Team:Nottingham/Description
Project Description
Our clostridia-based therapeutic will be engineered to increase the amount of D-β-hydroxybutyrate (DBHB) reaching neurons in the brain thus providing a baseline of neuroprotection to delay the onset of neurodegenerative diseases. Our solution will introduce DBHB production into C. sporogenes and will increase the DBHB levels within the blood that will eventually cross the blood-brain barrier to target neuronal cells. Research into DBHB has shown its ability to reduce reactive oxygen species as well as increase antioxidant gene transcription [1]. A recent study also showed its protective capabilities against MPP+ neurotoxin (1-methyl-4-phenylpyridinium) which causes dopaminergic neuronal death. With this project we aim to provide a new strategy to treat neurodegenerative diseases and open new doors to drug delivery techniques. Our project uses synthetic biology to engineer a bacterium which will protect against diseases which cause distress and illness to millions of people worldwide.
DBHB and Brain Interaction
One of the first papers we read during this process showed how DBHB could protect against the neuronal death generally caused by MPP+ neurotoxin [2]. This toxin causes the death of dopaminergic substantia nigral cells. However, when DBHB is added to neurons with the neurotoxin, neuronal death is not seen and the population remains relatively unaffected. This study showed real promise for DBHB as a neuroprotective therapeutic and led to our choice of project.
Despite this, the actions of DBHB in the brain are relatively understudied. Research has shown multiple effects that can be attributed to this ketone body. This vital research came after various studies showing increased memory of Alzheimer’s patients after a diet of increased ketogenic concentration [3]. DBHB has four main ways it can add to neuroprotection:
- Decreasing the production of reactive oxygen species (ROS) – Reactive oxygen species are produced naturally in the metabolism of oxygen in mitochondria. A large concentration of ROS’ can be toxic to the cell - an excess of these is called oxidative stress. ROS’ can cause damage to DNA, deactivate enzymes via the oxidation of their cofactors and oxidise certain amino acid residues in proteins. Their presence in the cell, especially in high concentrations, can cause apoptosis and are thought to contribute to many neurodegenerative diseases [4][5]. Therefore, decreasing their production via the reduction of the NAD couple in the mitochondria (normally produces ROS’) would help protect against apoptosis of neurons.
- Activate GSH-Px to increase elimination of reactive oxygen species – Glutathione peroxidase (GSH-Px) protects against oxidative stress [6]. This group of enzymes can produce water from hydrogen peroxide leading to the elimination of H2O2 - a known ROS.
- Increase ATP concentration – energy exhaustion has been linked with neurodegenerative diseases [7]. DBHB can also be used by the neurons to produce ATP and give the neuron enough energy to perform other vital roles.
- Inhibit histone deacetylases to then increase the production of antioxidants – This causes an upregulation of genes that encode antioxidant proteins such as SIRT3, SOD2 and FOXO3A [1].
Organism Selection
In our project we choose to use Clostridium sporgenes as the basis for NeuroTone, with a number of features making C. sporogenes a good fit for our project aims. For a more detailed overview of our strain selection see the Design page. Here is a video describing how we came to the decision of using this ‘spore loving’ bacteria.
Project Inspiration
Our therapeutic will be present in the gut despite its primary role of neuroprotection. These diffenrent locations will be overcome using the gut-brain axis, a route that already allows for communication between the brain and gut microbiota. Our fascination with the gut and brain axis is what spurred us on to further developing our project into designing a gut-based biotherapeutic.
With the support and expertise of our supervisors, the use of C. sporogenes was a no brainer. The accomplishments of last year’s Nottingham iGEM team on a C. sporogenes model will be a building block for our modelling which will be extremely important given our lack of lab time this year.
The iGEM competition has had many teams focus on poly-hydroxybutyrate (PHB) throughout the last decade. One example is the Wuhan iGEM 2019 team who successfully used Zymomonas mobilis for converting waste cartons into a polymer of β-hydroxybutyrate. However, those projects focused on its role as a biodegradable plastic. Our project focuses on its monomer’s health benefits which is a new and exciting way to think about DBHB. We believe this novel way to use synthetic biology to produce a gut-residing bacterium that protects against neurodegenerative disorders is a great application of synthetic biology.
By attending the UK virtual iGEM meetup we were inspired by so many ingenious ideas and enthusiastic students who did not view COVID-19 as a barrier to their projects. Despite the circumstances of working from home, iGEM teams across the UK were eager to raise the bar even higher and design projects which show innovative ways to model without wet-lab experiments. Inspired by everyone's ability to adapt their projects to suit the new COVID-19 regulations, this encouraged us to face our project with confidence and creativity without limiting our possibilities. With no lab work to direct us, more work has been put into literature searches, with reproducible and translatable results while producing significant and effective models. We have also put a lot of effort into human practices and outreach which we hope will increase the reputation of both our project and the iGEM competition.
This project is dear to us all in many different ways. Despite Luke Weir being the founder of the project, the whole team have personal connections towards the issues faced. Take a look at the team’s motivations towards the project below:
Luke Weir - Founder of project
"I had my first encounter with Parkinson’s diseases at a young age. My great grandmother was diagnosed with this disease just after I was born and fought the disease throughout my childhood. At the time, I did not really understand much about neurodegenerative diseases. This did not change until last year, when I studied abroad in the US where three main courses shaped my view on these diseases. In one I produced a review paper on Parkinson’s disease in general. This piqued my interest and gave me a great background into current research as well as great historical papers on the illness. Further to this, I collaborated in a 2-and-a-half-hour group presentation on Parkinson’s disease. In doing this, I became familiar with the problems in current treatment of neurodegenerative diseases. These treatments all focused on alleviating symptoms. This is due to there being no known cause of these kind of diseases although multiple causes have been hypothesised. With such a name as neurodegeneration I thought a way of helping the neurons survive could be effective in treatment of this disease. A treatment like this would have to be administered without full knowledge that a person would get a neurodegenerative disease which is a key stumbling block and one that I would mull over until I took the final course in spring semester. At the end of this course, I presented a short slideshow on intermittent fasting and how it affected the brain. The key feature was ketone bodies and how they protect neurons as well as how a ketogenic diet could improve memory in Alzheimer’s patients. With this knowledge, I proposed a project to engineer a clostridium that would produce DBHB in the gut with the aim of providing neuroprotection and delaying the onset of neurodegenerative diseases. I am very interested in the mechanisms behind the process of neurodegeneration as the origin of neuronal stress could be extremely diverse in different patients, but they have the same endpoint of neurodegeneration."
James Birch
"Our project is very close to my heart for a number of reasons. Using a biotherapeutic that colonises the gut to protect the brain is an innovative and fascinating concept which has the potential to be extraordinarily impactful on improving patient’s lives. It aims to extend the years of healthy life people prone to neurodegenerative diseases can enjoy, which separates it from treatments available now which prolong life but cannot maintain quality of life. I know from the experience of my family and friends, how devastating neurodegenerative diseases are on the patient, their family and their community. So the opportunity to help in the fight against neurodegenerative diseases was an opportunity I could not miss. I have also enjoyed the challenges this project has presented, exposing me to new skills such as bioinformatics and mathematical modelling as well as coding and testing my leadership as we work through a global pandemic. I feel proud to be involved in such an innovative project, and to be part of such an amazing team."
Saachi Bhalla
"An increased prevalence in neurodegenerative diseases in our constantly growing population has made it impossible to turn a blind eye towards the issue. Hence, our team decided to embark on ways of resolving the issue but with a twist – through the gut! Our project however, hits very close to home for me. Having a grandparent who has struggled with such diseases, I am aware of all the detrimental effects such conditions can have not only on the patient but also on the family members. Through our project, despite it being theoretical, we hope to find ways to combat such illnesses before their peak by targeting the functions of the brain through the gut. Additionally, through this project and the endless research we have done, I have been to gain a deeper understanding about such diseases and hope that we together as a team we can make a difference even if it is relatively small."
Aly Sadowska
"Being part of NeuroTone has been an exceptional experience for me. We have followed our team member’s novel idea of treating illnesses affecting the brain, from the gut. I have found it inspiring to work on something so innovative in the field of medicine, especially since this solution could help millions of people affected by neurodegeneration around the world.
Being able to work with our supervisors who are experts on Clostridia, and have a discussion with various professionals has been a fascinating exchange of ideas which gave me an opportunity to see into professional research and be part of it for this project.
It has been a wonderful learning opportunity for me as a mathematician, to study more methods for applying my mathematical skills in the real world. It has been particularly rewarding for me to use my knowledge of Maths in something that could really make a difference."
Kieran Bird
"With an aging global population, I found this project idea very topical and considered the implications it could have on the rising number people who will have neurodegenerative diseases. Neurodegenerative diseases themselves are depressing. Like with dementia, we can go from being a loved one to a stranger. The sense of hopelessness coupled with anxiety that comes to the families of those who have a member who is suffering from a neurodegenerative disease is something which only further pushes my passion for this project and the impact it could have on so many people across the globe. Although this project is only theoretical, what matters to me is enlightening myself and others on a possible therapeutic curated using synthetic biology. In doing so, also competing in a renowned global competition has provided me with new friends, work experience I will cherish for life and a further respect for those who are suffering from neurodegenerative diseases. "
Eugenia Vuong
"Our project this year is unique in the sense that we aim to tackle issues within the brain by using a bacterial strain that colonises the gut. What I find interesting about our project in particular is the gut-brain axis; using a biotherapeutic to delay the onset of neurodegeneration in the brain. The communication between the central and enteric nervous system with the intestinal tract has been an ongoing hot topic in the scientific world. Therefore, to be part of a project that utilises this route as part of the therapeutic delivery is something that excites me and the rest of the scientific community. As the project progressed, I was able to understand the barriers that patients with neurodegenerative diseases must face on a day-to-day basis. The more I learnt about the livelihoods of patients, the more I realised how many people our project could meaningfully impact. I feel honoured to be part of this project and to be part of such an amazing team, even if we met during a global pandemic and I have yet to meet the other half of the team!"
Alistair Cadoo
"I am super excited about the future and how new and emerging technologies such as synthetic biology, nanobiotechnology and personalised medicine can change our lives. The world is so complex and there is so much to learn! Every year, hundreds of teams from around the world are tasked with coming up with creative and innovative solutions to issues that affect our world. These can range from improving the nutritional content of the food we eat, to tackling antibiotic resistance in hospitals and the problem of plastic pollution in our oceans. It is a vastly broad, open-ended and multi-disciplinary project, but the main goal of iGEM is to impact the lives of people around the world with no borders."
Luke Barks
"For me, this project is a chance to work as a team on a real-world issue without getting too bogged down in the finer details. Working on a project based around neurodegenerative diseases interests me as it is research into bettering the lives of humans across the world and may have the potential to help people close to me as they get older. Working on a sensitive project such as ours also allows for us to tackle a greater number of issues, including ethical ones. Working on a project with a lot of variables is interesting to me as it poses a significant challenge for our team to overcome. "
Real World Applications of NeuroTone
Neurodegenerative diseases are a unique challenge in a world with an increasingly ageing population. In 2019, over 750,000 people were diagnosed with Dementia and a further 120,000 with Parkinson's disease [12]. This represents a large proportion of the population that will either be diagnosed or be affected by a neurodegenerative disorder. The current treatment options for these diseases focus on alleviating symptoms rather than preventing the neurodegeneration in the first place. Levodopa is the main treatment for patients in the early stages of Parkinson's disease [13]. This acts as a precursor to dopamine and is converted to dopamine in the brain. Levodopa replaces the dopamine that is lost via the death of dopaminergic neurons which usually produce dopamine. Treatments like levodopa can be used to inhibit motor decline, but their effectiveness is short lived as neurodegeneration continues to ravage the brain. Our project aims at neuroprotection before significant damage has occurred. At the moment, around 50% of neurons in the substantia nigra are already incapacitated by the time Parkinson's disease can be diagnosed and motor dysfunction is already visible. This highlights the need for treatment before diagnosis until biomarkers can be found for early diagnosis. We believe that finding a treatment to enhance neuroprotection would be a massive step to solving the neurodegenerative disease crisis and help increase the years of healthy life for patients.
References:
1. Yang, H., Shan, W., Zhu, F., Wu, J., Wang, Q. (2019). Ketone Bodies in Neurological Diseases: Focus on Neuroprotection and Underlying Mechanisms. Frontiers in Neurological Diseases, 10: 585, doi: 10.3389/fneur.2019.00585.
2. Kashiwaya, Y., Takeshima, T., Mori, N., Nakashima, K., Clarke, K., Veech, R.L. (2000). D-β-Hydroxybutyrate protects neurons in models of Alzheimer's and Parkinson's disease. PNAS 97(10); 5440-5444. doi: 10.1073/pnas.97.10.5440.
3. Ota, M., et al. (2019). Effects of a medium-chain triglyceride-based ketogenic formula on cognitive function in patients with mild-to-moderate Alzheimer’s disease. Neuroscience Letters 690; 232-236. doi: 10.1016/j.neulet.2018.10.048.
4. Nunomura, A. et al. (2006). Involvement of Oxidative Stress in Alzheimer Disease. Journal of Neuropathology and Experimental Neurology 65(7):631-41. doi: 10.1097/01.jnen.0000228136.58062.bf.
5. Ramalingam, M., Kim, S.J. (2012). Reactive oxygen/nitrogen species and their functional correlations in neurodegenerative diseases. Journal of Neural Transmission 119(8): 891–910. doi: 10.1007/s00702-011-0758-7.
6. Bhabak, K.P., Mugesh, G. (2010). Functional Mimics of Glutathione Peroxidase: Bioinspired Synthetic Antioxidants. Accounts of Chemical Research 43(11):1408-19. doi: 10.1021/ar100059g.
7. Abolhassani, N. et al. (2017). Molecular pathophysiology of impaired glucose metabolism, mitochondrial dysfunction, and oxidative DNA damage in Alzheimer's disease brain. Mechanisms of Ageing and Development 161(Pt A): 95-104. doi: 10.1016/j.mad.2016.05.005.
8. Millat, T. & Winzer, K. Mathematical modelling of clostridial acetone-butanol-ethanol fermentation. Applied Microbiology and Biotechnology 101, 2251–2271 (2017). doi: 10.1007/s00253-017-8137-4.
9. Kanai, T., Mikami, Y. & Hayashi, A. A breakthrough in probiotics: Clostridium butyricum regulates gut homeostasis and anti-inflammatory response in inflammatory bowel disease. Journal of Gastroenterology 50, 928–939 (2015). doi: 10.1007/s00535-015-1084-x.
10. Dodd, D., Spitzer, M. H., Van Treuren, W., Merrill, B. D., Hryckowian, A. J., Higginbottom, S. K., Le, A., Cowan, T. M., Nolan, G. P., Fischbach, M. A., Sonnenburg, J. L. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 551, 648–652 (2018). doi: 10.1038/nature24661.
11. Guo, P., Zhang, K., Ma, X. & He, P. Clostridium species as probiotics: potentials and challenges. Journal of Animal Science and Biotechnology 11, 1–10 (2020). doi: 10.1186/s40104-019-0402-1.
12. Available from: https://www.neural.org.uk/assets/pdfs/neuro-numbers-2019.pdf.
13. Available from: https://www.mayoclinic.org/diseases-conditions/parkinsons-disease/diagnosis-treatment/drc-20376062.
iGEM Nottingham 2020