Team:UAlberta/HP/Gold Integrated
The Promise of Protein-based Technologies
The diverse capabilities of proteins in biological systems have presented unique opportunities in the development of many novel products, and useful technologies, particularly for the pharmaceutical industry. Most notably, of the top-selling non-vaccine drugs of 2016, six were protein-based therapeutics. Five of these six therapeutics were antibodies treating conditions ranging from cancer to diabetes.1
Team UAlberta was greatly enticed by the potential of protein-based technologies, especially for therapeutic applications. However, as none of our members are experts in this field, we set out to gain insights from stakeholders and researchers connected to these technologies.
Dr. Mary Hitt
- Associate Professor
- Department of Oncology
- University of Alberta
One of our most motivational conversations was with Dr. Mary Hitt, an Associate Professor at the University of Alberta’s Department of Oncology. In our interview with her, we talked about the role that proteins have in medicine. She identified antibodies and peptides as both falling under the category of protein-based therapeutics, though, noted that each has their own place when it comes to treatments.
Antibody-based therapeutics are a prevalent treatment method for a wide range of diseases. Peptide therapies, which are compositionally similar, are drastically smaller and have simpler structures. Dr. Hitt discussed how antibodies can do much more than peptides, and exhibit greater affinity and stability than peptides. However, Dr. Hitt did note that the faster degradation of peptides can be a potential advantage as peptide-based drugs would not linger in a patient’s system as long as antibodies do. They are also relatively easier to manufacture compared to antibodies.
As an example, Dr. Hitt spoke about using peptides for imaging. Peptides specific to different proteins, such as overexpressed receptors on cancer cells, could be used as imaging agents as their relatively fast degradation, coupled with sufficient affinity, allow them to be introduced into the body for use in imaging studies without the long-term effects that a more stable antibody could have.
Our interesting conversation with Dr. Hitt revealed many insights into the field of protein-based therapeutics. Though challenges were identified, the promise of peptide therapies and the potential of their wider applications drew our team to further investigate protein-based technologies in the context of peptides therapies.
Screening Protein-Protein Interactions
Civilization has been using compounds found in nature to treat our various ailments since ancient times. Historically, drug discovery has been mainly serendipitous, but much effort has gone into developing more deliberate and informed strategies. Currently, the development of many therapeutics, including protein-based technologies, use natural proteins or compounds as starting points. However, wild-type proteins are often in need of optimization for use outside of their natural context 2. For proteins, this optimization is the realm of protein engineering, where the chemical and physical properties of proteins are optimized for use in industries such as manufacturing, medicine, and materials3.
Because our understanding of protein dynamics is still incomplete, optimizing proteins often relies on directed evolution. This process involves repeated cycles of mutating proteins and screening for improved variants to engineer protein-protein interactions with higher specificity and affinity. Due to the iterative mutagenesis required, directed evolution, and the screening associated with the process is extremely laborious.
Dr. Maya Shmulevitz
- Associate Professor
- Department of Oncology
- University of Alberta
Dr. Maya Shmulevitz, a researcher in the University of Alberta’s Department of Medical Microbiology and Immunology, has previously worked with the yeast two-hybrid system for screening protein-protein interactions. The particular system she used was based the expression of antibiotic genes regulated by the reconstitution of the yeast transcriptional machinery via the interaction of proteins of interest. The stringency of the screen is modulated with antibiotic concentration. If proteins of interest interact sufficiently, they confer antibiotic resistance to yeast, which are then selected.
However, what Dr. Shmulewitz found when using this system was that it was difficult to determine how many from a library of positive results should be selected, especially when no reference to controls are available. When Dr. Shmulevitz reduced the stringency of her test, she found many false positives, but when the screen was too stringent, many possible interactions are lost.
Our main take away message from our conversation with Dr. Shmulevitz was that the choice of reporter genes in assays like the yeast two-hybrid system is crucial to the results of a particular screen. In her case, antibiotic resistance did not provide an outcome that can be used to readily discern the relative strengths of protein-protein interactions, nor can it be used to separate desirable candidates from false positives. Though, as assays testing for protein interactions are not numerous, it was apparent that there is room for the development of other alternative screening methods to address these issues. In response, Team UAlberta aimed our project in developing a system that can provide a relatively quantitative readout linked to the strength of protein-protein interactions.
Jeffrey Wong and Phage Display
The scientific foundation of our project focuses on the idea of protein-protein interactions, and how best to engineer and optimize these interactions. One of the techniques currently used for the screening of protein-protein interactions is phage display. To gain a first-hand account of what phage display involves, we spoke to a researcher who gets up close and personal with the technique on a daily basis. Jeffrey Wong is a Ph.D. student in Dr. Ratmir Derda’s group in the Department of Chemistry at the University of Alberta. Jeffrey’s project involves using phage display to identify peptide sequences that can be further developed for cancer therapeutics.
During our interview with Jeffrey, he spoke at length about the work-flow researchers go through when carrying out the phage display technique. One of the things that stood out to us the most was how time consuming and labour intensive it was to conduct just one round of phage display. This realization set us on the track of looking to find a quicker and more efficient way of achieving the same results. Specifically, the idea of a system with the potential to be automated was quite appealing in that it could cut down the need for scientists to be physically present in the lab during the majority of the selection process. An automated system will not only increase efficiency and free up researchers for other tasks, but can also speed up the process of engineering protein-protein interactions. Using the information we have gathered from speaking with Jeffrey, the UAlberta team has worked to shape our RISE technology such that it allows for a more efficient and streamlined methodology that does not compromise the quality of results obtained.
Campbell Lab
Directed evolution is a technique commonly used in protein engineering to develop better variants. Our RISE system employs directed evolution in the engineering of better protein-protein interactions. While our team was familiar with directed evolution within the context of our project, we wanted to reach out to researchers who carry out directed evolution experiments and highlight the advantages and discuss potential challenges. We spoke to three members from the Campbell Lab in the Department of Chemistry at the University of Alberta. The Campbell Lab is a world-renowned leader in the development of fluorescent protein-based tools through protein engineering for use in cellular imaging. Landon Zarowny, a PhD student, Dr. Matt Wiens, and Dr. Eason Shen provided us with valuable insight into the workflow of directed evolution experiments.
For directed evolution, Landon discussed the multiple rounds of screening that needs to be performed to find a new variant. He told us that in their experiments, directed evolution is used until the differences observed between rounds of evolution begins to plateau. The information gathered from round to round screening is then used to assess and improve other photophysical properties of the fluorescent protein indicator. However, the successes achieved from multiple rounds of screening comes at the expense of the necessary time commitment. He emphasized that a researcher might need to screen tens of thousands of variants before they can be confident that they have exhausted that round of evolution. “It can be time consuming. We’re always looking for better screening methods, but they can be difficult to build or carry out. One method to get around the screening process would be automation. Some research groups do have that, such as at Janelia Farm.”
Dr. Wiens and Dr. Shen confirmed that directed evolution and the resulting screening that needs to be carried out can be time consuming and labour intensive. Dr. Shen estimated that while a round of directed evolution can be performed within a few days, this estimation assumes everything goes according to plan and does not include additional experiments required to verify and characterize identified variants. “Practically it takes longer. Molecular cloning can go wrong, things need to get sequenced, and purification of the protein needs to be carried out. This can extend a round to a week or two.” Dr. Wiens estimated that a typical project length might be a year. Dr. Wiens also discussed some challenges with directed evolution experiments, such as successfully improving one property at the cost of another property and not being able to achieve an indicator that has all of the desired properties.
Science Literacy and Today's Media
Dr. Trudie Aberdeen
As Team UAlberta’s outreach initiatives were focused on education, we interviewed Dr. Trudie Aberdeen, a lecturer at the University of Alberta who specializes in teacher education in Second Language Development and asked for her input on our methods for our outreach initiatives. She provided us with feedback on target audiences (with respect to both expanding our target audience demographic and tailor our approach according to our target audience) and suggested different approaches that could set us apart and influence a larger population. Our discussion with her lead us to develop our video called Explaining the importance of the Alberta Biology Curriculum.
Team UAlberta’s outreach initiatives were mainly focused on education. Initially, we did as all iGEM teams end up doing:. we reached out to high schools such as Archbishop Macdonald High School and set up presentations to explain synthetic biology and to demystify genetically modified organisms. However, after receiving feedback from the students whom we were presenting to, it was found that we didn’t achieve the impact we had hoped to.
In response to this, we reached out to Dr. Aberdeen at the University of Alberta who specializes in teacher education, and e discussed alternative strategies. . We discussed the role of formal education in students’ formative years, as well as how learning continues outside of a classroom setting, which we believe is something that is often overlooked. From this, we expanded our strategy so that we pay proper consideration to Canada’s diverse cultures and languages, as well as expanding our target audience from high school students to their parents, friends, and society as a whole.
From our discussions about our team’s preferred learning styles and the role of technology in education, as well as how to best leverage our team’s strengths for this undertaking, we concluded that the best medium sharing information would be through a video which can be accessed by anyone through our wiki. We planned to translate the video into many languages, striving to encompass Canada’s multicultural society.
Afterwards, we developed a storyboard for what the video should cover, and decided that the importance of the Alberta science curriculum at the high school level should be stressed as it is a good starting point in providing a foundation for the future.
Dr. Ryan Noyce
While speaking to Dr. Trudie Aberdeen, we came to understand some of the barriers facing effective science communication to the general public, such as misrepresentation of the facts. At the same time, Dr. Ryan Noyce, a research associate in the Department of Medical Microbiology and Immunology at the University of Alberta, was encountering the same barriers. Dr. Noyce works in the lab of Dr. David Evans, which studies poxvirus. Specifically, Dr. Noyce has spent over a year re-engineering the horsepox virus. The virus has been hypothesized to have gone extinct, but Dr. Noyce believes that re-engineering it could work towards developing a safer vaccine for the deadly smallpox disease, a close relative of horsepox. His work on recreating horsepox received lots of attention and sparked much controversy in the media, both traditional and social. Inspired by his work and curious about his thoughts on the public’s response to his work, we sat down with Dr. Noyce to gain an understanding of how both mainstream and social media’s perception of his work influenced the information actually communicated to the public.
As Dr. Noyce’s research was first becoming accessible to the public, many news stations such as the CBC wrote articles outlining the details of his work, which he believes were accurate. However, like any game of telephone, things began to change when people started sharing and spreading these articles via various social media platforms, such as Twitter. While Dr. Noyce’s research never involved studying smallpox virus, there was one report that aired on a morning radio show suggesting that their group was “one lab mistake away from releasing smallpox and decimating all of Edmonton.” This distortion of the facts highlights the issue that sometimes messages “get lost in translation”, as Dr. Noyce likes to put it. However, just because information may not always get across the way it was intended to, does not mean that science should stop focusing its efforts in ensuring it does. In fact, Dr. Noyce is of the opinion that “it is a scientist’s duty to communicate their knowledge to the public in a way that they can understand.”
Building off of the experiences Dr. Noyce has shared with us, we have made it one of our goals to focus on scientific literacy in our human practices component. His experience has revealed to us the importance of the accurate relaying of information, and emphasized that the onus for ensuring the public understands our work is on us. Without the proper transmission of information between sources, the information begins to deteriorate, until ultimately a skewed version of the truth is released to the public. In order to address this issue, we have designed our human practices to target multiple demographics, from high school students to their parents, and the general public.
Samantha Yammine @science.sam
Since the direction of our outreach began to evolve into addressing science literacy, we thought of individuals that might be able to share their insight with us. An important part of being able to stress the importance of scientific literacy is being able to communicate science to the public. Though there are many different platforms for sharing information, we focused on social media due to its pervasiveness in daily life. Platforms such as Twitter, Instagram, Facebook, and Youtube have unique ways of sharing information with the masses. As a team, we thought about the different science focused social media accounts we have encountered and followed over the years. Someone who was particularly awesome to us was a PhD student from the University of Toronto named Samantha Yammine. Samantha started her own instagram account, @science.sam, where people can get a glimpse into her life as a graduate student, as well as learn about science in a fun way. We reached out to her to hear her thoughts on science literacy and how to engage those that might not have a strong science background.
First, we asked Sam for her thoughts about teaching science literacy to the public. In contrast to the interview we had with Dr. Ryan Noyce, she argued that you can teach science literacy, but she emphasized that this needs to be differentiated from teaching science facts. To her, teaching people about the scientific process is more important about teaching scientific facts, and as scientists, we need to learn how to do this better. Sam also pointed out the problems with science communication, and how there is an inclusion problem. She stressed the importance of moving away from an “us versus them” mentality, and towards a less isolating conversation. Something really important that we learned from our interview with Sam was that although it is important to share science, it is also important to understand that not everyone is on the same page in terms of their understanding. Although as an insider, we might assume that certain scientific facts are common knowledge, we must be conscientious of the fact that forothers, these facts may be controversial and really challenge their worldviews. To appeal to an audience outside of the scientific community, Sam seeks to make her content accessible without isolating some of her audience. “There are more important smaller battles to be won,” Sam told us when we asked about how she communicates challenging topics. “We must be careful that we aren’t making echo chambers when inviting new people to conversations.”
We also asked Sam for her feedback on our idea to construct a video about the importance of the Alberta science curriculum and create science literacy modules aimed at critical thinking. Sam made the suggestion to make a science literacy quiz that is fun and shareable, and we have incorporated this into the module. Her insight on science communication through social media was very useful in the development of decisions we made while creating the science module.
References
1. The Top 15 Best-Selling Drugs of 2016 | The Lists | GEN Genetic Engineering & Biotechnology News - Biotech from Bench to Business | GEN. GEN (2017). Available at: http://www.genengnews.com/the-lists/the-top-15-best-selling-drugs-of-2016/77900868. (Accessed: 30th May 2017)
2. Brustad, E. M. & Arnold, F. H. Optimizing non-natural protein function with directed evolution. Curr. Opin. Chem. Biol. 15, 201–210 (2011).
3. Utsumi, S. Plant food protein engineering. Adv. Food Nutr. Res. 36, 89–208 (1992).
