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iGEM Competition and the University of Patras team: AI in sync with Pharmacogenomics

With this article I thought about starting a series of three articles that will present in a Q&A style-form the three Greek teams that participated at last year’s iGEM competition and won medals for their participation and project idea. For you that may not know, the  International Genetically Engineered Machine (iGEM) competition takes part in Boston, Massachusetts and is a worldwide synthetic biology competition that was firstly aimed at undergraduate students, but since its beginning it has expanded to other demographics.

In this first piece of the series I had the chance to ask some questions the team from the University of Patras, Greece. Their project “Hippocrates” has won the silver medal 🥈and has to do with pharmacogenomics, a scientific discipline that is believed to change healthcare and create ripples of positivity in the medical and clinical community. I can easily say, without hesitation, that the combination of Artificial Intelligence ( A.I ) and pharmacogenomics, will revolutionize personalized medicine. The “Hippocrates” project – among others – could set the stepping stones of inspiration and innovation that its needed in order to create the much desired change in the healthcare sector.

Without further ado…here is our Q&A that I hope you like as much as I did😊:

  • What was the exact purpose of the project “Hippocrates”?

The project “Hippocrates” aims for the easy and accurate determination of the required statins dose, a drug category which is administered to patients who suffer from cardiovascular diseases, that comprise the first death cause in the developed countries. More precisely, the team developed a portable molecular biology diagnostic laboratory and by combining Pharmacogenomics with Artificial Intelligence ( A.I ), it created a web-based application. This aims to subserve the doctors by creating a personalized dosing scheme for each patient, taking into consideration accordingly their respective genetic background.

  • What were the motives that pushed you towards choosing this project?

Pharmacogenomics is a relatively new scientific field that brings together the science of pharmaceutics with that of genetics. Contrary to other such university departments of the country, the Pharmacy Department itself of the University of Patras has an individual course devoted completely to pharmacogenomics. Through this course, therefore, we came first time in contact with something that seemed to be from the far-future but at the same time not inapplicable, as is the usage of patients’ genetic background for achieving personalized medicine. The cardiovascular diseases constitute the first cause of death and statins are the most abundant administered drugs used for their treatment, events that explain the development necessity of such a project.

  • What kind of difficulties did you encounter during the whole duration of the project and how did you deal with those as a team?

During those 15 months that our collective effort lasted there were certainly moments that we faced quite a few difficulties, mainly because we were the first team from Patras that participated to this particular contest and there was no one to guide us through the process. Unfortunately, due to the pandemic our journey till the Giant Jamboree was not as smooth as we expected when we first started our effort, approximately a year ago. From March and onwards we were living in a state of agony and of constant effort to keep pace with the deadlines that were defined by the organizing committee of the competition, which itself was trying to sync with the developing situation taking place in the COVID-19 front. The communication difficulty between the two sub-teams that were working either at the biological or the computational part of the project accordingly due to the different educational background of each one was a very big challenge for the team. Nonetheless, we managed to overcome all the challenges and stay united in order to achieve our common goal. With the appropriate guidance from our team’s coordinator and the division of tasks  between us, we managed to get over any obstacle coming our way and in the end to get the result we wanted.  

  • Who are the ones that played a pivotal role as your mentors and what do you admire in them?

A team to be successful in a competition, apart from efficient communication and cooperation, needs to have suitable and experienced mentors. This role in the iGEM Patras  2020 team was overtaken by Stavroula Siamoglou, Yannis Daramouskas and Charalampos Papakonstantinou. More precisely, Stavroula Siamoglou, who is a PhD candidate at the Department of Pharmacy at the University of Patras, was the coordinator of the lab team and with her knowledge coming from a multi-year involvement in research projects helped us into successfully conducting our laboratory experiments and to resolve any occurring issues that were arising. Yannis Daramouskas, a PhD candidate at the Department of Mechanical Engineering and Aeronautics at the University of Patras, guided the team through the artificial intelligence algorithm development and contributed significantly to the success of this system. Finally, Charalampos Papakonstantinou, equally a PhD candidate at the Department of Mechanical Engineering and Aeronautics at the University of Patras, counselled and supported the team during the development of the web-based application. We admire all three of them for their passion and interest for science, their perseverance and patience, as well as their values. More important for us is the fact that they believed in our team right from the beginning and till the end they were willing to assist us wherever and however it was needed.

  • What would be the ideal future of pharmacogenomics and could Greece play a pivotal role with its scientific workforce ?

The science of pharmacogenomics explains the reason why between two patients, who receive the same dosage, the drug could prove therapeutic for the first one while for the second patient it may be utterly toxic. The application of it in clinical practice could undoubtedly solve all those problems that occur due to adverse drug reactions. In Greece, the last couple of years, pharmacogenomics is successfully developing and evolving in the research realm. Nevertheless, the integration of it has not yet been accomplished as the medical community is not suitably specialized in the techniques which are being employed for such a genetic analysis. Undoubtedly, in Greece the workforce exists and can play an important part to the development of pharmacogenomics, as specifically in the Department of Pharmacy at the University of Patras there is a lab and a special course in the general courseware which is related to pharmacogenomics, offering the necessary knowledge for its further developability. Also, the combination of pharmacogenomics with programmatic algorithmic methods, such as artificial intelligence, can prove itself powerful for the evolvement of this scientific area.

  • Artificial Intelligence has been employed from you in combination with Molecular Biology. The BentoLab – AI system which has been developed by you, do you believe that it could be adopted by smaller and with less funding labs?

The BentoLab – AI system is a genetic analysis toolkit that gives the chance to each doctor to plan the patient’s dosing scheme, taking into consideration their respective genetic background. Its usage could be wide from labs that are much smaller in size and with less funding as the projected cost of performing genetic analysis with BentoLab is significantly smaller from a genetic analysis in a lab that uses conventional methods. On top of that, this mobile molecular biology lab can be transferred even in the most remoted areas that have less facilities and miniscule funding with an aim to support each individual clinical entity and its respective patients.

  • A creation of a global database that will hold our personal medical records, with an aim to receive personalized medical treatment in every part of the world that we may be located, is something that should be created. What are the benefits and salient points of such an endeavour, and which are liable to criticism on the grounds of bioethics?

In our days, pharmacogenomics is being developed more and more. Without doubt, the collection of patients’ records in a global database and the creation of everyone’s genetic profile, could be helpful by integrating pharmacogenomics into medical treatment. With this way every doctor will easily have access to the genetic profile of each patient, only when the patient gives formal consent, and can decide for the personalized treatment without the need to conduct any further analysis or examination. A venture like this is a given that it will follow the general data protection regulation and only each individual will be able to control who has control in their genetic profile, in order that data breaching will be avoided.

  • The discovery of the right medicine, for the right patient ( personalized medicine ), to the right dosage, how close in time do you think it can happen in big scale, and what is needed for this to be achieved?

Personalized medicine is gaining more and more ground the last few years in the medical space. During the application of it, there is no drug discovery happening, but investigation of genes that metabolize particular drugs. According to the genetic background of each patient, the rate at which that person can metabolize a drug can be faster or slower from the one we regard as a regular metabolic rate of a drug. Therefore, in the first occasion a dosage increase is needed as the drug does not stay within one’s organism for the required time span, while in the second occasion it is necessary to decrease the dosage as accumulation of the drug within the organism is observed, being the result of patient’s slow metabolic rate, thus leading to toxic effects. Hence, while pharmacogenomics has been scientifically developed, it is not yet applied in a very big scale but in certain only circumstances, mainly because of it high cost.

  • Finally, are you satisfied with the silver medal and what are your aspirations for the future?

The competition was undoubtedly an unprecedented experience for all of us. It is not a common event to have a team from Patras to compete with research teams coming from prestigious universities from abroad like Stanford or MIT. Nevertheless, we managed to discover relatively early in what we were good and so capitalize on these skills for the purpose of having a go towards competing with the other teams. With cooperation, perseverance, and lots of appetite for work we managed to receive the silver medal. This is just the beginning for our team, as we have decided to participate in the iGEM 2021 competition with an aim to win this time the gold medal!

What is your opinion about pharmacogenomics? Do you have any insights that you would like to share with me?

If so, I am really looking forward to hear your opinions about the Q&A and the expectations you have from pharmacogenomics in the not so far future!

Drop me an email, I will be happy to discuss!