From genes to enhancers and everything in between – PhD defense Anna-Karina Felder

Our DNA is like a code instructing our cells what to do. Genes are pieces of this code that contain the information for making proteins. Proteins have many functions in our cells, ranging from breaking down nutrients to transmitting messages. Different cells have different needs when it comes to protein production. A muscle cells requires other proteins than a brain cell, and a cell in an embryo has other needs than an adult cell. This means that the activity of genes needs to be precisely regulated in each of our cells. Cells can do this in different ways, one of which is through enhancers. These too are parts of our DNA code, but instead of coding for proteins themselves, they control the activity of genes like a genetic remote control.

Changing the distance

Enhancers do not need to be next to the gene they control. Sometimes they are very far apart, with long stretches of DNA in between. In order to activate the gene, the DNA strand then folds for the enhancer and gene to make contact. “This led us to wonder,” Anna says, “what would happen if you reduce the distance between an enhancer and a gene along the DNA strand itself.”

To test this, Anna and her colleagues developed a method called delete-to-recruit (Del2Rec), which removes a piece of DNA that normally lies between an enhancer and its target gene. They used the CRISPR/Cas9 technique, often referred to as ‘molecular scissors’, to very precisely cut out this piece of DNA. “By bringing enhancers and their target genes closer together, we were able to reactivate genes that are normally only active during embryonic development,” Anna explains. “This shows that the distance alone can influence whether the enhancer works.”

Future gene therapies

Although Anna demonstrated that this principle works for several different genes, her main focus was on the globin gene. This contains the information for making hemoglobin, the protein that carries oxygen in our red blood cells. Humans have different versions of the globin gene: the fetal version that is active during embryonic development, and the adult version that is activated after birth.

In sickle cell disease and beta-thalassemia, two genetic blood diseases, the adult globin gene is broken, which leads to serious symptoms. Anna and her colleagues investigated whether they could reactive the fetal globin gene to take over the function of the adult one. “We used the Del2Rec method to bring the fetal globin gene closer to its enhancer. This successfully led to activation of the fetal gene in red blood cells,” Anna explains. Del2Rec could thus offer a new approach to gene therapy. “While this is still in the early stages, it is an exciting step forward,” Anna says.

Rollercoaster

Looking back on her PhD, Anna sees many highlights. Being part of a Marie Curie doctoral network was definitely one. “It allowed me to take part in international trainings and connect with other PhD students from across Europe,” she says. “Another great experience was collaborating with Sanquin and a group from Erasmus MC — it was inspiring to work together across institutes.” She also has fond memories of the atmosphere in the lab and the social activities. Many colleagues became her friends. “And honestly, I really enjoy cell culture, even when the cells didn’t always behave! It’s such a nice space to connect with people on the floor and have those deep life discussions while feeding the cells,” Anna laughs.

Both the start and end of her PhD were challenging at times. Starting her PhD during the COVID pandemic, Anna initially struggled to build connections and settle in. And towards the end, her group leader Wouter de Laat moved to the UMC Utrecht. “This meant our lab was closing down and I was the last one standing. I’m very grateful that the Sonnen lab adopted me. It really helped me find the motivation for that final sprint,” she says. “Looking back, I can see how much I’ve grown, not only as a scientist but also personally.” To PhD students who just started, she says: “It’s a rollercoaster, embrace it! There will be highs and lows, but both are part of the journey and make it worthwhile.”