Team:Leiden/Safety
S.P.L.A.S.H.
Suckerin Polymer Layer to Achieve Sustainable Health
Safety
Scientific and technological advancements have been major contributors to a global increase in the standard of living [1]. Examples range from cheap and accessible vaccination to increased efficiency in food production. In his paper “The Vulnerable World Hypothesis”, Dr. Bostrom compares scientific progress to an urn filled with balls [2]. Each ball represents a breakthrough, a new technology. The balls come in a grayscale where light shades are harmless and beneficial inventions (e.g. smallpox vaccination), whilst darker shades represent inventions with the potential to be detrimental to society (e.g. fentanyl synthesis).
White balls: Discovery of technology beneficial to society, i.e. smallpox vaccine
Dark balls: Discovery of technology potentially detrimental to society, i.e. cheap fentanyl synthesis
iGEM is a great example of the efficiency with which we pull balls out of the urn. Each year, teams from across the world aim to pull a ball out of the urn hoping to pull out a light-shaded ball. For iGEM Leiden 2019 that is not enough. Filling in the safety form and complying with local legislation are the minimal requirements, the tip of the iceberg. We sought to develop standardized techniques that help assess the scope and risks of the project in hand, in relation to its societal effect now and in the future. In simpler terms, techniques to help us estimate the shade of the “ball” in question. Given that inventions are irreversible, we must be especially deliberate and careful with what we want to create. For instance, we cannot “un-discover” the genome of the Spanish influenza virus. Consequently, we contacted and closely collaborated with the Dutch National Institute for Public Health and the Environment (RIVM). They introduced to us the concept of “Safe-by-Design”. Safe-by-design is a framework that stimulates researchers to think from an early phase onwards about the effects of their research beyond the lab (moral issues, laws and regulations, environmental impact, et cetera). This is carried out as an iterative process by which iGEM teams receive input from experts in fields such as law, philosophy or environmental science and apply it to their work. In our case, this process was complemented by two coaching sessions with senior risk assessor Dr. Cécile van der Vlugt and policy advisor Ms. Korienke Smit from the RIVM where we discussed the implementation of Safe-by-Design to our project. In addition, we also created an infographic displaying the previously mentioned iterative process of contacting experts and applying their feedback to our project (found below). Following these sessions, we divided our focus on safety into three groups: consumers (potential patients that could benefit from using our hydrogel), world (wider global look at our impact on society and environment) and lab (focused on us and safe practices in our laboratory).
Consumer
World
Lab
Immune Response
Our proposed product consists of an antimicrobial hydrogel that promotes wound healing. After discussing the use of suckerin for a wound dressing with Prof. dr. E. Middelkoop, head of the Association of Cooperating Burn Centers (VSBN) and professor at the Free University Amsterdam in the Netherlands, she emphasized the importance of having a hydrogel that does not elicit an immune response. Because we still did not know whether suckerin hydrogels are histocompatible, she opted for targeting the treatment of superficial wounds rather than deeper wounds. This is because in superficial wounds, though the hydrogel might still cause an immune response, an immune response would not be as detrimental when compared to subdermal wounds. Fortunately, according to Dr. Deepan Kumar from Nanyang Technological University in Singapore, animal experiments with suckerin resulted in no immune response. Previous studies on suckerin films also showed in vitro to be viable as a structural scaffold for stem cell proliferation [3]. Therefore, we can conclude that suckerin-based materials are biocompatible.
Antimicrobial
The wound surface is colonized by a mixture of commensal (harmless) bacteria and pathogenic bacteria. Prof. P. Nibbering, from the Leiden University Medical Center, suggested that keeping the wound area sterile is essential for effective wound healing. To keep the wound area sterile there are two requirements: (1) the bacteria in the wound area must be eliminated and (2) the wound area must be isolated from its environment. To fulfill the first requirement, we would incorporate antibiotics into our suckerin-scaffold. Given the nature of hydrogels, any hydrophilic antibiotic could be added to the aqueous solution used to create the hydrogel. The second requirement was addressed by looking at the current techniques to keep the wound area isolated. A band-aid-like material could be used to keep the hydrogel in close contact with the wounded area, as well as serving as a border between the hydrogel-wound environment and the “outside”.
GMO and DNA-free
Dutch legislation prohibits selling GMOs [4]. We came up with a processing system that systematically removes any GMO and any modified genetic material, thus making our product sellable. This treatment relies on lysozyme and DNase. Lysozyme is a well-known cell-wall degrading enzyme that will eliminate any possible bacterial contamination. Since we are using E. coli which is lysozyme-sensitive, this treatment should be sufficient to eliminate any GMO. On the other hand, DNase will degrade any possible genetic contamination.
Antibiotic resistance
The increase in antibiotic resistance is a global crisis that threatens to take society back to the pre-antibiotic era [5]. In order to prevent collaborating with this increase in resistance, we decided against using actual antimicrobial peptides in our proof-of-concept for the detection system, instead we would use GFP. Furthermore, the theoretical detection system would directly help reduce the increase in resistance. This is because antimicrobial peptides targeting the pathogen Staphylococcus aureus would only be released from the gel in the presence of the pathogen, since the linkers are cleaved by proteases secreted by S. aureus. Thus, we would reduce the exposure of antimicrobial agents to bacteria resulting in a decreased chance to develop a resistance mechanism.
Degradation of suckerin
While developing this project we tried to maintain an open mind aiming to foresee future problems that this technology could pose. Given the harmless nature of our product and the minimal possibilities for a negative dual-use, we focused on its degradability. The question we wanted to answer was: if in the future we decide to mass-produce this protein, what would be the best way to recycle it? We believe that a circular economy approach would be the best solution. Currently, protein waste is lysed with extreme pH or protease treatment and used as feedstock for microbes [6]. Therefore, our product could be used in the medical field and afterwards re-used by breaking it down to its components (amino acids). These amino acids could be used as feedstock for our microbes to produce more hydrogels, thus closing the hypothetical circle.
Safety course
All team members received a course from Andre Kamp, Safety Officer of the Biology Institute in Leiden. The aim of the course was to learn how to safely handle GMOs and general laboratory safety.
Choice of hosts and techniques
We decided to use non-pathogenic model organisms for the recombinant expression of suckerin. The following organisms were used: E. coli BL21 (DE3), E. coli DH5α, S. lividans, and S. cerevisiae, all of which can be safely handled in an ML1 laboratory. In addition, we used a marker (sfGFP) for the proof-of-principle of the detection system instead of an actual antimicrobial peptide. Lastly, the virulence factor proteases from S. aureus were obtained commercially. We did not use S. aureus at any point, thus complying with iGEM regulation.
Our RIVM infographic
This is the infographic we made in collaboration with the RIVM, as mentioned above.
References
- Peck M., Molnar J., & Swart D. (2009). A global plan for burn prevention and care. Bulletin of the World Health Organization, 87(10), 802-803.
- Bostrom N. (2018). The Vulnerable World Hypothesis. Future of Humanity Institute University of Oxford.
- Ding D., Guerette P., Fu J., Zhang L., Irvine S., & Miserez A. (2015). From Soft Self‐Healing Gels to Stiff Films in Suckerin‐Based Materials Through Modulation of Crosslink Density and β‐Sheet Content. Advanced Materials, 27(26), 3953-3961.
- Country Reports: GMOs in EU Member States: The Netherlands, GMO Compass (2007). Available: http://www.gmo-compass.org/eng/news/country_reports. Accessed on September 12th, 2019
- Aslam B., Wang W., Arshad M. I., Khurshid M., Muzammil S., Rasool M. H., . . . Baloch Z. (2018). Antibiotic resistance: A rundown of a global crisis. Infection and Drug Resistance, 11, 1645-1658.
- Li S., Ng I., Chen P., Chiang C., & Chao Y. (2018). Biorefining of protein waste for production of sustainable fuels and chemicals. Biotechnology for Biofuels, 11(1), 256.