Human Practices

Our project is focused on developing a software that allows cell specific protein expression. Specificity is one of the main challenges mRNA technology-based applications are facing. The ability to express a protein in a specific type of cells, while preventing it in others could be a game changer in many fields. Some examples are cancer treatment, vaccination, personalized medicine and bioproduction. Achieving specificity in cancer therapies could prevent side-effects such as aches and hair loss and could even reveal new methods for treating incurable types. Using our software, researchers could improve bioproduction in the microorganism community and enable studies that were not possible before. Those examples are just a taste of the enormous potential implications.

From the beginning of our project, we followed the human practice cycle. We built a diverse IGEM team and recruited new members for further diversification. At the beginning, we initiated meetings with participants of past TAU iGEM teams such as the captain of the iGEM 2020 TAU team. Afterwards, we paired up and reviewed past iGEM projects from all over the world to inspire and familiarize us more with iGEM. Later, each pair brainstormed ideas for our project and presented it to the team in our weekly meetings. We consulted with academic experts from Tel-Aviv University regarding our ideas and their feasibility and safety. Among them were Prof. Itai Benhar, Prof. Avigdor Eldar and Dr. Natalia Freund. The insights we gathered have led us to reconsider some of the ideas and to make some required adaptations. In the end, we have concluded that the most beneficial to the world, yet feasible project is the one we have described earlier – enabling targeted protein expression.

The idea was inspired by the success of the COVID mRNA vaccines. We believe that efficient design of RNA-based products is a topic that will clearly have a strong positive impact on the world. Specifically related to cancer therapy, biosensors, vaccines and manipulation of microorganisms communities. We met with additional relevant researchers, synthetic biology companies and potential users, such as other iGEM teams, to get their feedback on our work. All of them were very excited regarding our project and its importance to humanity and gave us important feedback on how to improve our project. We understood that our software should be suited for many types of organisms and have the ability to address different cases. For example, addressing different requirements regarding expression levels, such as prioritizing low OFF expression levels in favor of high ON expression levels.

After we established the idea for the project, we have diversified our team’s skills by splitting into sub-teams: Model, Biology, Human Practices, Funding and Wiki. Each team member could join more than one sub-team, according to their skills, in order to maximize their contribution. Furthermore, we decided to integrate human practices into our project by performing additional meetings with relevant experts from the industry and academia, as we elaborate about it in the integrated human practices section.

Following all those human practices actions, we have constantly made adaptations for the sake of our project. When the results were starting to form, we have started to present it in various opportunities, when the end goal was to present it to as many people and institutions as possible to get feedback and improve required aspects of it:

Israeli SynBio Association Inaugural Conference

We attended the synthetic biology conference held by the Israeli SynBio Association at the Reichman University in Herzliya, Israel. At the conference many interesting lectures were given, covering diverse topics of synthetic biology. The conference also included a poster session where we presented our project’s poster and explained to the people in the conference about it. We answered their many questions and they showed great interest in our project. Followed by that, we won a prize for one of the three best presented posters.

Efi and Tal receiving the prize for one of the best presented posters as a part of the Israel Synthetic Biology Conference.

Tuller's Lab Conference

The conference included several lectures about synthetic biology, computational models of translation optimization and the effect of silent mutations. Moreover, we participated in the poster session held in the conference which included a two minutes presentation for each project. In that short presentation we gave a glimpse about our project’s main themes.

Tal presents our project in Tuller's lab conference.

4th Year Biomedical Engineering Projects Day

The Biomedical Engineering students in our team have presented the project throughout a poster session taken out during the Biomedical Engineering Projects Day, held by the Biomedical Engineering department at Tel Aviv University. The poster was presented to the engineering faculty professors and to second and third year students who showed great interest in synthetic biology and in our project in particular.

Roee, Tal, Yulie and Efi presenting our project on the biomedical engineering projects presentation day.

Israel Mini-Jamboree

We participated at the mini-jamboree held by the Technion_Israel iGEM team. At the mini-jamboree we heard a lecture about standing in front of an audience from Anna Shreder, the coach of the Technion's debate team. Later, each Israeli iGEM team presented its project and received feedback and advice from the other teams. For example, we were advised to present more human practice activity in our project’s presentation. This conference has led us to form a new partnership with the BGU_Israel team.

Tal presents our project in the Israel mini-jamboree hosted by the Technion israel iGEM team.

Read about how we integrated human practices into our project in the integrated human practices tab!

Group Guidance

Our team attended monthly meetings with an organizational consultant as part of our aspire to improve the interpersonal relationships between the members of the team. In accordance with a worldview which is shared among many iGEM teams which the value of teamwork should be extolled and emphasized, we decided to participated in monthly meetings with an organizational consultant. Those meetings have substantially helped us to overcome many obstacles we encountered along the way and improved our working capabilities and communication skills. Since most of us did not have prior experience with such demanding project, requiring a versatile set of both professional and mental skills, going through an official and approved treatment method was a wonderful experiment. That has helped us a lot to improve many aspects required for a proper team functioning. We may assure current and future iGEM teams that going through such an experience will only be beneficial for the team's success.

Education

The Israel Arts and Science Academy - IASA

We have presented our project and the field of synthetic biology to high school students at IASA, a boarding school located in Jerusalem. Many students were excited to hear about our project and the current findings in the field, so we have raised the possibility of registering to the iGEM competition as a high school team. This experience was very meaningful for us and has taught us much about the force of synthetic biology to generate interest and curiosity.

Efi presents the iGEM competition and our project to the students of IASA.

Molecular Biology Class

We have presented our project in front of the students of the molecular biology course given at the Faculty of Life Sciences at Tel Aviv university, and have talked also about the iGEM competition in general in order to evoke interest among the undergraduate students.

Entrepreneurship

Following all of those occurrences, we have submitted a provisional patent application, with the kind aid of Ramot, the commercialization company of Tel Aviv University, accompanying research facilities while trying to commercialize their ideas. The advice we have got has led us to develop a wide and generic tool, accustomed for the use of various potential end customers and for many therapeutic and biotechnological goals, enabling specific translation of proteins in a wide number of different systems and organisms. In the light of the mentioned above, it could be inferred that much of that would have not been achieved unless the massive net of human practices events we have taken part in. Also, a thorough consideration of how to implement our project in a beneficial manner could be witnessed, and even more importantly, an evolutionary process of our work throughout the project while being based on the many human practice events we have settled.

Integrated Human Practices

We have conducted many meetings with professionals and research authorities in order to learn more about the emerging field of synthetic biology and how we may adapt our project to the currently common scientific knowledge. Contacting them was a source of inspiration for us for many new ideas and developments in our project. To get the most out of these meetings, we have decided to approach them while keeping in mind four general principles, according to which previous TAU iGEM teams of 2020 and 2021 and the Exeter iGEM team of 2019 have designed their HP section. These four principles are inspired by the AREA Framework for Responsible Innovation, first generated by Richard Owen[1]: Anticipate, Reflect, Engage, Act.

To make it more intuitive to us and more adapted to our needs we decided to change the order of these four principles:

Anticipate - What is the end goal of the meeting? What did we want to know by meeting that specific person?
Engage - Who is the person we have approached in order to get that information?
Reflect - What were the conclusions of the meetings, or what did the specialist we have met told us?
Act - How did that information affect our project?

Figure 1: Our integrated human practice four principles cycle.

Meeting with Jacqueline Valeri

Anticipate: Since our solution is based upon a toehold switch, a secondary mRNA structure located at the 5' UTR of it and enabling or disabling translation according to the presence of environmental required cues such as trigger RNA molecules, we wondered if we could utilize the STORM (Sequence-based Toehold Optimization and Redesign Model) library [2]. This model is a deep learning tool for characterization and optimization of toeholds based on a large data set, containing many ON/OFF protein translation ratios.

Engage: We have arranged a meeting with Jacqueline Valeri, who is a biological engineer and a PhD student from Massachusetts Institute of Technology and is the first author of the article introducing this model.

Reflect: We have learned that STORM is specified for prokaryotic systems since it is based and trained on data generated from prokaryotes. Moreover, she explained to us that for generating a deep learning tool we will have to get a large amount of data. Hence, she recommended the use of basic computational learning methods like a regressor, which can generate beneficial results with less data.

Act: Her recommendations led us to abandon our first direction of generating a deep learning tool. In addition, it led us to initiate a meeting with Prof. Alexander A. Green and eventually to generate the linear regressor from his data, as elaborated below.

Our zoom meeting (Efi, Ilan, Nitay and Rei) with Jacqueline Valeri from Massachusetts Institute of Technology.

Meeting With our Steering Committee

Anticipate: To get initial feedback from well-experienced researchers regarding different aspects of our planned project.

Engage: We have consulted the steering committee of our project, composed of four leading researchers residing in Tel Aviv University: Prof. Martin Kupiec, Prof. Uri Gophna, Prof. Itai Benhar and Prof. Avigdor Eldar.

Reflect: Members of the committee suggested that we should consider expanding our program to be also applicable for prokaryotic Toeholds, as opposed to only eukaryotic ones. They also emphasized the need to consider mRNA structure in different phases of its introduction into cells. In addition, it was our first opportunity to present our ideas to experts outside the group. Therefore, they advised us to emphasize the challenges we are trying to solve rather than explaining in detail the current limitation of RNA therapies.

Act: Regarding the early stage of the project, the remarks helped us better focus our project ideas. More specifically, it is after this meeting that we decided to add prokaryotic to the scope of our program. In addition, according to their feedback, we changed our way to present our ideas and focus on how we are planning to solve the specificity challenge in RNA therapies.

Our steering committee, clockwise from top-left: Prof. Uri Gophna, Prof. Martin Kupiec, Prof. Avigdor Eldar and Prof. Itai Benhar.

Conversations with Prof. Alexander A. Green

Anticipate: Since our project was based upon the concept of toehold switches, we have thought it would be a good idea to discuss its various possibilities with the researcher that has introduced its applicability to the scientific community.

Engage: Prof. Alexander A. Green from the Biomedical Engineering department at Boston University.

Reflect: We have exchanged emails with Prof. Green. By that, we have learnt that we might examine the data produced by him during his toehold research [3]. He provided us with that data so we could use it for our project.

Act: Following the described above, we have generated from that data a linear regressor for the cause of analyzing it. This regressor is now part of our pipeline and enables us to design good toeholds.

Meeting with Dr. Shue Wang

Anticipate: Since we were directed on toehold switches adapted for eukaryotes, we were excited to learn about the design process of it from someone who has tried to utilize those.

Engage: We have arranged a meeting with Dr. Shue Wang, who has published an article relating to an application of the toehold switch in a eukaryotic environment [4].

Reflect: We have learnt about certain aspects of the toehold’ structure Dr. Wang has established, such as what were the dimensions of the different parts of the toehold she used in her article.

Act: In our initial design of the toehold sequence we used the dimensions we received from Wang. This allowed us to run our first cycle from which we learned for the next cycle.

First Meeting with the R&D Team of Lonza Company

Anticipate: We have arranged a meeting with the Lonza Company, presenting our project throughout which and reporting our progress, in order to gain feedback also from professionals from the industry that are working on RNA technology.

Engage: The following people from Lonza were present at the meeting:

Alessandro Di Cara - Head Bioinformatics and Data Science, Biologics R&D
Ariel Gilert - R&D Manager
Bernadette Sweeney - Director R&T
Iris Geffen Gloor - Director of External Innovations, Biologics R&D
Maya Gonen-Wadamy - R&D Manager
Telmo Graca - Head of mRNA Process Development
Katarina Radosevic - Global Head Biologics R&D

Reflect: We have received feedback regarding the challenges of specificity of mRNA molecules delivery to cells. In addition, they brought up the fact that there might not be a particular gene that is expressed only in cancerous tissue and not in a healthy one and therefore affects the ability to achieve high specificity in cancer cases. We agreed to meet again in order to report our future progress.

Act: Following the meeting, we decided to focus our project only on the mRNA expression in the target cells without dealing with its delivery to these cells. By improving the specificity of the mRNA expression, delivery to non-targeted cells could end with fewer consequences. Moreover, we examined a new direction for finding mRNA molecules that would differentiate between the target cells and the other types of cells instead of gene expression levels. For example, to differentiate cancerous tissues from healthy ones by targeting common cancerous mutations.

Meeting with the Lonza Company. (Participating: Efi, NItay, Rei, Tal, Ilan, Matan and Tamir)

Meeting with Dr. Yoram Zarai from OncoDecipher

Anticipate: We have desired to examine the potential of designing a toehold switch for specific translation in cancerous cells, based on common mutations.

Engage: We have arranged a meeting with Dr. Yoram Zarai, a researcher in a small start-up called OncoDecipher which is developing a computational platform to identify and understand complex (e.g. silent) cancer mutations.

Reflect:Following the meeting, we have learnt about the option of implementing our tool upon a data set of cancerous mutations. Dr. Zarai agreed to provide us with relevant data and helped us to understand it.

Act: We analyzed the dataset according to Yoram’s instructions and following his advice looked for common mutations. We then created 30-nucleotides windows around those mutations in order to find the window that best differentiates the mutant sequence from the wild-type sequence. We designed a toehold switch sequence based on the best window and modeled the interactions of this switch with the mutant and wild-type sequences. We present the results of this work as part of our POC (for more details, visit our POC page).

Second Meeting with the Lonza Company

Anticipate:We have arranged a second meeting with the Lonza Company, presenting the progress since the first meeting, in order to gain additional insights.

Engage: The following people from Lonza were present at the meeting:

Alessandro Di Cara - Head Bioinformatics and Data Science, Biologics R&D
Ariel Gilert - R&D Manager
Bernadette Sweeney - Director R&T
Iris Geffen Gloor - Director of External Innovations, Biologics R&D
Maya Gonen-Wadamy - R&D Manager
Telmo Graca - Head of mRNA Process Development
Sonke Stocker - Head of Growth & Innovation mRNA

Reflect: Not only that we have got additional feedback concerning our work, but also regarding safety issues, such that Uridine rich mRNA can trigger an immune response and lower the molecule’s stability.

Act: Following the last remark, we have designed an algorithm for Uridine depletion, which depletes Uridines from the final mRNA, and implemented it into our pipeline. In addition, the Lonza company has decided to financially support our project (via a donation) as they were very impressed by our project, initial results and our team.

Meeting with Alagene (The Israeli Center For Synthetic Biology)

Anticipate: We desired to get feedback and advice regarding our project. from experienced Israeli professionals in the emerging field of synthetic biology.

Engage: Dr. Or Rotem and Dr. Hadar Less of Alagene Ltd company, the recently founded first Israeli synthetic biology biofoundry.

Reflect: We have received feedback concerning the cancerous mutations subject described earlier, advising us to be focused on more frequent cancer types. In addition, we have been informed about the possibility of utilizing toehold switches to generate logic gates. They also gave us various remarks on the presentations.

Act: We indeed considered the suggestion regarding the cancer mutations when we performed the analysis. We also implemented their suggestions in our presentation and website. Their ideas regarding logic gates are presented now as a future work in our presentation as we can not achieve this goal before the jamboree.

Our zoom meeting (Efi, Tal and Tamir) with Dr. Or Rotem and Dr. Hadar Less from Alagene.

Collaborations with Other iGEM teams

Anticipate: We have arranged many collaborations with other iGEM teams, in order to spread our project throughout the iGEM community and get feedback and advice.

Engage + Reflect + Act: The partnership with Aboa team, for example, has led us to generate sequences of toeholds switches using our developed tool for E. coli, a prokaryotic model organism that was not initially planned to be utilized by us. However, the strong collaboration that has been formed led us to generate sequences for the Aboa team's verification via wet-lab experiments.In addition, we changed our rating system according to a new rating metric introduced to us by Aboa members. Moreover, we collaborated with BGU_Israel team and sent them a rated list of sequences in order to validate our ranking metric and linear regression model. We have also got useful feedback and advice, which we have implemented in our work, while meeting the Waterloo and Technion_Israel teams throughout different events.

Some of the iGEM teams we have collaborated with (Aboa, BGU_Israel and Technion_Israel)