Team:MIT/Human Practices

Human Practices

If you are looking for our other Human Practice contributions such as our collaborations, community outreach, and educational work click on the links here or the other tabs under Human Practices on the bar above!

Integrated Human Practices: Considering Society in our Project’s Design

As a team on the foundational track, we know that our project could lead to many applications. From the outset, we wanted to design our project such that it would be beneficial to the scientific community now, and to the world in the future. In designing our project, we considered many possible routes, including projects related to AMD, Cystic Fibrosis, and cholesterol levels. Team MIT ultimately decided to focus on inducing chemotaxis by engineering leader cells, as a Foundational Track project. We chose this track because although we feel that our project will have many future applications in medicine and therapeutics, we also see this project as an opportunity for other iGEM teams and future projects to use when looking to use synthetic biology as a tool to understand immunology and immune cell behavior and communication. For that reason, much of the work we did was focused more on creating a general toolbox for immunology and not directing our work towards one particular medical problem that may be connected to immunology. We felt that we should work on a project further from in vitro work, in consideration of the controversy over genetically engineering human cells and tissues. Although our project still involves engineering HEK (human embryonic Kidney) cells, we felt that it was more ethical than other project ideas because our system would not be implemented in human beings. We also drew strategies for working with neutrophil-like cells and chemotaxis from the UCSF 2009 iGEM team.

Team MIT chose to contact experts in the fields of synthetic biology, microfluidics, and immunology, and we also reached out to the public and students with an interest in synthetic biology. We felt that the synthetic biologists and microfluidics experts would have valuable input in the development of our cloning strategies and assay plans. In fact, they did recommend helpful assays and ways to think about our project. We contacted immunology experts in order to better understand the cells and systems we wanted to replicate, as well as determine feasible applications. Finally, we reached out to the public and students (through our presentations at the MIT Museum and Biobuilders) in order to get the average person’s view of our project and its ethical and societal implications.

Our project could lead to therapies for autoimmune disorders (given many years of future research), by theoretically allowing doctors to draw neutrophils to, or away from areas of interest. Our system could also potentially restore swarming motion that is compromised following organ transplants. On a shorter timescale, it could help immunologists learn more about how neutrophils work and better quantify the chemotactic response of neutrophils. We do recognize that our system could cause negative effects in the body, which is why we encourage much research before it is used in vitro.

Meetings With Experts

Dr. Jesse Torduff, Ph.D., MIT

Early on in our project’s development, Team MIT met with Jesse Torduff. She helped our team learn how to use Morpheus software to model our system. She recommended that we use Morpheus to model chemotaxis, so that we could compare our physical results with what should be happening, according to the models. We took her advice, and decided to use computer models to simulate swarming in addition to our physical experiments.

Dr. Jiandong Wu, Ph.D., UMCAS microfluidic neutrophil assay developer, University of Manitoba

“For your purpose, maybe you can first validate your research idea using the supernatant from the chemoattractant secreting cells” -Dr. Wu

While planning out our summer experiments, we consulted Dr. Jiandong Wu in our search for applicable assaying techniques. Dr. Wu is a researcher at the University of Manitoba who specialized in microfluidics. We talked with him about how to create a chemokine gradient and discussed which assays may be helpful for us to use for our project, given his experience with HL-60s. He informed us of diffusion gradients and the time frames that we can expect and gave us several options, such as the under-agarose assay and microfluidic assay. We actually attempted to employ under-agarose assays in determining the chemotactic ability of our HL-60’s, though we were unsuccessful in implementing them due to difficulties cutting ibidi chamber walls. We met with Dr. Wu twice, once when we were just planning our project, and again right before we began running assays.

Dr. Ritu Raman, Ph.D., EBICS, Langer Lab

We also met with Dr. Ritu Raman, a researcher in Biobots; she focuses on the formation, maturation, and responsive behaviors in skeletal muscle movement. We spoke to her about cellular sense and response mechanisms and directed cell movement. Dr. Raman also gave us a framework to consider the ethics of our project by offering us an ethics module that she wrote. We used this module to shape our discussions about the ethics of our project, particularly the ethics of using human cells and potentially introducing an engineered system to the human body. This, along with public input from various presentations (see below) led us to investigate kill switches. Dr. Raman’s largest influence on our project was the framework of her ethics module, but she also suggested experiments, namely using an empty ibidi chamber and comparing it to an ibidi chamber with HEK cells with regards to chemoattractant production. It also led us to consider possible effects of emergent behavior in our system. When we worked through her module, we came up with pros and cons of our project from the eyes of stakeholders such as medical professionals and the general public. We determined from her module that we should consider implementing a kill switch into our leader cells such that when cells swarmed the leader cell would stop attracting them.

Dr. Michael Mansour, M.D., Ph.D., Massachusetts General Hospital

“You have taken on the cutting edge of neutrophil biology” - Dr. Mansour

As we were working through some problems with our HL-60 growth that was delaying our assays, our team contacted Dr. Michael Mansour. He is an MD/PhD at MGH who specializes in infectious diseases, currently studying neutrophil responses to fungal infection in organ transplant patients. He told us “modeling swarming is very complex”, and suggested that we attempt to model waves of neutrophils rather than a linearly dense stream, since real neutrophils approach in waves. Dr. Mansour advised our team to tag our HL-60s by pre-staining our neutrophils with nuclear dye in the UV wavelength to quantify their swarming intensity without interfering with cellular functions. Unfortunately we were unable to do so due to time constraints, but we followed the bottom line of his advice: we tracked Hl-60 movement using our microscopy experiments in order to quantify their movement using image processing software. Dr. Mansour also helped us develop a clearer idea of potential applications of our project. He expressed that in his research, some patients had negative auto-immune responses due to deficiencies in swarming. He felt that our project could be the basework for a treatment for this deficiency by restoring normal swarming motion. In line with this application, he directed us to look into how we could package our HEK cells for actual use in the future. Unfortunately, due to the timing of our meeting, we were unable to actually implement many of Dr. Mansour’s suggestions, but we did change our assays to try and quantify swarming, as well as investigate future directions we could take this project. We were also directed to Professor Daniel Irimia, a neutrophil assay expert, by Dr. Mansour.

Professor Daniel Irimia, M.D., Ph.D., Massachusetts General Hospital

Team MIT also took a field trip to speak to Professor Daniel Irimia, one of the foremost neutrophil experts in the world. He has been researching neutrophils for the majority of his life, and is a contributor on around a third of papers about neutrophils. Like Dr. Mansour, Prof. Irimia recommended adding neutrophil waves to our model, to account for neutrophils’ chemokine production. He also warned us that IL-8 is not the most effective chemokine, but we could not induce synthesis of LTB4 because it is a lipid and too difficult for the scope of our project. He did recommend an assay that we later ran: co-plating HEK cells and HL-60s to see if HL-60s would go to individual HEK cells. He also advised us to remove all FBS, because starved HL-60s will respond to FBS, which would mask their response to IL-8. Finally, he provided us with more information about neutrophils that contributed to our ideas of future applications.

Professor James J. Collins, Ph.D., IMES, MIT

Our final expert was Professor James Collins, who works in synthetic biology at IMES (Institute for Medical Engineering and Sciences) at MIT developing diagnostics using synthetic biology. He recommended us to look into about collective behavior of immune cells. He thought it would be interesting to see if the leader cells could “trick” follower cells into going to a place that would not normally attract them. He was also especially interested in applications of drawing neutrophils away from a site in order to reduce inflammation. Professor Collins also recommended that we devise further definitive measures of success of our system in order to quantify overall success.