Introduction

Goethe once said, "Conformity is always the highest need of all good-minded people." Collaboration is also one of the principles that iGEM participants follow carefully, and it has deeply influenced the exploration path of successive iGEMers. Collaboration with other iGEM teams can simplify complex problems and enable the development of collective wisdom to find the best solution, which is the embodiment of the efficiency, vitality, and innovation of an iGEM team. This year, we have established a solid collaborative partnership with NMU-China, and the two teams are working hand in hand to create a new chapter in problem solving, innovation and development.

Build the bridge

In early April this year, ZJUintl-China initially established the project of Ambrosia-T, aiming to design and assemble CAR-T cells to target and kill organ senescent cells to reverse aging-related phenotypes (represented by liver fibrosis and cardiac fibrosis). During the group chat of iGEM China, we found NMU-China, which is like our project, so the leaders of both teams contacted and had preliminary communication. We established a communication group of both teams, and then carried out a meeting and exchange meeting for all members of both teams to fully present the research content. We are very honored to have NMU-China actively communicate with us, which is one of the reasons why our team was able to successfully complete the IGEM-Ambrosia-T project.


Figure 1. The first online meeting between ZJUintl-China and NMU-China

Interconnection

Wet lab

Seeking assistance

In the process of plasmid construction, we designed the IL-6R gene and Chimeric Antigen Receptor (CAR) gene in the negative feedback mechanism into a plasmid and found that the transfected cells basically expressed only IL-6R but not CAR. We have tried many ways to solve this intractable problem, but we have not found the root of the problem. Later, we sought help from the NMU-China. After careful consideration by the NMU-China wet experiment team, we found that the MND activity of the IL-6R gene promoter was much higher than that of the CAR gene promoter SV40. After finding the problem, through the redesign of our wet experiment team and the discussion with NMU-China, we redesigned two schemes: 1. The promoter of the CAR gene was changed to the more active p2A. 2. The promoter of IL-6R gene was changed to CMV to enable the normal expression of CAR. This collaboration provided a lot of help for the normal operation of our experiment, and deepened the tacit understanding and cooperation between the two teams.


Figure 2. Schematic diagram of plasmid reproduced by ZJUintl-China

Dry lab

Data analysis

NMU-China communicated with us about how to screen out highly expressed targets in senescent cells. We elucidated the public data sets for differential expression analysis and the specific organs to focus on. And we shared the Python crawler code we wrote about membrane protein information retrieval with NMU-China. When the shared Python crawler was processing Uniprot web pages, it encountered problems of Uniport web page update and different module changes. Our teams worked together and optimized the code to solve the problem. This exchange on data analysis of the dry experiment further deepened the relationship between our two teams and solved the problem more efficiently and objectively.


Figure 3. The NMU-China group displays Python crawler methods shared by ZJUintl-China

Model building

To build a model, the relationship between variables should be established according to the basic principles or laws of actual problems. However, the complex variables in iGEM subject require very careful thinking, which is why NMU-China hopes that we can discuss the modeling process together. We discussed with NMU-China about the oscillations of the initial simulation results of the prey and predator model and suggested that NMU-China should add a logistic term to consider the relationship between environment and cell population, so as to make the model more comprehensive. It is proved that the simulation results of the improved NMU-China model fit the real situation. As shown in the figure below, the proliferation of tumor cells and CAR-NK cells proved the feasibility of this suggestion after NMU-China listened to the factors of adding environmental variables. The cooperation in modeling enables the two teams to have a deeper understanding of the subjects of both sides and provides opportunities for in-depth cooperation.


Figure 4. Proliferation of tumor cells and CAR-NK-92 cells before and after adding environmental variables

Cost

Since ZJUintl-China is the first to contact chimeric antigen receptor related experiments, there is no relevant experience in the evaluation and control of experimental costs and funds, which is why we refer to the cost control of NMU-China related experiments. NMU-China shared their plans for cost control, and we discussed the costs of plasmids construction, instrument use costs and related consumables. In the end, ZJUintl-China evaluated the final funding for the experiment. This cooperation provides an opportunity for the two teams to deepen their communication on cost control.


Figure 5. Experimental cost plan shared by NMU-China (Unit: RMB)


Figure 6. Experimental cost plan set by ZJUintl-China (Unit: RMB)

Publicity

Synthetic biology, as a new and vigorous discipline, is growing in constant exploration. Based on the history of synthetic biology over the past 20 years, synthetic biology has its own ideas, basic technological developments, and permeated many different application fields. To make the synthetic biology knowledge map more comprehensive and innovative, we invited NMU-China and five other teams to jointly write the "Co-create Map" on synthetic biology. NMU-China is responsible for the improvement of synthetic biology cross information in "Co-create Atlas" and has achieved good results.

Conclusion

This year, ZJUintl-China and NMU-China partnered to establish a "solid, reliable and mutually beneficial alliance" to encourage both teams to participate in this partnership actively and fully. Our collaboration, to a large extent, has solved the various problems and disputes we have encountered, and made our values converge. We fully practiced the spirit of collaboration advocated by iGEM and paid more attention to and respect for each member in the process of collaboration, which also improved the overall efficiency of our two teams. Our collaboration is making the broader picture of synthetic biology clearer, and we hope that our two teams will achieve satisfactory results this year. Finally, we'd like to give a special thanks to NMU-China, have fun!

References

[1] CAR T cells: development, characterization and applications, 2022. , Methods in Cell Biology. Elsevier. https://doi.org/10.1016/S0091-679X(22)X0002-2