Epigenetic regulation of Transposable Elements in human brain development and disease

What have you been working on during your time as a Ph.D. student? 

“Over time, my research has evolved. In the beginning, my focus was on epigenetics. Now, I would say the main focus extends past the scope of “just” epigenetics and takes into consideration different approaches that show how transposable elements (TEs) and their activity can influence human brain development, as well as neurodevelopmental and neurodegenerative diseases. 

About half of our DNA consists of transposable elements. For a long time, they were dismissed as ‘junk DNA,’ but we now know they play roles in evolution and development. At the same time, increased TE activity has already been linked to disease, inflammation, and aging. For example, their dysregulation has been observed in diseases like Alzheimer’s and Parkinson’s Disease, to name those more widely known, but the mechanisms are still not well understood. This makes them both challenging and exciting to study. 

In many ways, TEs are still a black box. Even protein-coding genes, which make up only about 2% of our DNA, are far from fully understood. There is still so much to learn. 

What we do know is that TEs are controlled, as much as they can be, through what are known as epigenetic repressors. In Epigenetics and Chromatin Dynamics research group, led by my PhD supervisor Chris Douse, we are interested in what happens when those repressors fail. On the other hand, I was lucky to also be a part of the Molecular Neurogenetics lab, co-supervised by Johan Jakobsson. There I got so much knowledge about TE mechanisms and how they contribute to a wide array of transcriptomic complexity, from neurodevelopment to neural disorders. Together this was the perfect match for me to really appreciate the full picture.  

To study this, we silence or mutate specific epigenetic repressors and looked at the consequences. I looked at the epigenetic changes using a multi-omics approach, including long-read RNA sequencing, which is very useful for studying repetitive elements like TEs, due to their repetitive nature. 

Later, we also modelled disease-associated mutations found in patients with neurodevelopmental disorders. We used three model systems: neural progenitor cells, induced pluripotent stem cells, and unguided cerebral organoids. The organoids allowed us to study brain development in a 3D context that more closely resembles what happens in the human brain during development."

Were you always interested science? 

“Yes actually. Many people in my family work in the medical field. My grandmother and aunt were nurses, and one of my uncles is a surgeon. I've been very much influenced by them, and have always been interested in the medical sciences, or just in general, about how the human body works and biology. These are people that I've really looked up to for a big part of my life and still do. When I thought about my future when I was younger, it was always either medicine or biology 

My older brother attended a school that sent many students abroad, and I followed a similar path. I moved to Germany for my bachelor’s degree in biochemistry and cell biology. At the time, I became really interested in molecular mechanisms and development. I felt a genuine passion for understanding how things work at a fundamental level. 

At the same time, I knew that if I hadn’t chosen biology, I probably would have studied computer science. So when I discovered bioinformatics which just happened to be the perfect mix between data analysis and biology, I knew that was what I wanted to do next.” 

How did you end up with us here in Lund? 

“I’m from North Macedonia. I moved abroad when I was 18, which felt like a leap of faith, but honestly, it was one of the best decisions I’ve ever made.  

While I was studying in Germany, I heard about the bioinformatics master’s programme at Lund University. A friend of mine had started the programme a year earlier and spoke very highly of it. What appealed to me was that students came from both biology and computer science backgrounds, and the programme was designed in such a way that you would get basic knowledge of both subject areas. You start fresh in some ways, but you also build on what you already know while learning a lot from people with very different skill sets. 

During my master’s thesis, I worked in Johan Jakobsson’s lab under Chris Douse. When Chris later started his own group here in Lund, I was lucky enough that he offered me a PhD position. I had to think about it a little, but I knew I wanted to continue in academia, I felt like there was still so much I wanted to learn, so I decided to continue with the PhD and join his team.” 

Can you tell us more about your thesis cover? 

“One of the things that my parents instilled in me is a love for movies and the cinema in general. I've been a cinephile for as long as I can remember. One of my favorite trilogies is Lord of the Rings, I think I saw the first one when I was like five or six and still have very clear memories from when I watched it the first time.  

I wanted to highlight that this has very much been a group effort rather than one person doing this on their own. So, I decided to incorporate Lord of the Rings into my cover artwork. 

Here, we have the Fellowship, representing everyone that has helped me along the way, who are going on a journey together. You can see that they are walking on a path of nucleosomes, which are very important when you are studying chromatin, and the path is decorated with H3K9 and H3K4 trimethylation. 

Together, they are walking through a forest of unknowns which represents the TEs and how much there still is to learn about them. The Fellowship very bravely goes through the woods and starts climbing towards the Tower of Mordor, which here represents the culminating effort of the fellowship. As you go further up the tower, you can see that the colors go from darker to lighter shades. This is because the Fellowship are shedding light on the final goal, which is learning more about the human brain.   

I have to give a big thank you to Sylvie on our team who drew this image by hand. At the top you see the northern lights. I had just thought to have a light shining down on the brain, to represent them shedding light, but Sylvie was very creative and drew in the northern lights. They represent my journey here in Sweden.” 

What have you enjoyed most about your PhD? 

“I would say first and foremost, the group of people that I was surrounded with both in and outside of the lab. Many of the people that I work with have become my closest friends. It's very interesting, I've always wanted people around me that are going through the same experiences. During the PhD, I think that's been necessary. 

 It is a challenging time, to be focused on the same goal for four years and needing to be in high performance mode most of the time. It's been nice to have people that are going through the same thing. To help relieve some of the pressure and stress, and you grow closer together, which is very nice.  

I’ve also really enjoyed being surrounded by high-calibre scientists and people that can talk about science and explain it in a way that shows that they have a passion and a drive for it. It really is a one-of-a-kind opportunity which I am very happy to have had.   

Lastly, and maybe this is a bit surprising, but I found writing my thesis was very enjoyable. Don't get me wrong, it was stressful, but it was really nice to see how all your efforts over the past four years lead towards something. During the process, you are hyper focused on the details of these projects and trying to make sure that everything checks out. You go from this project, to the next one. You don’t often step back to look at the big picture. But once I started writing my thesis, I could really appreciate that moment when you see how the red thread connects all your projects. I didn't think I would enjoy it that much, but I did.” 

What did you find most challenging? 

“The fact that you're supposed to be focused on the same goal for four years is quite challenging. I mean, bachelor's and master's programmes are also like quite long, but they are divided into specific years, specific classes, projects, courses that you take and so on. The PhD is not like that. It is a constant upgrading and learning new things, while also constantly going back, explore something new, and then get back on track. I think that was the most challenging for me.  

Also, going directly from a master's programme to a PhD. During the PhD there is much more emphasis on being in charge of your own time. This can be a little bit challenging in the beginning because you go from being given a structure to follow to having to make one for yourself. With that comes prioritization, like what is the most important thing to do from all these things you have to get done. 

With that said, it was nice to have the supervisors that I did. I was quite open with them about this, and they were also helpful. When I asked them for their input as to what the current priority was, they would help me structure my work in a way that was helpful for them, for myself, and for the projects.   

Overall, I think keeping on goal, structuring your own time, and being responsible were the most challenging aspects. You are given much more responsibility transitioning from being a master's student to a PhD student in the lab, which is very understandable, but it's also a hurdle that you have to get used to it over time.” 

What’s next after the defense? 

“During my halftime, I was sure that I would be making the switch to go into industry. Then after I was done with my halftime, one of my opponents advised me to not close the door on academia yet.  

It was nice to hear that from someone in academia, and from outside my lab. Because as a PhD student you do not always feel like you belong in academia, the imposter syndrome can be quite strong, or at least it was with me.  

Since then, I have found a lot of details of my job that I realised that I really enjoy. For example, when it comes to scientific discussion and outreach, scientific writing, exploration of topics that are always novel. I learned to appreciate these sub tasks of my job, and now I’ve switched back a little bit. Now I am a postdoctoral researcher in the lab of Molecular Neurogenetics, where I continue to study the developing human brain and human neural disorders.

I think previously, I saw that continuing in academia as a much bigger challenge than going to the industry. Not saying that the industry is easy, but for me it always seemed like more of a challenge. But just because it's challenging doesn't mean it's bad. I learned this when I started doing bioinformatics, where if you challenge yourself with something new and something intimidating, at the end, you grow so much more as a person.” 

Any advice to current or future PhD students? 

“I was told in the beginning, that this is not a sprint, it's a marathon. I think that is important to keep by your side. Having a burnout is quite a common thing among PhD students. So, my advice is to learn to keep your strength, and make sure you recover whenever you can. If you take a little bit of a break, when you come back, you will be reinvigorated to continue with your science.  

The second thing is, I think the more you learn, the more you understand that there is so much more knowledge out there. I think it might have been Chris that said this to me, but when you are doing your bachelor's, at the end, you think that you know everything. Then at the end of your master's, you kind of understand things, so you think you are a specialist in a field. Then, when you are done with your PhD, you understand that you do not know anything. That really resonated with me. 

Another thing, that I learned during the Professional Development Program, is that your work is not who you are as a person. It is very easy to get lost in that a little with unsuccessful experiments or making a mistake. But all of that is normal in science, there are mistakes and we learn from mistakes. It is very important not to only associate yourself with the work that you do though. Using myself as an example, you have the professional Nino, but then you also have Nino the friend, Nino the partner, Nino the son, the brother, and so on. There are so many more aspects of everyone, you should not just attach yourself to one specific thing and let that be the final value of who you are. 

Then, my last piece of advice is to just enjoy. Four years sounds very long, but honestly, I feel like I started two weeks ago. Time passes very quickly when you’re having fun!”