the gold-standard treatment for lung cancer, as well as mention the negative side effects of this technique. After that, we should introduce our own concept and explain why our concept can circumnavigate existing negative side effects. By doing this, it should be easier to convince companies to invest in our project.

He also explained that we should dive deeper into the further implementation of our project. We were mostly focused on isolating vesicles and functionalizing them. He advised us to also do research on implementing our concept in animals and humans. He asked us the following questions. What is the half-time of the vesicles at 37 degrees celsius? Which immune cells will be targeted by the vesicles? Will the vesicles be injected as a vaccine, or can they be used to train immune cells in vitro?

Lastly, he mentioned that it would be good to do a risk-analysis for our concept. What are potential harmful side effects of our product and how can we mitigate those risks?

Implementation

We conducted an extensive literature review on the tips he provided, carefully analyzing them to gain a deeper understanding of their potential impact. By applying these insights, we aimed to improve our approach and present a stronger, more well-rounded project, both for potential new sponsors as well as for (international) meet-ups and the Grand Jamboree. This literary research has enhanced our understanding of how our therapy would function within the human body, allowing us to make more informed decisions about the most appropriate preclinical tests to conduct. More information on this can be found on our implementation proposal section.

Outlook

We kept refining the project and engaging with multiple stakeholders. Till told us he was open for another meeting in a couple of weeks to discuss the progress of our project in the laboratory. For that meeting, he also wanted to invite some colleagues that are experts in antigen functionalization and delivery for cancer. We kept this in our mind and wanted to reach out when we had some promising results.

Purpose

Prof. Dr. Jürgen Kuball has expertise as a hematologist and immunologist. He particularly has experience with stem cell transplantation and T-cell engineering for cancer therapy. While our project focuses on administering a vaccine to activate B-cells and T-cells rather than modifying immune cells directly, we sought to understand whether our approach could effectively target tumors despite the immunosuppressive environment they create. Additionally, we aimed to explore the benefits of our method with other technologies, such as checkpoint inhibition and CAR-T cell therapy, and gather insights on improving our design and its persuasive power.

Contribution

Prof. Dr. Kuball provided several key pieces of advice for our project. He thought that bacterial membrane vesicles (BMVs) were innovative and saw potential in using them for a cancer therapy. Moreover, he emphasized the importance of demonstrating why BMVs were superior to vaccines using traditional adjuvants. Furthermore, he said that it would be essential to identify and highlight specific compounds within the BMVs that would enhance the immune response. For instance, if there were proteins on the membrane that worked as adjuvants, this could have been particularly interesting since it is not typically done in vaccine development. Given the complexity and limited understanding of the immune system, Prof. Kuball suggested focusing on creating a broadly applicable treatment rather than one tailored to a small patient population. Lastly, he pointed out that screening for specific responses was not often done, and a universal approach could have been more practical and effective.

Implementation

As we could not use M. BCG in the lab, we delved into existing literature to understand the interaction between BCG-derived BMVs and immune cells. This research informed our strategy and validated the potential of BMVs enhancing the immune response. Additionally, we investigated the effect of different components of BCG-derived BMVs on immune cells and the antigens fused to the outside of the membrane. Furthermore, we explored whether our vaccine should work locally or systemically to be superior to existing methods.

Outlook

We conducted a thorough literature review to understand the interactions between BCG-derived BMVs and various immune cells, including B-cells and T-cells. Next to that, we specifically examined the advantages of using M. BCGas an adjuvant and explored the potential benefits of combining BCG-derived BMVs with other therapies, like checkpoint-inhibition.

Purpose

After the meeting with Yosta, we searched for alternative vectors for M. smegmatis. We found it quite challenging to identify suitable options, so we reached out to Alexander Gräwe, a postdoctoral researcher at the our university. Given his extensive expertise in immunology, microbiology, biochemistry, genetics, and molecular biology, we sought his advice on which plasmid to use for expressing the fusion proteins in M. smegmatis.

Contribution

We reviewed pYUB28b and concluded that it was not suitable due to its use of Gateway assembly, which offers the advantage of being reversible but adds complexity to the process. He demonstrated how to find similar sequences using nBLAST and pBLAST. We discovered that the 2023 iGEM team from William and Mary had used the plasmid pCHERRY3. He then advised us to read more papers on the expression of membrane-associated fusion proteins in M. smegmatis.

Implementation

We considered using pCHERRY3 as a replacement for pYUB28b and found it to be a far more suitable option for our needs. While pYUB28b required the more complex Gateway assembly, pCHERRY3 offered a streamlined approach by allowing the use of Gibson assembly and induction with tetracyclin.

Outlook

The next step was to design the DNA constructs for the Gibson assembly of the fusion protein genes into pCHERRY3.

Purpose

We wanted to get Tom’s perspective on our modeling approach since he is an expert on biological modeling and has been an iGEM PI for a very long time. Our aim was to identify what was feasible and useful. In order to better integrate the lab and modeling, we attended this meeting with the lab and modeling subgroups. We had a lot of ideas on things to optimize within our complete personalized pipeline. Our main ideas after talking to Luke Rossen and doing more research were either ODE modeling of the BMV production to optimize yield or to automatically select antigens for personalizing the treatment.

Contribution

Based on our research and Tom’s insights we concluded that there was too little data on our host organism (which is not a model organism) or on the metabolic chain for BMV production to accurately or usefully model this process. We also considered active learning, which would involve less data upfront. However, this would involve many different growth conditions in the lab experiments, which was not feasible given the time and costs of our protocols.

He also stressed that informing our process through modeling could take many forms. We do not have to optimize the experiments that we do the lab, but we could also use modeling to fill the gaps of our treatment pipeline that we would not be able to do in the lab. In this way we can inform the future of our treatment beyond iGEM.

We also realized that integrating many existing modeling approaches for our problem is still innovation and that we could always add complexity later on when necessary.

Implementation

We continued with the implementation of the pipeline for selecting antigens. In areas where we identified gaps, we planned to consult with relevant experts to gain deeper insights and ensure the robustness of our approach.

Outlook

Following our conversation, we made the decision to develop a personalized pipeline for selecting antigens. We conducted more research and started programming the pipeline. More information can be read on our modeling page.

We are ready to enter the laboratory!

Decription

Over the past months, we have been preparing to enter the laboratory by working on the laboratory protocols and compiling a list of materials we needed to order or request from our sponsors. Next to that, we held a meeting with Liesbeth Varion-Verhagen, our university's biosafety officer, and Peggy de Graaf, our lab manager, who approved our choice of bacterium, possible inserts and provided us with safety measurements. Additionally, we participated in a Safe Microbiological Techniques (SMT) course to ensure we could work safely in the laboratory.

Based on advice from the fourth PI meeting on May 21, we decided to use both M. smegmatis and E. Coli. The PIs indicated that relying solely on M. smegmatis posed a significant risk, as no one had previously worked with this bacterium within the university. In the event of failure, it would be difficult to determine whether the issue stemmed from our approach or the bacterium itself, so they suggested starting with a proof of concept using E. Coli. Using this did not require a new meeting with Liesbeth and Peggy, as E. Coli had already been used widely within the university; however, we did reach out to notify them of this.

We held multiple meetings with various individuals, including Yosta de Stiger, Alexander Gräwe, and the PIs, to better prepare ourselves for the laboratory. Recognizing the urgency to begin our experiments, we officially started working in the laboratory.

Feelings

First of all, we felt really happy that we received approval from Liesbeth and Peggy to enter the laboratory. The SMT course and the introduction to the laboratory helped us understanding the safety measures and made sure we were able to work responsibly and safe in the laboratory, which made us feel relieved.

As for the protocols and plasmid designs, we were well-aware that we probably need to keep updating them based on the results in the laboratory. That was something we could easily accept, as we felt like it was part of the process and how an engineering cycle works. We trusted the process and felt like we were ready to try the first things we had on paper in the laboratory.

Evaluation & Analysis

We encountered several hurdles in designing fusion proteins intended for incorporation into our bacterial membrane vesicles (BMVs) and in creating plasmids for an uncommon bacterium to functionalize them. With limited literature available, we managed to establish a sufficient library and a solid plan to test various approaches in parallel. However, we recognized the need to broaden our perspective rather than delving deeper into similar solutions to the problem. The PIs advised us to explore alternative methods for functionalizing the BMVs, as developing different strategies was crucial to avoid becoming stuck during our lab work. Our team had a tendency to be overly optimistic and reliant on a single strategy, so the feedback from our PIs was valuable for helping us formulate a more robust plan.

Conclusion

We successfully secured approvals to begin our laboratory work. The inclusion of both M. smegmatis and E. Coli in our research strategy mitigated the risks associated with the limited knowledge of M. smegmatis and provided a robust proof of concept. We also expanded our functionalization strategies by employing recombinant expression and micelle mixing. These additions resulted in a solid plan for finalizing the wet lab protocols and initiating experiments.

Action Plan

Our immediate priority was to finalize the experimental plan, ensuring that all protocols and plasmid designs we ready for implementation. Once the experimental plan was completed, we ordered materials and initiated wet lab experiments, starting with E. Coli to establish a proof of concept before proceeding with M. smegmatis. Besides, we wanted to keep exploring modeling opportunities to support our experimental work.

Purpose

Dr. Ronald ten Berge is an accomplished professional with a PhD in Pharmacology and extensive experience in business development, strategic advising, and consulting within the pharmaceutical and biotech sectors. Currently, he is an Impact Developer at Biotech Booster and a Consultant at Fontys University of Applied Sciences, where he uses his skills to boost innovation and commercialization of biotech findings.

The purpose of this conversation was to get to know how to identify suitable target problems and groups, get insights on how to conduct a comprehensive market analysis and addressing intellectual property concerns to ensure the project's success.

Contribution

Dr. Ronald ten Berge provided valuable insights and recommendations for the project. He emphasized the importance of selecting cancer types based on factors such as prevalence, impact and ease of market entry, suggesting an analysis of data availability, preclinical testing models, tumor accessibility, treatability with immunotherapy, and competition from other technologies. For market analysis, he advised relying on both literature and discussions with experts in similar technologies, like Sacha Wissink from MSD. He highlighted the necessity of filing a provisional patent to protect intellectual property (IP), attract biotech collaborations and recommended consulting Maarten Merkx and Willem Mulder for IP strategy.

Implementation

The team decided to focus on analyzing various critical factors for selecting a tumor type that aligned with their therapy, considering impact, relevance, funding, preclinical models, and expected effectiveness. This analysis would also aid in understanding competition and identifying market entry pathways. Next to that, plans were made to establish contact with Sacha Wissink from MSD for insights on checkpoint inhibition and regulatory strategies. Additionally, the importance of patenting was again recognized.

Outlook

The next steps involved analyzing relevant factors for tumor type selection. A competitive analysis would be conducted to compare the technology with others and identify pathways for market entry. The team wanted to initiate contact with Sacha Wissink through Ronald ten Berge to gain insights on checkpoint inhibition and regulatory strategies. Further discussions would be planned to review progress and findings. Lastly we considered cooperating with the Biotech Booster program after the iGEM project, to see how we can develop this project in the future.

Purpose

The purpose of the conversation was to gain insights from a CEO of an anonymous Tech Start Up Company about the process of spinning out a startup from a research group within the university. Specifically, the discussion aimed to understand the rationale behind the choice of specific cancers targeted by the companies treatment, the steps necessary to go from research to a functioning company, and advice on navigating the journey from an idea to a marketable product. We wanted to get insights into why, when and how to spin out.

Contribution

The CEO provided valuable advice on several fronts: selecting target cancers based on the innovative application, emphasizing thorough market research to identify where the technology stands out, and the importance of protecting the idea and having proof of concept data. He also highlighted the need for a clear development path, starting with minimal resources and then seeking aligned investors, and detailed the steps necessary for clinical trials and scaling production, stressing the importance of engaging with doctors to ensure the technology addresses real problems.

Implementation

Based on given advice, our team decided to focus on validating the problem-solution fit by engaging with doctors to understand the issues with conventional treatments and to identify our technology's unique selling points. We also planned to conduct detailed competitive research to determine our market positioning and develop a clear, step-by-step development plan to protect and advance our idea while keeping an eye on the competition.

Outlook

The next steps involved further investigating the problem-solution fit for our technology by starting conversations with doctors to identify significant problems with current treatments and assess if our solution is viable. We planned on determining our technology's unique selling points, wanted to know how to bring it to market considering effectivity, availability, and financial feasibility, and needed to focus on crucial business development steps to attract potential investors.

Purpose

The purpose of conducting this interview was to deepen our understanding of immunotherapy in clinical settings. We sought insights into alternative therapies that might be preferred, exploring the drawbacks of immunotherapy and uncovering reasons for its potential limitations. Additionally, we aimed to receive feedback on our project idea from a doctor and hoped to gather more information on the complexities of lung cancer pathology.

Contribution

The interview offered a new perspective on our approach and provided us with a deeper understanding of the state of the art in immunotherapy. It primarily focused on the drawbacks of immunotherapy. Through this, we learned that immunotherapy is currently not very specific, making targeted therapy a more favorable option for cancer treatment. However, it is often unsuitable for lung cancer due to the high mutation rates, which are frequently caused by smoking. In such cases, immunotherapy would be a better choice. Additionally, we discovered that immune cells are often located far from the tumor and can struggle to penetrate it. These new insights allowed us to reassess and refine our project accordingly.

Implementation

Following the insightful interviews, we incorporated several key considerations into our project. One such aspect involved conducting more research on the tumor microenvironment and considering how it might influence our project strategy. Understanding that tumors use both mechanical and chemical mechanisms to hinder immune cell infiltration was another key area we aimed to explore further. These crucial insights helped us navigate the complexities of immune responses within the context of a tumor and guided us in refining our project approach accordingly.

Outlook

The next step was to conduct further research into the possible drawbacks mentioned above. As tumors can grow a resistance towards immunotherapy, it would also be profitable to look at a fast-working therapy that could implement dendritic cell activation. Our team wanted to gather more knowledge on these new topics and conduct more interviews with professionals to make further progress in our project accordingly.

Purpose

The purpose of interviewing Dr. Becker-Commissaris was to gain a better understanding of how cancer treatments were selected. Learning about the various factors considered in these decisions was important for shaping a new strategy. We aimed that the interview could provide us clearer insights on how patients responded to different treatments and which ones were most suitable.

Contribution

Our goal was to develop a more effective immunotherapy for cancer patients, and speaking with Dr. Annemarie Becker-Commissaris provided us with valuable insights into how current treatments were addressing—or failing to address—patient needs in the clinic. Gaining understanding of how immunotherapies were being implemented allowed us to design our therapy to better meet the needs of both patients and doctors. Additionally, learning about the benefits of alternative therapies highlighted aspects we could incorporate into our approach, giving us clearer direction in developing a more successful treatment.

Implementation

The accumulated knowledge about patients and treatments were used to develop appropriate questions for the patient surveys that were sent out. By understanding which aspects of their therapy worked or did not work on a daily basis for both patients and doctors, we gained a clearer picture of the real-world implications of treatments. This knowledge was crucial for implementing therapies that considered practical, day-to-day factors, ultimately making our surveys as comprehensive as possible and improving patient care.

Outlook

The next step was to validate the patient difficulties that Annemarie had brought to our attention by sending out surveys. Additionally, we wanted to reach out to more stakeholders, including healthcare professionals, researchers, and patient advocacy groups. Engaging a broader range of voices would not only help us gathering more comprehensive data but also ensured that our approach addressed the diverse needs and experiences of all those involved in cancer care. This collaborative effort would ultimately strengthen our project and enhance the effectiveness of our proposed solutions.

Purpose

Dr. Sacha Wissink is Therapeutic Area Lead of Oncology/Devices Regulatory Affairs Europe at MSD. Dr. Mariëlle van Hulten is Senior Director at Regulatory Affairs Europe Oncology and has experience in regulatory strategies for oncology and vaccine development, and GMO/ATMP product development.

The purpose of this conversation was to gain insights on checkpoint inhibition and identify whether or not our solution could solve the problems of resistance towards checkpoint strategies. Furthermore, we wanted to know more about the commercialization potential and what we would need to do to be able to start clinical trials in the future.

Contribution

Sacha and Mariëlle recognized that new therapies to improve the effectiveness of cancer immune checkpoint inhibitors are needed and agreed there could be potential in improving the effectiveness by stimulating the immune system via our cancer vaccine; it would be unique selling points for our therapy if it could alter the tumor microenvironment for higher efficacy with potentially causing fewer side effects. We showed them our roadmap towards clinical trials. They agreed that a financial plan is very important. If you generate IP, a company could jump in at different stages within the development roadmap to further develop the treatment in a partnership. To show that it is successful enough to proceed in clinical trials, you need effective preclinical data. During this process, we have to consider whether GMP production is possible.

Implementation

We had to find out what the next steps would be after the iGEM competition to validate our proof of concept and get preclinical data. This way, we would be more attractive for investors and we could collaborate with large companies such as MSD. Furthermore, we should consider whether we do this in an academic environment, or in cooperation with a company. This depends on the phase we are in. If we do more research on how the concept works, probably an academic environment would be better. If we are more interested in scaling up and already have IP and/or good clinical results, working with a company might be better.

Outlook

The next steps involved making a timeline and financial plan to validate our proof of concept. Here, we considered cooperation with the BioTech Booster program. We considered to plan a follow-up meeting possibly also with an R&D developer. This way we could discuss the project in further detail and see how we could potentially improve our road to success.

Purpose

The last meeting with the PIs had taken place quite some time ago, so we felt it was necessary to update them on the decisions we made and the progress we had achieved. Specifically, we wanted to discuss the initial results from the lab, including vesicle formation and isolation of E. Coli, as well as the PCR results for the pCHERRY3 vector into which our gene would be inserted. We also sought their opinions on our IP process and explained the advantages and challenges we had encountered. Additionally, we asked whether they had, or knew someone who had, experience in obtaining access to (raw) data for modeling. We had been searching for options for a while but found it difficult to gain access as students, which required a lot of administration and time. At the end of the meeting, we thought it would be nice to update them on our finances, HP process, and the organization of both the Mini Jamboree on October 7th and the Challenge Day on September 11th.

Contribution

When we presented our lab results on vesicle formation and isolation. The PIs said we needed more information to be certain we had isolated vesicles. Based on the Cryo-TEM image and DLS output, they felt it was definitely possible that we had, but they emphasized that more evidence was required for certainty. They advised us to perform TEM and explore staining possibilities to obtain more and better information. Additionally, they recommended doing Cryo-TEM of the medium to compare it with the Cryo-TEM of the (hopefully) isolated vesicles. They also suggested conducting further literature research to see how others had validated similar results.

Regarding the pCHERRY3 PCR, we already knew it had not gone well, as we had obtained bands at half the expected length. We already tried different annealing temperatures to improve primer binding, and wanted to check the possibility that the extension time was too short. The PIs advised us to indeed try a longer extension time and, more importantly, to ensure that the primers were not binding elsewhere in the sequence.

As for the modeling data, the PIs had no relevant experience and could not provide further assistance. They recommended that we continue with our current approach and suggested talking to Willem Mulder, as we were already collaborating with him and he would have more experience.

Concerning our IP process, they were somewhat skeptical about our ability to file a patent. They believed there was too little time, insufficient data, and too much uncertainty regarding who would continue the project in the future. Willem Mulder had previously expressed interest in working on it, so they advised us to have a discussion with him and, after that, reach a final conclusion.

Implementation

Regarding the lab, we followed their advice and discussed it with our supervisors. We also scheduled a meeting with Willem to explore how he could help us obtain the data we needed and to discuss his thoughts on the IP matter.

Outlook

Our next step was to try out the advice in the laboratory after discussion with our supervisors. Next to that, we wanted to discuss intellectual property (IP) possibilities with our supervisors Willem and Anna, as they had more experience. Furthermore, we wanted to finalize sponsorship, as we were almost at our goal of 43,000 euros. Lastly, we were busy with preparations for the Challenge Day and the Mini Jamboree.

Purpose

Sacha Massop and Hana Schlorová work at ThermoFisher as R&D Validation Engineer Life Science and Project Manager. They are experienced in commercializing research projects and wanted to help us with our business development. We aimed to present our idea and the business case we had built around it. We sought to validate our unique selling points and the competitive analysis we had refined after the meeting with MSD. Additionally, we wanted to review who our customers would be and what our cost structure and revenue streams might look like if we launched as a startup.

Contribution

Sacha and Hana were enthusiastic about our project. They advised us to focus even more on the benefits of our approach with respect to treatments that are still in development, but have potential to reach the market within 5 to 10 years since these will be our direct competitors. They advised us to also include the fact that personalization is a possibility with our treatment, but it is not necessary. This would allow us to reduce costs in case of a general approach, but improve efficacy on a more personalized approach.

In considering our business model, we faced a significant decision: should we solely focus on being an R&D company that licenses our technology to other companies for market implementation, or should we attempt to bring the product to the market ourselves by outsourcing various tasks? After discussion with Sacha and Hana, we concluded that our optimal path forward would be to sell to pharmaceutical wholesalers. These wholesalers would have the capabilities to conduct clinical trials, manage distribution, and handle the necessary steps to bring our technology to the market efficiently.

Implementation

Sacha and Hana were overall impressed with the steps we had taken and the way we were commercializing the project. However, there were still some areas that could be developed in more depth. For example, we needed to demonstrate that our therapy would be superior to the cancer vaccines currently in development to attract investors and ensure we remained competitive. This was something we had already begun addressing, but our arguments could be stronger and supported by clearer visualizations. Strengthening these points could contribute to a solid business slide deck for attracting investors in the next stages of the project.

Regarding the business model, given our status as a small company, we lacked the infrastructure to handle certain tasks independently. Additionally, the financial burden of outsourcing these functions was prohibitively high. Establishing licensing agreements would allow us to achieve a faster return on investment and align with our core strength: our expertise in biomedical engineering.

Outlook

Following our conversation with Sacha and Hana, our next steps involved several key actions. First, we added the option for personalization versus no personalization to our unique selling points to better differentiate our offerings. We also enhanced our visualizations for the competitive analysis to provide clearer insights. Refining our business strategy became a priority, which is why we planned on consulting with an R&D company experienced in licensing technology to larger pharmaceutical companies to gain a better understanding of the process. We also worked on developing a comprehensive business model, financial plan, and a compelling slide deck.

Purpose

Marit van Buuren is a senior director at BioNTech, a company that is working on novel therapies against cancer and infectious diseases with help of the immune system. Her responsibility is to develop T-cell therapy. She researches what mutations are present in cancerous cells and how to generate a T-cell product that is able to recognize DNA damage. She has lot of knowledge about neoantigens, which was something we also planned on using in our project. We thought Marit would be able to validate our approach and provide us with a lot of useful input. Next to that, we hoped she could tell us more about working for NEON, a start-up that was bought by BioNTech.

Contribution

Marit was able to ask us some critical questions about our approach. She liked the idea of recruiting more immune cells to the tumor by working with bacteria and also though it would be successful, because of the EPR-effect. However, her (and our) main concern was that when the T-cells are recruited, they probably still do not end up in the tumor, especially not when the tumor is “cold”, like the case with lung cancer. She expects that eighter the T-cells or the TME has to be modified, in order for the T-cell to go through the barrier and be able to kill the tumor. She advised us to first try our approach with “hot” and easier tumors, like melanoma. Although this might not be ground-breaking and something new to the market, she advised us to take small steps in our approach and not to think too big immediately. That is also how it works with clinical trials: start with the easiest and then build towards more complex systems.

As for the modeling, she thinks our approach could definitely work. Also here, she advised us to first work with easy and accessible open-source data to build the model and start getting results quickly, so that we can expand and include new data. Moreover, the strongly advised us to look at antigens and responses that already have been described in literature, so that we can use that to validate our model and use it as our ground-truth to build upon.

We also asked her what she thinks has more potential, a general vaccine that could help lot of people or a personalized vaccine. Her response was that developing personalized vaccine is very expensive and that the main drawback is that it is time consuming. By the time we have the data of patients and know how to compile the vaccine, the patient becomes sicker and chances of remission continue to decrease. Lot of people try making their therapy personalized, but it remains a challenge. She advised us to look at two products from the company: FixVac and iVAC. One is more general and the other is more personalized. From that we might receive some inspiration. In the end it is all about engaging investors and hoping for the best results. When the results stay out, it becomes really hard to continue research & development, because you eventually cannot convince new investors. NEON was sold to BioNTech because clinical results (i.e. effectiveness) were not forthcoming. However, it was not a weird decision, since BioNTech was already into developing therapies to fight cancer with neoantigens. They wanted to buy NEON for their T-cell therapy.

Implementation

We received more insight into our approach and identified possible pitfalls. We planned to explore the tumor microenvironment (TME) further to see if we could find a way to transform a "cold" tumor into a "hot" tumor. We aimed to refine our clinical trial process by conducting more literature research and engaging additional stakeholders and companies in our project. Marit provided us with useful search terms and advised us to look beyond academic papers, such as those on PubMed, and to investigate what companies were already doing. She also offered to share her thesis, which she believed contained a lot of relevant information for our project. Additionally, we were allowed to send her a list of people we wanted to engage, so she could see if she could assist us.

Outlook

We made use of her proposal to send a list of companies we were planning to reaching out to, so she could see if she could help us. For CMO scaling up and production, we planned on reaching out to Lonza. Next to that, we will work on our business plan and do more in-depth research about the TME and T-cells, which was the major concern in our product development.

Purpose

The purpose of the meeting was to gain a deeper understanding of patients' experiences both in and out of the hospital during their treatment. Another key objective was to gather insights on the current treatments, with a focus on their practicality. Given that nurses have close, continuous contact with patients, they offer invaluable perspectives on the patient experience. This is why we sought to meet with Janneke van der Stap specifically, to better grasp the full scope of what patients go through and to identify areas where the patient experience might be lacking. Our goal was to enhance our therapy by addressing these aspects more effectively.

Contribution

This interview provided valuable insights into the major issues patients face with their current treatment, particularly regarding the time lost due to hospital visits and waiting periods. Janneke offered a detailed account of the patient's experience, painting us a clear picture. She described how frequently patients visit the hospital, the various processes they encounter, and the different types of consultations required for different treatments. Through her detailed descriptions, we gained a deeper understanding of what patients go through and learned a great deal about their overall experience.

Implementation

As we sought to continue developing our therapy, we took into account the potential issues highlighted by Janneke. It was valuable for us to address not only patient needs but also the requirements of health workers who would be administering the therapy. To this end, we leaned towards a vaccine or pill format, as these options were more practical and less time-consuming for patients. By minimizing the need for frequent hospital visits, we aimed to make the treatment more convenient for patients, allowing them to manage their care at home. Additionally, this approach reduced the workload for nurses, enabling them to treat more patients efficiently.

Outlook

The next steps involved exploring the feasibility of transforming our treatment into a vaccine or pill. We wanted to assess how the therapy should be registered for patients and identify aspects that can be adjusted to optimize its effectiveness for both patients and nurses. This included making the treatment simple and portable, so patients can manage it at home, either independently or with a nurse’s assistance.

Purpose

When working with GMOs (Genetically Modified Organisms) in the Netherlands, strict laws and regulations are in place to ensure public and environmental safety. In our meeting with the RIVM (National Institute for Public Health and the Environment), we sought to gain a deeper understanding of the potential environmental risks associated with the production and use of our therapy. Specifically, we discussed how GMOs could potentially be released into the environment after exiting the human body post-treatment or during manufacturing in the lab. The meeting provided a clear overview of the key areas we need to consider when planning for scale-up, with a focus on minimizing these risks.

Contribution

During the meeting, new insights and potential challenges were brought to our attention. The primary issue raised was that scaling up BSL-3 experiments (classified as ML-III in the Dutch system) could potentially lead to an MI-IV classification, which would result in significant economic drawbacks. Additionally, it was highlighted that while the production of our product falls under the strict laws and regulations governing GMOs, the isolated product itself might not, depending on whether there are living GMO’s in the end product or not. This means that once the therapy is used in a clinical trial, it is no longer subject to the GMO regulations, as it is no longer considered a GMO.

Implementation

We acted on the feedback by immediately reviewing the various aspects of our lab work, identifying the BSL level associated with each experiment. In addition, we specifically analyzed which elements of our therapy's production process classify it as BSL-3, allowing us to better understand the factors driving this classification. We also examined the key safety regulations for higher BSL-levels, which we are not currently operating in, to gain a deeper understanding of the requirements at those levels and prepare for potential future scale-ups.

Outlook

The next steps involved exploring strategies to ensure that the production of our bacterial membrane vesicles can be classified as BSL-2 (ML-II), while avoiding the escalation to MI-IV during the scale-up of BSL-3 processes. To address this issue, we will conduct interviews with established contract development and manufacturing companies to identify more effective approaches for navigating the challenge of scaling up BSL-3 classified experiments. Finding a solution to this problem is crucial for the long-term viability of PROMISE.

Purpose

After discussions with our PIs and supervisors, we concluded that the project is worth pursuing beyond the iGEM competition. To publicly disclose the invention while retaining control over its development and commercialization, we decided to file a (provisional) patent application. We have drafted an Invention Disclosure Form (IDF) and scheduled a meeting with the business developers at The Gate to review the description and determine how they can assist us in the patenting process.

Contribution

Nataša believes the idea was definitely worth protecting and suggested the patent could have broad coverage. However, as we discussed earlier, she emphasized that you cannot patent mere ideas; we had to present solid data to move forward. Bart also stressed the importance of having in-depth discussions about ownership and inventorship. We needed to clearly define who made intellectual contributions to the concept and involve our supervisors and PIs in the conversation.

Implementation

We took Nataša’s advice into account and understood that while the patent can be broad, our current IDF draft focused specifically on our project: developing a personalized cancer vaccine using antigen-functionalized bacterial membrane vesicles (BMVs). However, we had to focus on the fact that the technology has broader potential applications, such as for cancer, infectious diseases, and autoimmune diseases. Additionally, although the data we had generated was limited, we had to analyse and process everything to move the patenting process forward.

Outlook

We planned to revise the IDF to reflect a broader scope, considering the technology’s potential applications beyond our focus. Additionally, we planned to identify the inventors in our team and create a clear development plan. Since we only have one year after filing the provisional patent to collect more data, these steps were crucial. When handled properly, The Gate wanted assist us in finding patent attorneys, and TU/e would cover the funding for the patent application.

Purpose

Bart van Dijk is a member of the development team at Lonza, a contract development and manufacturing organization (CDMO) company that does productions for pharma-companies, and knows how to go from an idea to a clinical trial. A fun fact is that he graduated from the same studies as most of us are pursuing now. The purpose of our meeting was to gain more insight on the transition from R&D to GMP production. We wanted to know how and if we are able to scale-up in the future. Also we were curious to figure out when exactly one knows it is right moment to do so. Next to that, we were also curious about Lonza as a company themselves.

Contribution

In general we are not doing something completely different from things that have never been done in a lab, so scaling up should in principal be possible. However, the main concerns were about our bacteria being Biosafety Level III and using an ultracentrifuge for isolation of the produced vesicles. Biosafety level III requires lot of precautions and there are not that many labs available for such processes. Not many manufacturing sites have the capability, and if they have, it is more expensive. Having an ultracentrifuge in the process of scaling up can be a big hurdle, since you will be limited by the capacity of the centrifuge rotor. One should seek for other purification steps or make smaller batches, which could be inefficient due to the fact all batches need to be tested which takes a lot of time and will increase manufacturing costs.

Another question we received was to think early on whether your product is generalized, like a cocktail for multiple patients, or personal. We should have in mind that making personalized medicine can cost you between half a million to one million euros a patient which is extremely expensive. Next to that, the two are completely different when scaling up, so before doing that, one should decide which way to go.

Finally, we discussed how and when a company as Lonza could jump in and help with production process. The answer was that they could be supportive at different moments, from early stage and helping with development to commercial phase and doing production. Bart believes that involving a company always increases success chances, but you have to weigh money and knowledge. Companies as Lonza can be great for giving feedback, helping with research and development and offering facilities, but often you need to take all or nothing. That is why, as a start-up, you often need to have trust from lots of investors to be able to buy those facilities to really grow into a business and unfortunately many do not succeed. It is strongly advised to keep in mind different exit-strategies as a start-up or small business. Since Lonza is a manufacturing organization, they will not often buy a start-up. This is outside of their goals, to make products in Lonza name. A pharma company like Pfizer (that makes its own pharma products) will do this if they think the start-up is valuable to them.

Implementation

When considering scaling up, we needed to examine whether we wanted our medicine to be general or personalized. Additionally, we had to explore how to move from Biosafety Level III to lower levels, as this would increase our options for finding labs and scaling up. Furthermore, we looked into replacements for ultracentrifugation, noting that Tangential Flow Filtration (TFF) is often used in the protein industry and could be a viable option. Size Exclusion Chromatography (SEC) and other chromatography techniques also seemed interesting. An important point raised was to never skip quality control and to utilize various analytical methods to ensure the product's quality, as this remained a significant challenge for everyone in the field.

Outlook

Our next steps included working on our business case and thinking about how to set up a clinical trial, with the advice from Bart in the back of our head. We tried to search for alternatives of ultracentrifugation and look into possibilities to reduce the biosafety level of M. BCG when we want to use it in the future. We tried to make every process step as easy as possible.

Purpose

For modeling we wanted access to non-open-source data, alongside open-source data. This because we encountered that open-source data does not contain information on healthy cells and we thought this potentially could be important to be able to compare this with cancer cells. We contacted people who manage non-open-source data and they wanted to grant us access if we would send them the text to be reviewed thirty days in advance of publication. Next to that, they asked about our ethical review process, and we told them we had undergone a fast-track procedure which formally allows us to reach out to externals. They were not sure whether our ethical forms were enough, since access to patient data was not included in our review. That was because when we filed the application in May, we did not yet know we wanted access to this kind of data. We contacted Jolanda Habraken from the Ethical Review Board of our university to ask for advice on how to handle the situation and how to access the data properly and according to the rules.

Contribution

We explained our situation and gave more background information to Jolanda and asked what steps we need to take in order to handle the data properly and comply with both the governmental and universities rules. We were notified of the fact that our current application was fast-track, because it was only to reach out to stakeholders, for which reading the rules and making an informed consent was enough. The universities Ethical Review Board trusts that we handle responsibly and have the right to check at any time what we are doing ethically. Since our application did not involve receiving access to patient non-open-source data, we should fill in a corrected ethical review that will be reviewed within two weeks. Based on what we told Jolanda, she did not expect any problems with our corrected application, however we should still let it be reviewed by the Board.

Implementation

We were more aware to handle responsibly with the access that has been granted. We stored the data in a safe research cloud and delete it afterwards. Moreover, we only used it for a specific research purpose, which is to see whether healthy data is really needed as comparison for the cancer cells and to check our conclusions. Since we had very limited time and already received access, we worked with the data for now. Also, because we needed to submit written text at least thirty days in advance to the data managers. Would our application be rejected; we plan a new meeting with the Ethical Review Board to see what we can and what we cannot do.

Outlook

Our next step was filling in a corrected ethical review form to be reviewed and making sure to comply with the demands of the data managers and the Ethical Review Board. We started working with the data already so that we will be able to hand in the written text thirty days in advance.

Purpose

To create a successful product for the market, it is crucial to consider the needs of those affected. Therefore, distributing a survey became a key part of our human practices approach. We understood that lung cancer patients' lived experiences were invaluable in guiding our efforts, so gathering their insights was crucial to designing something that balanced both effectiveness and quality of life. To make this effort as impactful as possible, we reached out to Longkanker Nederland and asked if we could collaborate by utilizing their network to target lung cancer patients.

Contribution

We had multiple discussions via email with Christel van Batenburg, the project leader of Longkanker Nederland, who played a vital role in supporting our efforts. She assisted us by brainstorming how best to present the survey and gave us valuable feedback before we moved forward with publishing it. Additionally, she wrote a piece about our project on the Longkanker Nederland website, which directed people to our survey. Her contributions were instrumental in ensuring that our survey reached the lung cancer community and was designed in a way that resonated with patients.

Implementation

After collecting the survey responses, we carefully analyzed the results and documented our findings on our Integrated Human Practices section, right before this timeline. This analysis was particularly rewarding as it aligned closely with the input we had previously received from the healthcare community. By validating our insights with both patient perspectives and healthcare professionals, we were able to confirm that we were creating a solution that was meaningful and beneficial for society. This thorough implementation process not only strengthened our approach but also reinforced our commitment to developing a product that genuinely addressed the needs of the lung cancer community.

Outlook

We planned to share our results with Longkanker Nederland, as they recognized the relevance of the survey input for their community. In addition, we intended to write another piece for publication on their website, allowing us to communicate our findings back to the community. This would help ensure that participants understood the impact of their contributions and the reasons behind the survey. By doing so, we aimed to foster a greater connection between our work and the lung cancer community, reinforcing the importance of their involvement in our research.

Purpose

The purpose was to get a greater understanding of the immune system activation by neoantigens. This was to improve the context around the computer modeling because there was still a disconnect between the practice and the theory on the modeling wiki. More specifically, we predicted the neoantigens based on some metrics but did not understand why these metrics were important and why the neoantigens would activate the immune system.

Contribution

There were a few flawed assumptions or misunderstandings around immune system activation that made the description on the modeling page less consistent and clear. The modeling team learned a lot about how immune system activation worked which allowed us to make a stronger case for our vaccine.

Implementation

We identified a few key papers to read on the background of immune system activation.

Outlook

We planned on reading more about this background and rewrite some parts of the modeling wiki.

Purpose

The purpose was to get more insight on how our treatment would be used in practice. In particular we were interested in how our software and process could be integrated into the medical world to enhance the treatment of a patient. The interviewee was an oncological surgeon who treats patients with various types of cancer, specializing in colon and breast cancer.

Contribution

An important distinction was made between oncologists and oncological surgeons. While they create a treatment plan together, the oncologists have more knowledge of immunotherapy and chemotherapy. Our target group was oncologists.

The main obstacle to integrating our treatment was timing. In the Netherlands, after a diagnosis is made, guidelines suggest starting treatment within five weeks. Of this, the first would be spent on routine tests and scans, leaving very little time for cell cultures, sequencing, running the software and creating the vaccine. The logistics of the treatment are quite complex, meaning our treatment personalization would need to have few steps and be very fast to be feasible.

The second consideration was price. Cell cultures and creating a personal vaccine is quite expensive. Additionally, for some patients there is little advantage over conventional, less expensive, treatments. Hospitals use metrics that limit how much an additional year of life can cost on average. So to justify a more expensive treatment an analysis is made of tumor characteristics, growth behaviour, TNM classification, lymph/angio-invasion or Oncotype DX --- which is a test based on DNA estimating the likelihood of metastasis.

Regarding our software, there were different details which are important to a researcher like us and a clinical practitioner. Up until now we showed a lot of details on how the prediction was made which is not interesting in practice. What the doctor wants to know is how he can help the patient. The most important output should be the chance that a given treatment will work. Details such as quality metrics or how the prediction was made should be available on demand. We can take inspiration from other software programs such as Predict Breast Cancer which only asks a few questions and has a simple output.

Implementation

While a personalized treatment would be the most effective, we needed to consider the timing and cost aspects. If we create a vaccine based on population common markers, this would speed up the treatment. Additionally, we could scale the production and thus bring down costs. We might be able to strike a balance between personalization and scaling by creating a set of vaccines and doing a histocompatibility test which specific vaccine would be most effective for a patient. We wanted research this idea in more detail.

Our target group for the current software was not the doctor, but rather other researchers. In the future we might develop software helping doctors implement our treatment, but this should have very different features than what we have now.

Outlook

The next steps included reevaluation of our business case to take treatment feasibility into account and changing the target group of our software to biological researchers with less programming experience. This would affect the design and documentation.

Purpose

The purpose of the conversation was to gain a clearer understanding of how clinical trials are conducted, including the typical duration of each phase and the time required for preparation, such as filing documents and handling regulatory requirements. We also wanted to learn about how data is analyzed, which tasks are outsourced to other companies, and which responsibilities remain with the company running the trials. Additionally, we sought insights into common errors and challenges that arise during trials, so we can avoid potential pitfalls. Another key area of interest was learning more about Contract Research Organizations (CROs) and how R&D companies can collaborate effectively with them to optimize trial outcomes.

Contribution

Her contribution was invaluable, as all the advice and information she provided could be used to shape our own clinical trial plan. In addition to her insights, she also pointed us toward resources and specific guidelines that can further assist in developing our plan. These references helped us ensuring we follow best practices and meet regulatory standards. The information she shared will also be taken into consideration when crafting our business case, helping to align both the clinical and business aspects of our project.

Implementation

We immediately got to work by researching the specific guidelines and regulations for immunotherapy and pharmaceutical clinical trials. With this information in hand, we began refining the business case, making necessary adjustments based on the new insights gained from the conversation. At the same time, we started drafting the clinical trial plan, ensuring it aligns with the relevant standards and timelines. This proactive approach helped us lay a strong foundation for both the clinical and business aspects of the project.

Outlook

The next steps included implementing the valuable information provided during the conversation. The clinical trial plan would be drafted, following the recommended guidelines and keeping the suggested timelines in mind to ensure an efficient and realistic schedule. Additionally, the business case would be further developed, incorporating insights from the discussion. This involved adjusting key elements and adding details based on the new information gathered, ensuring that both the clinical plan and the business strategy were well-aligned.

Intellectual Property and Provisional Patent!

Decription

Over the past months we had been exploring possibilities for intellectual property (IP) in collaboration with the Gate and more specifically Nataša Maršić. On the 30th of April we decided to seriously consider going for a provisional patent. Since then we had multiple (small) sessions to discuss what the next steps should be. In the beginning we worked on an invention disclosure form (IDF) to give a proper description of the invention. We use a and a non-disclosure agreement (NDA) when talking in full detail to stakeholders. The NDA was also signed by all group members and supervisors as advised by the Gate. During the project, we did an extensive search on the innovativeness of our idea and came to the conclusion that our idea indeed is patentable. After that, the next step was to hand in all the paperwork including methodology and results, so that the Gate could work on claims and send it to the patent attorneys to come up with claims. For that, we also had to look into funding possibilities and the most logical approach was to work together with the Technical University of Eindhoven (TU/e).

Feelings

We were very happy that the Gate helped us with the patenting process and that TU/e agreed to fund our provisional patent, as this allows us to keep control over the commercialization of our project and ensures continuity. The Gate worked diligently to ensure we filed the patent before the 30th of September, which would allow us to share our work publicly on the wiki. If the filing was not feasible within the short time we had, we would prioritize sharing our findings at the Wiki and Grand Jamboree over pursuing IP, as our goal was to share everything with the iGEM community. Nonetheless, obtaining the patent was significant because our team captain and supervisors planned to continue this research after iGEM. While we anticipated being busy with the submission process, we also needed to handle results processing for the Wiki Freeze, allowing us to work on both tasks at the same time. It still felt unreal, and we were excited to see how everything would develop.

Evaluation & Analysis

We took a considerable amount of time to make our decision, as not everyone was confident that our idea would be truly innovative. The tight timeframe added to our challenges, leading to numerous discussions with The Gate, our supervisors, and PIs. While the PIs appeared somewhat skeptical, Willem and Anna (our supervisors) did everything they could to support us. We dedicated significant effort to creating a business slide deck, completing the various forms, and processing results, ultimately convincing TU/e and The Gate to move forward. We found this accomplishment fantastic and were grateful for the opportunity.

In hindsight, starting the process a bit earlier would have given us more time, but we realized that we needed stronger results and claims before moving forward. While patenting can be a long and energy-intensive process, it is also exciting and rewarding, especially when you have something innovative and promising to protect. However, we think that patenting is only feasible if a team is confident that they have a solid idea and a plan to continue the research after iGEM. A clear development plan is essential, as pursuing a provisional patent is an investment, and securing a full patent within a year requires delivering more concrete results.

Conclusion

In summary, our exploration of intellectual property possibilities over the past months, particularly in collaboration with The Gate and Nataša Maršić, has been a significant learning experience. Our decision to pursue a provisional patent led to crucial discussions and valuable documentation, allowing us to establish the patentability of our idea and secure funding from TU/e. The support from our supervisors, especially Willem and Anna, was instrumental in overcoming initial scepticism and driving the project forward. While the process was time-consuming and required considerable effort, the potential for continued research and innovation made it worthwhile.

Action Plan

We focused on finalizing our documentation to ensure a smooth submission process. We collaborated with The Gate and patent attorneys to file the provisional patent by the deadline, making certain that all claims and results were accurately represented. Additionally, we worked on the documentation required for the Wiki to effectively share our findings with the community. Finally, we prepared a presentation for the live stage talk at the Grand Jamboree, where we will discuss our experiences with intellectual property and the importance of this process for future iGEM teams.

Purpose

The purpose of the meeting with our PIs was to update them on our progress, as it had been a while since our last discussion. We wanted to review our lab results with them and get their advice on how best to present this data on the wiki. Additionally, we sought their input on which experiments were still feasible within the remaining short timeframe and what could be done to add value to our research. Next to that, we also wanted to give some updates on several other aspects of our project, including our model, entrepreneurship efforts, human practices decisions, education outreach, the upcoming mini jamboree and finances. Another key point was to present our designs for the wiki. Since we were deeply involved in the project, we were unsure if the designs were easy for outsiders to understand, so we wanted their feedback on how clear and accessible the content was.

Contribution

During the conversation, the PIs made several valuable contributions. At the start of the presentation, they immediately pointed out that some visualizations of the lab work could be clearer. They asked what certain elements meant, noting that this confusion should not occur—everything should be directly understandable.

Regarding experiments, they offered practical suggestions for relatively easy tests that could significantly enhance our project if successful. For instance, they suggested trying synthetic liposomes to demonstrate the binding of SpyCatcher and potentially using a microscope for visualization if the Cryo-TEM apparatus would not be available. When discussing our FACS data, they confirmed that our explanations seemed correct, highlighting that we had some very promising results but also a few unexplained anomalies. They mentioned that we could aim for the Best Composite Part Prize, but emphasized the need for excellent Cryo-TEM imaging to support our claims. Additionally, they felt our DLS results were promising, giving us confidence in that part of the project.

As for the other updates we provided on our model, entrepreneurship, human practices, education, and the mini jamboree, the PIs did not have much feedback but expressed that we were doing a great job and felt we were on the right track overall so close before the wiki freeze.

Implementation

After receiving the feedback from the PIs, we took time to discuss our lab goals with the team, making sure to keep their suggestions in mind throughout the process. We revisited the visualizations of our lab work and reworked them to ensure they were clearer and more intuitive. We wanted anyone viewing the data to understand it without needing further explanation, as the PIs had pointed out. For our FACS data, we investigated the anomalies together with our supervisors and worked on improving our understanding of the unexplained results as far as possible.

Outlook

As for the lab, we planned to make a final sprint and wanted to do some final experiments including a doxycycline test to optimize protein expression in M. smegmatis, assembling micelles with Spytag and Spycatcher, restriction ligation of one of the pCHERRY3-based plasmids and Cryo-TEM to (hopefully) be sure we have created the vesicles. For the rest, we worked on the wiki pages.

Purpose

Lily Frank is a Philosopher and an Assistant Professor of Philosophy and Ethics at Eindhoven University of Technology. Her areas of specialization are biomedical ethics, biotechnology, moral psychology and ethics in general. Our meeting had multiple objectives. First, we aimed to address ethical concerns related to clinical trials and animal testing. In addition, we sought feedback on the decisions made in the clinical trial proposal and identified potential ethical challenges we might encounter in the future. Lastly, we worked to strengthen the justification for the choices made throughout the project.

Contribution

Lily contributed by offering feedback and highlighting key points we had not previously considered. She brought up the ethical considerations of conducting animal testing on species with fewer sensory capabilities before moving to those with more complex sensory systems, emphasizing that this approach is both more ethical. Next to that, she raised important questions about the financial aspects of the therapy, questioning whether it would be fair to invest significant resources. She emphasized the need to consider who would ultimately benefit from the therapy and whether this justifies the amount of money being invested. At the end, Lily provided us with papers and frameworks that could help justify our clinical trial.

Implementation

Based on Lily's advice, we made several adjustments to our clinical trial, which are detailed in the implementation proposal section. Specifically, we revised key elements regarding which aspects should be randomized and blinded, ensuring that our approach would be ethically responsible. Furthermore, we documented how we took the patients into account during the planning of the clinical trial and identified ways to best address their physical and mental needs throughout the study.

Outlook

After our conversation, we identified several key tasks based on the advice we received. We needed to develop the project framework, implement changes to the clinical trial, and write a comprehensive ethical justification for both the clinical trials and animal testing. We also planned to clarify how ethical considerations were integrated into the project. Given that we had only one day to complete these tasks, we recognized the urgency and committed to working together efficiently to meet our objectives.

What a year!

Decription

We have arrived at the final stage of our iGEM journey. To ensure that our project, PROMISE, is beneficial and responsible for society, we actively engaged with as many stakeholders as possible throughout each phase. We consulted approximately 30 stakeholders from diverse sectors, including industry, science, and safety. Their insights provided valuable feedback across all facets of our project. In addition to these discussions, we conducted a survey with lung cancer patients, whose responses aligned with the feedback we received from stakeholders.

Feelings

We are extremely proud of everything we have achieved in such a short amount of time. It has been a challenging journey, but we are excited that we managed to incorporate the valuable feedback from our stakeholders, which helped shape our project in meaningful ways. Although we had hoped to connect with even more people, time was not on our side. Still, we are proud of the impact we have made with the resources we had.

As the Jamboree approaches, we are excited to showcase what we have accomplished and see how far we have come. We cannot wait to share our work with others, but we are just as excited to meet the other teams and witness their incredible projects. It is going to be an inspiring experience to celebrate everyone’s hard work and creativity.

Evaluation & Analysis

At the start of our journey, we held a brainstorming session to identify all the key stakeholders relevant to our project. With those stakeholders in mind, we developed a plan to assess whether our project, PROMISE, would be beneficial and responsible for the world. We incorporated the feedback we received into the design of PROMISE by cross-validating it with other stakeholders and supporting literature.

Our Human Practices page outlines all the work we have done in this area. We utilized several frameworks, including stakeholder identification, value-sensitive analysis and a timeline with reflections and milestones based on the adapted AREA framework from iGEM TU-Eindhoven 2022 and the Gibbs Reflective Cycle. By leveraging these frameworks, we not only built upon the work of previous iGEM teams but also contributed insights of our own, which future teams can continue to build on in the coming years.

Conclusion

Our iGEM journey has been a rewarding experience, where we engaged with approximately 30 diverse stakeholders to ensure that PROMISE is both innovative and socially responsible. Despite time constraints, we are proud of what we have accomplished and the impact we made by incorporating valuable feedback and using frameworks like value-sensitive analysis and the adapted AREA model. As we head to the Jamboree, we look forward to sharing our accomplishments and celebrating the creativity of the iGEM community.

Action Plan

As for our project, our team captain, Milou, will continue research together with the supervisors after the Grand Jamboree with the goal of turning the provisional patent into a full patent and maybe spinning of a start-up.

We hope that all the work we have done so far will serve as a valuable resource for future researchers and iGEM teams. By building on existing knowledge and contributing new insights, we aim to inspire others to continue advancing science and innovation.