Kalliopi Trachana, PhD

Interns Kalea, Maria, and Zainab in this in depth interview with Dr.Trachana, Technical Program Manager in Clinical Genomics in the Hood-Price Lab at ISB, discuss her journey, hopes for the future, and helpful advice for navigating the STEM field:

What was your journey to becoming a Technical Program Manager in Clinical Genomics and what inspired you to pursue this job as a career? 

So let me explain my background. First of all, I have a PhD in bioinformatics that I completed at the University of Heidelberg in Germany, and when I initially started at ISB I was a research scientist working for Dr. Lee Hood was a completely new technology at that time- single cell and stem cells. At the time I came here at ISB, and where I think a lot of my journey started was the start of merging new technologies (single cell, genomics, analytics, gene and cell therapies) into the clinics. During my progression, I could see the interesting outcome that comes from combining the academic, cutting edge thinking with the process of the industry. I then decided I would like to take a path where I can do mostly innovative projects bringing knowledge from industry partners, health system partners, but also ISB. The transition happened naturally. Once we got affiliated with a huge health system in the USA (operates in seven states), we started thinking how, for instance, we can bring genomics (probably the most mature genome sequence technology and interpretation in the clinic) to help physicians and patients improve their health. This is, more or less, how the role and the title emerged. My role is to think about strategic initiatives, how we can bring the ‘know-how’ that ISB has to analyze large, new data sets into the clinical or industry settings where other research times are thinking about those problems.

Throughout your career, you have released many publications, what is your favorite research work you’ve done so far and why? 

This is an interesting question because you can publish something that not a lot of people want to read but you have such fun doing and producing the research. There are other papers, for instance, my publications with a world recognized source called ‘ECNOG’, the go-to database when it comes to compiled genomics, with over a thousand genomes. When I was back in Heidelberg, my team and I created this source for the whole world web community. So, in terms of how you build a database, it can be very tedious, repetitive, and not a lot of innovation; but at the end of the day, it can impact the field. For me personally, I gained so many citations because people are using the resource constantly. On the other hand, I have a research paper I worked on with Sui Huang’s group, here at ISB, that is about how stem cells make the decision to differentiate within a cell’s time. Those papers, at the time we published them, was such a new idea and many people in the field were not able to understand how complex this system’s theory (used mostly for theoretical physicists and mathematicians) can apply to biology. It was something new and something that definitely helped me start thinking very differently about how physics and philosophy can have a role in a biological problem

You mentioned combining interdisciplinary approaches with physics and philosophy into biology research – how exactly did you incorporate this into your work?

Essentially, we were a team of very diverse backgrounds (physicists, biologists, computer scientists) thinking about how single cell technology and stem cells have important systems. I think that the revolutionary idea came from Sui Huang, who interacted with physicists, mathematicians, and philosophers over his career. He knew something we call ‘tractor systems’: a behavior of complex adaptive systems. Here we are able to learn about the ‘properties’ of biological systems, not in a mechanistic model way, but rather how the network interacts and how each factor has a role. Once you tap into a network of people who are thinking so differently about a single problem, you are able to learn a lot from them and start building your own ideas about how theory and other sciences are coming together with biology.

What is an ugly truth of your research/job and what are some ways to navigate it?

There are always challenges coming from very simple communication. For example, maybe you have an idea that the scientific community will not accept. Or, it contradicts what most people believe today. So how, for instance, you will take a complex idea that is not accepted and communicate to your colleagues, and convince them to perform experiments. But even later on when you’re completing a paper, the reviewers and scientific community are all very important communication challenges that will likely happen. Of course we are writing a lot of papers, but I feel that we don’t have good training on how to take something complex and break it down into very simple items and components that we can communicate. The other one is that there are constantly new tools, but not really any standards. I will take my tool-bioinformatics- even to do the genomic analyses, there are so many different tools you can use, but even today we have standards on next generation genome sequencing and genomics in particular. It took decades for people to organize the community around these standards and make sure that everyone accepts them and make the data usable for interpretation. This is the way we are doing science. And it’s a good way because on one hand you allow everyone to innovate, but at the same time because everyone is innovating and wants to have it their own way, it is very hard to compare work between different labs and come to common conclusions. Some examples of this include electronic health records and COVID-19. I could go on and on about challenges, but I think for me communication is number one. And the second is how to maximize the value from the data and money we spend by standardizing procedures and creating resources that everyone in the community can use, and help the reproducibility of research

Where do you hope to see the field of human physiology going in the future?

I hope to see fundamental changes in gene editing and CRISPR and how we treat rare diseases and cancer (t cells, cell therapies). These need genomic, physiological, and clinical information. There are so many different levels of information that need to come together. On the other hand, other types of technologies (ex: surgery’s digitalization) help us understand physiology and treat a disease. Fundamentally, if we are successful, we will be creating interventions in gene and cell therapies. This will happen to medicine in the next few decades.

Interns Kalea (upper left hand corner), Maria (upper right hand corner), and Zainab (lower right hand corner), with Dr. Trachana (lower left hand corner).

I know you care to advocate for women in STEM and build awareness of systems biology and P4 medicine. Can you explain what you saw in the scientific community throughout your career that motivated/motivates your advocacy for change?

I love science. I think that you’re not deciding to get a PhD if you don’t think that science and technology can fundamentally change our lives. For me, STEM education is important not only to grow new talent that will understand and will innovate/develop the next frontiers of science and technology, but I think more importantly education needs to come from critical thinking. I feel this is very important and sometimes gets lost in academia – it’s very often in academia you see we are doing research for research. We try to deepen our understanding only for the good of human knowledge without necessarily having an application. This can be good; for instance, referring to CRISPR, we would not be able to do gene editing today if someone hadn’t spent decades understanding the genomics of bacteria and an understanding of the physiology of the whole mechanism. So, basic science is good and we need to do basic science but at the same time I feel there is a big gap between the academic side and the industry side of science. Perhaps we could create a pathway and see how the new knowledge we create will be applied. This gap is important in STEM education; ideally, we don’t only need people who understand the technology (e.g. AI), but also people who think about things like ethics, economics, etc (critical thinking). Try to solve a problem thinking about all the different aspects such as the environment, society, etc and not just science, industry, and profit. I hope to see more STEM professionals start building critical thinking about their everyday, environmental, and social lives.

What advice would you give to anyone who may be hoping to pursue a career in healthcare or the STEM field, but think it’s impossible due to their socioeconomic background, sex, ethnicity, etc.?

This is interesting in that if you think about it, we have a large number of immigrants from India and China in the US today because they have STEM education and there are not enough Americans to do these jobs. I was reading somewhere that probably in the next couple of years there will be another half a million of STEM-related jobs and there is not enough supply here in the US, which means that in one way or another, you need to start hiring talent from elsewhere. But I have to say, I have lived in other countries aside from my mother country [that is Greece] — I have lived in France and Germany, and now here in the US for most of the time– I have to say that one of the things I like about the US is that you have opportunity. You have opportunities even as an immigrant to pursue what you want to pursue; not that there aren’t regulatory issues that can box you, but I feel it is easy for people to see the value that you bring and try to promote you. I think honestly I didn’t have as big a problem as an immigrant than I did as a woman. You see, I feel that the gender here is more important than if I am coming from Greece or not. And the reason that I’m saying this is that despite all the great progress we have made about accepting females in STEM, I think the biggest problem is not about educating more female students or having more females getting their PhDs. In fact, I think we are equally successful. I think it’s about how you will go from early to senior career and beyond.

Can you explain why you think it’s important to decentralize Precision Medicine moving towards the future?

Yeah, absolutely. So decentralization is going back to the topic we were talking about. It’s related to making research and care more equitable. For instance, today we know that the majority of people enrolled in clinical trials will be through academic medical centers, so we are talking about people in urban environments who have access to these medical centers, and mostly Caucasian people. So, if you manage to decentralize your operations and outreach in the community (and especially rural community), you will be able to close the gap that exists between clinical trials and diversity. There are actually staggering numbers; for African Americans, 13% of the population, they are only <1% of the population in clinical trials. And that’s the whole idea, let me say something extremely important: let’s go back to the case of a new type of medicine we see coming like gene and cell therapies. For those therapies, you create a personalized treatment. Let’s take the case of the chromatid immunotherapy we see. They will take the bone marrow, they will take your immune cells, they will engineer and do whatever mutation they want to introduce and then throw them back to your body. This means as you’re doing this, this is part of a clinical trial. Imagine how big the gap is if you’re not in a place where they know how to do something like this, or you are not able to access this process simply because you’re in a rural environment. So, figuring out how we will start with simpler trials, how we are going to do the engagement of those communities, how we are going to build the operations to serve those communities, and eventually transition to more advanced therapeutics that we want to see is such a good way to utilize what I know today. I feel very passionate about this

Can you explain some of your current research projects?

I am working very closely with the health data science team at ISB which is led by Andrew Magis, and we built a platform that essentially allows patients to be educated about clinical studies we are doing and consent and organize how their samples are going to be collected without the need for them to come in. So, they can do everything digitally from where they are. To give you one of the examples of where we have used the platform, there is a population genomics project that we are doing with Providence and the whole idea is that we are going to collect blood samples from 5,000 people across 7 states where the system has physicians. We have the need for our audience and potential participants to educate them about genome sequencing and about the program and what are the steps for them to participate (from consent, to giving a sample, to receiving a sample, to receiving back results, to talking to their physicians if it is necessary). So we educate them, we enroll them, we organize their sample collection and if, for instance, we identify that they have a mutation that predisposes them to cancer or some other disease, we make sure that their physician will be notified, they will get genetic counseling, they will get informed, and maybe even have a personalized prevention plan to make sure we catch a potential transition due to cancer or heart disease or neurological diseases. Imagine that right now we can do this in 3-4 different states without even hiring people to do this, which is wonderful. This also needs to project both our values and health system values. We believe that not only does a patient need to be educated but there needs to be transparency and they need to understand what are the risks for their privacy and how we are going to use their information. This allows them to understand how people want to use their genomic information [and go one step further to allow them to think about protecting their privacy].

Any advice to leave off on?

I’d say, every time you start a new project, guide and become experts on the subject. Always try to deepen your knowledge, become an informative person in this field. I very often feel that science is offering so much but we sometimes miss the bigger picture and what other people are doing. So always have an idea of what other labs (if they operate in the same space) are doing and publishing. It is very important to think about how your research fits into the ‘bigger picture’ and community (back to what I was saying about communication).

Number one- become experts and know the field very well.

Number two- just because you are women, do not be afraid to participate in IT.

Kalliopi Trachana, PhD

When I mean ‘IT,’ I mean data, cloud, writing python, learning code, and everything else that has to do with computer science. This helps us understand data architecture and how data connects to different organizations. Do not think this is something that only males can do, women can not only do it, but can excel and be very good at it. Do not be afraid of computers! I believe this is very important. For good or bad, this is a digital world, a lot of value comes from data analyses. So learn computer science and be experts in your fields. Lastly, be fulfilled. If there are things that you do not like, raise your concerns and do not be afraid of that. Make an environment for yourself where you can thrive. Make an environment where you will be trusted to pursue your ideas and interests.

Link to ISB Profile: Kalliopi Trachana, PhD | The Hood-Price Lab for Systems Biomedicine (isbscience.org)