Interview: Tumoroids from colon cancer, including WGS-strategy

Federica Di Maggio is a post-doc at CEINGE-Advanced Biotechnology in Naples, Italy where she studies the use of three-dimensional cell models, such as tumoroids, as a model system for cancer, with a focus on the development of personalised precision medicine. We caught up with Federica to talk about the use of three-dimensional cell models in cancer research, the challenges she has faced in her work, and the impact nanopore sequencing is having on our understanding of cancer mutations.

You can also learn more about Frederica's work by watching a recent webinar where she discussed her research on colon cancer.

Watch talk

What are your current research interests?

I am very interested in the use of three-dimensional cultures as they are a good model to study both pre- and post- clinical aspects in the research field.

What first ignited your interest in cancer genomics?

Since I was a student, I was always fascinated by cancer research, and I started my research career in a group with great experience in genomics. Thanks to the presence of state-of-the-art equipment in the laboratory, I had the opportunity to closely study all the genes related to cancer predisposition and move in the direction of personalised medicine as a main goal.

How is nanopore sequencing helping in our understanding of mutation patterns in cancer, in particular the relationship between predisposition and pathogenic mutations?

Nanopore technology has great advantages, such as short library preparation time, and the possibility of using different basecallers, depending on the type of analysis you want to do. There is also the possibility to investigate not only single nucleotide variants, but also structural variants, as well as methylation analysis. In our case, it has certainly helped us in understanding some mutations, but as the bioinformatics analysis is still in progress, we should wait until the end of these to be able to give a final answer.

What impact could the use of three-dimensional cell models have on the study of cancer and the development of personalised precision medicine for patients?

Today, these three-dimensional systems are probably the most studied because they could give advantages in both pre- and post- clinical use. Thanks to research carried out in recent years, it has been noted that these 3D cultures can resemble the cells from which they derive, which is an obvious advantage as they have the potential to improve the study of both cancer development and progression, as well as drug discovery. So, they could therefore be a good model to proceed in the direction of personalised precision medicine.

What have been the main challenges in your work and how have you approached them?

In our work, there are challenges to face every day, but for me, probably one of the greatest challenges was the optimisation of the whole procedure for the stabilisation of organoids. I had just started my PhD and so had no experience and had never worked with fresh cancer tissues before. It took months to optimise, and at a certain point I understood that each tissue was different from the other and so each should be treated with different precautions.

What's next for your research?

In the next few months, I will look to deepen all the aspects of this research we’ve started, expand the case studies, and begin to use drugs to continue towards a potential personalised precision medicine approach.

To learn more about other applications of nanopore sequencing in cancer research, click here.