Faster, effective and safer gene engineering

Innovation takes many forms – from a tweak that improves technology, all the way to the development of new medicines. Translating science is about adapting research, moving research beyond the lab, or closing gaps in technologies so that it can be used to improve our lives. Valentina spoke to us about spotting those opportunities and progressing our science into tangible outputs. 

I'm part of the R&D team, with Andrew Basset in the Cellular and Gene Editing Research team and my main aim is to develop new technologies in the gene editing space. At the moment, I’m working on a Translation Committee Fund project. The project comes from a currently unanswered question - can we establish regions of a stem cell’s genome that are open and safe to engineer? In doing so, can we have an effective transcription of engineered genes of interest during differentiation from stem cells to specialised cells?

Let’s imagine we have a book, an instruction manual. Each cell has the same instruction manual, but because each cell performs a different function in our bodies, the different parts of the manual are underlined, highlighted or put in bold. For a muscle cell, for example, a specific part is highlighted. Also, not all chapters of the book are open in all cells except stem cells, before they develop into a specialised cell, such as a liver or brain cell.

So, when we engineer a cell, we need to engineer it in the open chapter. If we engineer a blood cell or a muscle cell, the chapters are different, and here lies the challenge - we don’t know which chapters are open. Our project intends to find those open chapters so that we can effectively and safely engineer those stem cells. In other words, there is not a universal place in the genome that we can target, as was thought in the past but depends on the cells we are trying to develop.

How are we doing this? We add a fluorescent gene into the chapters that are open in a stem cell. As the stem cell develops into a more specialised cell, we can see, under the microscope, if it is still fluorescent or not at the end of the process. If it is, we then know that where we added that gene is the bit that is open, the open chapter or chromatin, and hence the place in the genome where we can safely engineer.

Once we understand this, we can screen for different combinations of genes that might drive stem cell differentiation into specific lineages. Further down the line, this will enable us to develop cells in the lab that are very close to the ones we have in our bodies, allowing us to perform experiments, such as drug tests, that we can’t effectively do at the moment.

How did the Translation Committee Fund enable you to do this?

My job, as a staff scientist in the gene editing R&D team, is to fully support the academic groups within the Sanger Institute. This means that I don’t really have the chance to decide what I will be working on unless there is interest. So, the translational grant allowed me to work on something I am personally passionate about and to hire someone who I manage directly, Dr Ivan Gyulev. Ivan helps me not only with experiments in the lab but is also the person I can discuss with daily about the technology we are developing.

We are also extremely lucky to have a part-time PhD student (part-time Technical Specialist in the gene editing team, Michaela Bruntraeger who has helped us immensely to progress the project and the technology derived from it, which we recently patented.

So this for me has been the biggest change - we are more brains constantly thinking about the same problem and exchanging ideas and also freeing time from my experiments overload! Most importantly, this has allowed me to manage more people and expand the R&D side of gene engineering further.

How did you become so interested in the R&D part of the job?

I have an academic background in epigenetics, the study of the information that is not written in the DNA but that can be inherited. Going back to the book analogy, genetics is the study of the words, but epigenetics is the study of what is highlighted, in capital letters or in bold This can help us understand what is important to “read” in a specific cell type.

In 2012, when I joined Professor Tony Kouzarides’ lab as a Postdoctoral Fellow, the lab focus shifted from epigenetic research to epitranscriptomics. The aim was to study RNA modification in the same way that we look at histone or DNA modifications in epigenetics, and at the impact of these modifications. Even though we know now that epitranscriptomics plays a critical role in the regulation of gene expression, thanks to pioneer work also from our lab, its study was still certainly in its infancy back in 2012.

At that point, there were not many reagents and methodologies in the field and I loved the challenge of solving the problems we were encountering. I found myself relishing the R&D part of the job. I’d say I was thrilled. Being the first author of an academic paper lost its importance, I started looking for new challenges to solve.

Professor Tony Kouzarides was also an inspiration. He is one of the co-founders of Abcam and the Director of the Milner Institute in Cambridge. He also founded Storm Therapeutics whilst I was a postdoc in his lab - I worked with him for eight years - and I started to see how academia can interact and collaborate with companies, adding clinical relevance to our research.

That’s when I started thinking - I love what I do, but I want to do something that is much more relevant for patients, without totally jumping out of academia. I wanted to challenge myself and start something new. That’s when my career shifted and I came to the Sanger Institute. I wanted to know more about genome engineering and this seemed like the right place to do this.

When I think of my career until now, I do believe that perhaps I could’ve become a PI, but with this work, I feel that I am making a difference in other ways. Furthermore, the Sanger Institute is the perfect environment to get the best of academia but with opportunities to engage with industry too.

I joined Sanger in February 2020, and everyone knows what happened a month later - the pandemic hit. We were all home and because I hadn’t started the new project yet, I had plenty of time to think. You very rarely get the opportunity to have three to four months just thinking about science. I used that time as best as possible and that was when I started looking at the things we lack in genome engineering - new challenges to work on.

I think that coming from a naive point of view about it helped. I didn't know many of the papers in the field, so I wasn’t conditioned in my questioning. After each idea, I’d talk about it with a colleague, Dr Thomas Burgold, or Dr Andrew Bassett, my line manager. Most of my ideas didn’t make sense, but some of them did, and one of them in particular - to combine different types of gene editing methodologies. We combined different CRISPR-Cas9 technologies with site-specific recombination, and delivered all reagents simultaneously, making it possible to engineer large inserts into a specific region of the genome in a faster and efficient way.

How was that novel?

The novelty was due to the combination of the two technologies and especially to the delivery of all reagents in one step.

This was the idea which gave you the base for a patent?

It was. The idea worked and now we have a system that is fast and safe (as it is characterised by a non-viral delivery of the reagents) and which has been patented. The ability to engineer the genome of human cells is extremely important in the context of fundamental research, disease modelling and development of cellular therapeutics.

Most techniques have limitations, as you can unintentionally target parts of the genome that you’re not interested in, especially if you use a viral delivery system (not site-specific), with the potential to even cause damage to the cell itself. Moreover, the efficiency of CRISPR-Cas9 technology decreases with the size of the insert (the cargo) that you want to engineer your cells with. We hope that our technology, overcoming some of these limitations, will make genome engineering safer, more effective and crucially, faster.

What would you say you enjoy most about your work?

I’ve been working on this project for a long time, with trial and error, putting our knowledge to the test and I’ve relished the whole process. Innovating in this way, seeing that me and the team can make a difference in how cell engineering can improve, ultimately becoming safer in the clinic, is something that fills me with a huge sense of pride and satisfaction.

Recently, I applied for another Translation Committee Fund project to test whether we can directly target primary immune cells, known as T cells, enabling us to make off-the-shelf CAR-T cells and it was successful! This will allow one of my colleagues, Dr Ivan Gyulev, to stay longer with us and test our hypothesis, which, if it works, can have a clinical impact for cancer patients!