Thesis defense Marloes Blotenburg: Profiling epigenetic modifications and lineage specifications using single-cell multi-omics

Development of an embryo starts with one single cell, a fertilized egg. This cell begins to divide and continues to divide to eventually form a complete organism composed of numerous different cell types like neurons, liver and muscle cells. All these cells originate from the same single cell and therefore share the same DNA code, yet they differ greatly in form and function. This raises the question how a single cell decides its fate during embryonic development.

Epigenetic modifications

In her PhD project, Blotenburg addressed this question by looking into the role of epigenetic modifications. “Epigenetic modifications are marks placed on top of the DNA that can determine whether a chunk of DNA is used or not, without altering the genetic code,” she explains. By turning on and off various regions of the genetic code, epigenetic modifications play an important role in the formation of different cell types during development. “During neuron development for instance, activating epigenetic modifications are placed on the pieces of DNA that are necessary to form a neuron. Inhibitory marks are placed on all parts of the genetic code that are necessary to form other cell types and therefore need to be switched off.”

A new method

To further dissect the role of epigenetic modifications in cell fate decision-making, Blotenburg developed a new method called TChIC. “This technique allows simultaneous measurements of the epigenetic modifications and which parts of the DNA are turned on and off, in one single cell”. She applied this technique to gastruloids, an embryo-like structure that is grown in the lab from stem cells. “In this model, you start with a number of cells that can form any type of cell of the embryo. You place them together in a dish so they form a ball of cells. And over a few days, they continue to divide and choose different cell fates. Where one cell can decide to form a heart cell, another cell can decide to form a gut cell or a neuron”. Blotenburg managed to measure where epigenetic modifications are placed in the genetic code during development. “Thanks to this study, along with all of the other research out there, we can hopefully start understanding what is truly happening during development and how cells actually differentiate into the specific cell types they need to make.”

PhD experience

Looking back on her PhD, the first thing that comes to her mind are the group meetings when she just started. “I remember the fact that I was sitting there and not understanding half of what was said. And then I thought: this is a good place for me, because here I can learn.” Overall Blotenburg experienced her PhD trajectory as having quite some ups and downs. “Still, I am quite happy with the way that I was able to finish everything.” A true highlight for Blotenburg were the people. “I could always approach anyone in the lab for help and they were always open. By just walking into an office, we ended up having a scientific discussion, which gives you new ideas about how to move forward when you are stuck with something.”

Freedom; a possibility and a challenge

“In your PhD there is a lot of freedom. This is very nice when everything goes perfectly fine, because it gives you a lot of opportunities. The downside of that freedom, on the other hand, is that you need to be very independent. Sometimes this means withdrawing yourself from a project if things are not working”. Blotenburg remembers that this can be very challenging. “Looking back, I already kind of knew about a project that it did not work, but I was too focused on the details and too deeply invested to realize this. I was going in circles for a long time and wasted a lot of time. In the end, I needed someone else to tell me to try something else.”

Science and people

With this experience, Blotenburg advises current PhD students to spread the risk by having multiple projects. “If one project is not working, you still have the other ones,” she says. Blotenburg also stresses the importance of finding someone who can pull you out if needed. “Surround yourself with people that can give you the advice you need, not necessarily the advice you want to hear,” she says. And are you a student and still unsure whether you want to do a PhD? She advises to interview in many places, both inside and outside science. “If you give yourself the opportunity to apply for five or ten places, you will start seeing the differences. Only then will you start discovering what you prefer. Maybe this one lab is studying the topic you really like, but the way they go about it does not suit you. You will only realize this if you see an alternative. A PhD is not just about science, but also about the people you surround yourself with and about how the lab works.”