Proposed implementation

Overview

Triple-Negative breast cancer is the most aggressive subtype of breast cancer as it has a mortality rate of 40% with at least 46% of patients being likely to develop distant metastasis.(Gonçalves Jr et al,2018). The only treatment option currently recommended is chemotherapy with limited success as tumors frequently develop chemoresistance (Nedeljković, M., & Damjanović, A, 2019).

With this in mind, we needed to work on providing a new method of personalized treatment. Providing by that a novel therapeutic solution for TNBC. That could either help in fighting the cancer either by itself or as an adjuvant to chemotherapy

In this page, we document our thought process towards imagining the real world implementation of our project guided by our integrated human practices and various other resources. We detail how we perceive our vaccine being produced and used by others, we outline our anticipated implementation hurdles and we discuss the safety aspects of our design.

Implementation & Potential Challenges

Putting all this to our mind we figured that the implementation of our project can be achieved on three main milestones which are

Milestones	Description	Anticipated challenges	Potential Solutions	Steps taken to achieve it
In vitro proof of concept	The first milestone in our project is to get our vaccine into the lab and assemble it to be able to experimentally test it and its efficacy in vitro	During the time that we live in, our main challenges would be to get into a lab during Covid-19 pandemic to test this experimentally followed by the problem of getting the funds needed for our project	This could be solved by applying for internal & external grants as well as finding a safe lab to be able to work in it.	We applied for internal grants As well as Deliberating potential partnerships to grant us both the funds we need and access to freely open labs.
Animal model studies	The second milestone is to test our vaccine on animal models to see its effect and how effective it would be in a live setting.	We see that here in egypt we have a lack of animal studies facilities which would pose a problem in how we could do this	We think that we could propose a potential collaboration with research centers to experiment with animal models	We discussed a partnership with the Egyptian Center for Research and Regenerative Medicine
Clinical trials phases I, II & III	Our final milestone is to get to clinical trials and test our vaccine on phases to allow us at the end to measure its efficacy and safety and get approval for its use.	The main challenge would be strict regulatory systems in egypt that restricts research & clinical trials	Recently a new law has just been approved that governs clinical trials so we might benefit from it.	We familiarized ourselves with the current laws & systems of Egypt as well as trying to find solutions in order to bypass the hurdles the might come in our way

What next? The vaccine would be present for administration by a physician that regards that his patient’s case would benefit from this kind of therapy. But who are those?...

Proposed end-users

Our vaccine is intended to help those with Triple-negative Breast cancer subtype As It's our vaccine’s main target However it can also be beneficial to a huge base of society forming around 12% of females and 1.2% of males worldwide of people diagnosed by breast cancer. As it can help prevent the development of breast cancer to this subtype.

Also These cases might include

Those who are already in chemotherapy to use our vaccine as an adjuvant to elicit immune specific response against cancer
Those who are on treatments that don't work for them as frequently the cancer becomes resistant to traditional methods.
Those who can’t tolerate the side effects of other treatments as our vaccine only induces the immune system and targets tumor cells only, not the whole body.
And finally even those who have been treated from it as it can prevent recurrence of the tumor again as immune cells would have memory to fight the tumor in case of recurrence.

Vision

We see that our vaccine would be administered only by physicians for those with TNBC or those expected to develop the disease providing them with personalized therapy.

We also see that our project would help upcoming igem teams in many ways as we provided them with the methods & parts needed to develop and design a replicon-based vector whether it is for the sake of making a multi-epitope vaccine or for any other reason

while also supplying them with tools & techniques that would help to evade immunity for safe delivery of the desired vector to ensuring safety of the design while having control over it

while also showing them techniques that would enable them to find hotspot shared & targetable neoantigens for targeting any disease and not specifically TNBC

We guided them through the process of prediction of targetable neo-epitopes using different tools and showed how to find the most appropriate linker between every two successive epitopes to achieve the best stability in our structure

We showed them how to validate epitope prediction by comprehensive steps & verify these epitopes stability to HLA-complex & also showed the whole process of engineering a multi-epitope vaccine from start to finish showing the main points of consideration to be noted as well as mistakes made in the process and how to correct them while also showing multiple approaches to design and engineer a DNA-Replicon based plasmid.

We guided them into the process of optimizing parts & sequences, whether to find ways to increase these parts' function or whether to choose between multiple viable options to select the best one and to get the highest efficacy out of your vector overall.

And we didn’t stop at that as we continued even until the very final steps as to show them methods of assembly of replicon plasmid using multiple ways as well as how to design assemblies that they would be able to use to compare and get experimental data on certain parts.

Safety aspects

In our design we had several concerns about the safety and security of our vaccine and design that we made sure to cover as we used parts of alphaviruses that can cause diseases such as encephalitis.

Other Solutions	Our Solution
live attenuated vaccines have the risk to revert to virulent state & the risk of recombination with wildtype viruses	By searching the literature, we found that Replicon vaccines are safe as they cannot escape the cell they are replicating in making them better and safer than live attenuated vaccines as we found that replicons are self-limited.
Traditional DNA Vaccines have the risk of integrating into the patients genomes	DREP based vaccines doesn’t pose that threat as they doesn’t integrate with the DNA but rather replicate and transcribe the desired peptides or antigens
Viral delivery systems have the risk of causing a viral disease to the patient	We also only used parts of the alphaviruses that are responsible for replication only and that is not part of the virus’s integral part to cause a disease.

(Pijlman, 2017)

Also we didn’t rely only on that as we designed an off-switch in our vaccine that can ensure safety of the vaccine and stop it completely and provide control over it. By taking all these points into consideration we ensured safety of our vaccine.

References

Gonçalves Jr, H., Guerra, M. R., Duarte Cintra, J. R., Fayer, V. A., Brum, I. V., & Bustamante Teixeira, M. T. (2018). Survival study of triple-negative and non–triple-negative breast cancer in a Brazilian Cohort. Clinical Medicine Insights: Oncology, 12, 1179554918790563.
Nedeljković, M., & Damjanović, A. (2019). Mechanisms of Chemotherapy Resistance in Triple-Negative Breast Cancer—How We Can Rise to the Challenge. Cells, 8(9), 957.
Pijlman, G. (2017). Environmental safety of synthetic replicon particle vaccines – risk for RNA recombination with wildtype viruses (RepliSAFE). https://www.nwo.nl/en/research-and-results/research-projects/i/21/28821.html