Team:City of London UK/Description
PROJECT RIBOTOX
Screening for Preeclampsia Using RNA
Pre-eclampsia is a condition prevalent around the globe that causes high blood pressure during and after pregnancy. Currently, It is detected after symptoms have arisen by old, antiquated methods such as a blood pressure cuff that often result in misdiagnosis and missed-diagnosis [1], ultimately leading to preventable complications in pregnancy such as foetal growth restriction, low birth weight and life-threatening seizures and blood clots [2].
Project RIBOTOX’s primary aim was to overcome the drawbacks of antiquated diagnostic methods, by developing a genetic engineering based cell-free test for microRNA (miRNA) biomarkers that can detect cases much sooner into pregnancy, so medication such as aspirin and statins can be taken and patients’ symptoms can be tracked by their doctor.
The secondary aim was to create a framework with which researchers and igem teams in the future can develop tests for multiple microRNAs at low concentrations, and also to develop a software tool to increase the use of in-silico experimentation, saving costs in the lab.
The final goal was to spread awareness about a condition which, despite its prevalence, is relatively unknown, and too often damages lives in both the developed and less developed worlds.
‘We still rely on a two hundred year old technology to diagnose preeclampsia’.
‘There isn’t an established test for preeclampsia, and that’s one of the problems. If you can create a test that screens for even half the cases of Preeclampsia, that would have a huge effect.’
MicroRNA Biomarkers
MicroRNAs are small, 15 - 20 nucleotide long, non-coding RNAs that regulate gene expression and play an important role in the regulation of placental development[3].
MicroRNAs circulating in human serum have been shown to be upregulated in certain conditions, such as Preeclampsia, allowing them to be used as biomarkers in disease detection[4].
In Preeclampsia, placental dysfunction and hypoxia leads to abnormal extracellular miRNA secretion and we found two miRNAs - miR 210 3p and miR 517 5p- which are upregulated between the 10th and 13th week of pregnancy, before symptoms have arised [4] [5].
This is twice as early as traditional detection methods, such as a blood pressure cuff (which detects the condition after symptoms have arisen at 20 weeks), can sense the condition[4].
‘[Current diagnostic tools are] antiquated and result in missed diagnosis and misdiagnosis. An accurate and rapid diagnostic/screening tool for preeclampsia would certainly contribute to reducing mortality'.
Toehold Switches
We designed three generations of toehold switches, improving their efficacy each time to consider both specificity and cost.
Gen2
When few microRNAs are present, the ribosome binding site of an mRNA coding for luciferase is folded up, so the ribosome cannot unzip the long stem and move down the strand to the start codon to initiate translation. However, when a microRNA binds to the trigger site, the switch unfolds, decreasing the length of the stem, and exposing the start codon, so translation of leuciferase - a reporter protein - can begin. Both gen2 switches were designed using a Python script we developed which predicted the secondary structure of RNA complexes based on different linker regions, and selected the ones which were most likely to unfold.
Gen3
After designing the gen2 switches, we realised that detecting two microRNAs using two different switches would require more hardware than if we could detect both in the same switch, and this problem would increase if we wanted to detect even more microRNAs. With this in mind, we decided to develop a novel AND-gate switch to demonstrate how more complex RNA diagnostic tools can be used to simplify other aspects of a detection kit, such as hardware. This switch works by binding both microRNAs together with an antiRNA and then detecting that complex with a complementary trigger binding site. It's not inconceivable that teams in the future could scale up our design to detect cocktails of 3, 4, 5 or even more microRNAs with the same toehold switch, and this is part of our framework for future research.
Read more about how we designed our switches, and how they work on our design page.
RPA
Having tested both our gen2 and gen3 switches, we decided that difficulties in discriminating between leaky expression, and low miRNA concentration, in addition to not knowing the true concentrations of the miRNAs in human serum meant we should find a way to amplify microRNAs. This decision was further confirmed by talking to researchers such as Dr Ciara O’Sullivan and Dr Alex Green.
Not only is PCR difficult to perform on microRNAs due to their short length, we wanted to find a solution that would allow amplification to take place isothermally, in a single tube, increasing the accessibility of our tests, especially in countries with less access to expensive equipment such as thermocyclers. For this reason, we designed a new amplification strategy by combining Recombinase Polymerase Amplification, or ‘RPA’, with miRPA. This process is explained in detail on our design page.
Outreach and Human Practices
After initially asking friends and family whether they had heard of Pre-Eclampsia, we quickly realised that awareness was not as wide-spread as it should be. Therefore, we conducted a random-sampling survey amongst our peers to gain an understanding of their knowledge of pre-eclampsia.. The results of the survey made us quickly realise that more awareness is needed on this topic.
In order to combat this, we started off by making leaflets that we spread around our schools. The leaflets included information such as: symptoms, diagnosis and treatment of pre-eclampsia. To reach a wider audience, we recorded a podcast mini-series. This proved to be an effective and easily-accessible method of communication. We recorded episodes with Dr Andrew Shennan who is a professor and consultant of obstetrics at King's College London, and he works closely with APEC, which is the UKs leading preeclampsia charity. We also interviewed our head teacher Mrs Brown, who has previously had pre-eclampsia, about her experience and how it affected her.
We also designed an app which provides on-hand information about pre-eclampsia for those who are keen to learn more. The app consists of details about our project, the disease and different methods in which people can learn more about it.
In addition to this, we provided a cost model and entrepreneurship strategy which analysed how we could clinically implement our project into the real world.
Throughout human practices, we have contacted numerous other teams that are taking part in the project as well. This includes King’s College London and Moscow. We also were in contact with different professors, charities and people from the iGEM ethics committee. All of these interactions helped shape our project by making sure that we followed all ethical and social guidelines, whilst effectively spreading awareness.
Learn More
To learn more about these aspects of project RIBOTOX, as well as our hardware, software, modelling and more, visit the pages below.
Refrences
- Human Practices
- nhs.uk. (2021). Pre-eclampsia - Symptoms [Online]. Available at: https://www.nhs.uk/conditions/pre-eclampsia/symptoms [Accessed 19 October 2021].
- David P. Bartel (2018). Metazoan MicroRNAs [Online]. Available at: https://doi.org/10.1016%2Fj.cell.2018.03.006 [Accessed 19 October 2021]
- Condrat, C.E. et al., 2020. miRNAs as Biomarkers in Disease: Latest Findings Regarding Their Role in Diagnosis and Prognosis. Cells, 9(2), p.276. Available at: http://dx.doi.org/10.3390/cells9020276. [Accessed 19 October 2021]
- Reza M. A. N., Kolsoum S. et al., 2019. Quantification of circulating miR-517c-3p and miR-210-3p levels in preeclampsia. Pregnancy Hypertension, Volume 16, 2019, Pages 75-78, ISSN 2210-7789. Available at: https://doi.org/10.1016/j.preghy.2019.03.004 [Accessed 19 October 2021]