The DNA repair analyst
In order for the human immune system to effectively fight off pathogens, B cells need to smash up and reassemble their own DNA. Michela Di Virgilio searches for factors controlling this important process, which also have crucial implications for our predisposition to cancer.
The whiteboards in Dr. Michela Di Virgilio’s office never stay white for long. They are constantly overrun with structural formulas of molecules, arrows and abbreviations: IgG1+, CSR, DSBs, 53BP1. On the “collaboration board” behind her desk, she recently explained antibody diversification to a mathematician so they could jointly develop models for it. On another board, she keeps track of upcoming publications. “We plan all the experiments on it and discuss them as a team,” Di Virgilio says. She speaks English quickly with an Italian accent and an information density that could fill several whiteboards in just a few minutes.
Michela Di Virgilio is a molecular biologist and cancer researcher. At the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), she heads the junior research group “Genome Diversification & Integrity.” With her team of ten, she investigates how B lymphocytes, also known as B cells, ramp up the immune defense, and which molecular processes help them modify their DNA so effective antibodies can be created.
When pathogens enter the body and meet B cells, the cells begin to multiply and produce a special enzyme called activation-induced cytidine deaminase (AID). This enzyme edits nucleotides, much like changing words in a sentence, by making substitutions in the part of the antibody genetic blueprint coding for the receptor that recognizes the pathogen. This enables B cells to produces antibodies that exactly match the pathogen – thereby rendering it harmless.
A risky maneuver
The AID enzyme also initiates a second important process that leads to B cells producing a different class of antibodies to broaden the immune response. For this class switch recombination (or CSR), it is again necessary to change the genetic information of B cells. Both DNA strands need to be broken and reassembled – a very risky process. If something goes wrong during the formation or repair of these DNA double-strand breaks, for example, the DNA is cut in the wrong place or assembled incorrectly, tumors can arise.
“Any abnormalities can have catastrophic consequences in our lives,” Di Virgilio says. But in most cases, the finely tuned control of DNA repair enable the immune system to keep a variety of pathogens at bay. “I’ve always found the idea that evolution allows us to benefit from such a daunting mechanism fascinating,” Di Virgilio says. She hopes to further examine the molecular processes by which B cells manage to maintain the balance between the formation of DNA breaks and their repair, and what can disrupt this precision.
A variety of proteins are involved in this balancing act. Di Virgilio discovered one of them during her time in New York. After studying the basic mechanisms of DNA repair in cells as a visiting student at Columbia University and finishing her doctoral dissertation, she moved to Rockefeller University as a postdoctoral fellow in 2007. There she focused on repair processes in B cells – and in 2013 discovered Rif1 plays a key role protecting broken DNA ends.
Ten years earlier, researchers had discovered that after double-strand DNA breaks, a protein called 53BP1 protects the severed DNA ends from other proteins nibbling away too much of them. Now it turns out that 53BP1 can’t do its valuable work at all without Rif1. “It recruits Rif1 to the break sites and only afterwards is it able to clear the way for the correct type of DNA repair,” Di Virgilio says. The findings were published in Science. Exactly how Rif1’s function is regulated is still unclear.
Hard-core basic research
When Di Virgilio came from New York to Berlin-Buch in the Fall of 2014 to establish a cancer research group at the MDC, these and many other questions were still open. Hard-core basic research has been driving her since then. “Any protein can become the basis of a diagnostic method or cancer therapy,” she says. Her team is feverishly searching for new DNA repair and CSR factors and trying to decipher the workings of those already known. Among other things, they are using CRISPR/Cas, the “gene scissors”.
In 2018, Di Virgilio discovered ZMYND8. This protein is crucial for class switch recombination. However, rather than be involved in repair, ZMYND8 helps direct AID to the right spot in the genome during DNA break formation. “Breakage and repair are probably much more closely regulated than we previously thought,” Di Virgilio says. In 2019, having just accepted her junior professorship at Charité – Universitätsmedizin Berlin, her team came across a mutated form of 53BP1. “This was a very exciting chance find. We then spent six months doing nothing but analyzing the mutant protein,” she says. The result challenges the belief that 53BP1 is only important for class switches because of its ability to protect the broken ends. “53BP1 has other functions during CSR that are crucial to efficiently support the process, and we are determined to define these additional activities”
She and her team made their latest discovery in the summer of 2020. Using CRISPR/Cas, they found the protein Pdap1, which ensures sufficient quantities of AID are produced in the first place, enables antibodies to switch classes. It also protects the B cells from stress-induced cell death. This is an important piece in the complex puzzle of protein activity.
Sometimes she can’t get to the office fast enough
She is adding another layer of complexity to her research by looking at RNA molecules with regulatory mechanisms in CSR. Di Virgilio opens a notebook with digitalized handwriting on her tablet, which is something like the matrix of her research. “In the left column, I jot down questions about current projects, next to them ideas for follow-up projects, and on the far right, long-term questions that I’m interested in,” she says. The right-hand list is the longest. When she drinks a coffee in the morning from her favorite blue enamel mug, leaves her office door slightly ajar and looks out the window, this list often grows even longer. “It’s good to have far-reaching questions, but often it’s the concrete questions that pull me back to my work. Otherwise, the system would get out of balance.” Step by step, she hopes to approach her long-term goal: understanding all the processes in B cells that play a role in genome stability, thereby helping to prevent cancer and immunodeficiencies.
Nowadays, much of her work involves communication. Her office door is almost always open, her whiteboards are where all the threads of her team come together, and she also maintains virtual contact with researchers around the globe by organizing conferences. In 2017, she launched a Helmholtz initiative on “Immunology & Inflammation,” involving 23 labs from five Helmholtz Centers. “I like bringing people together because it helps to advance science,” she says.
On the sideboard, above which hangs a portrait of Simone de Beauvoir that her brother painted for her – “because I can be pretty intense sometimes” – are piles of scientific articles from international journals. She has reserved her Fridays for reading and pouring over them. “Then I can take interesting thoughts with me into the weekend and develop them further,” she says. Does she find it easy to switch off at home? Di Virgilio waves off the question, saying her two sons are sometimes annoyed by all the B cells talks. When a thought begins to occupy her attention, she can’t get back to the office fast enough.
Basic research into fundamental molecular mechanisms, she says, is both the most beautiful and the most terrifying area to work in. “You need to continually come up with new ideas that, even if they are good, often lead to nothing,” Di Virgilio says. She has had to painstakingly learn to deal with setbacks in a constructive way, she says. The giant pink eraser on her desk was given to her by her sister. “For really big mistakes” is written on it. “In science, you have to allow yourself to make mistakes, just like in other areas of life,” she says. “Otherwise, you will never make meaningful discoveries.”
Text: Mirco Lomoth