Ronja Struck received an EACR Travel Fellowship to travel from her home institute in Ireland to Vilnius University and the National Pathology Centre, Lithuania between July and October 2022.

The EACR has joined forces with Worldwide Cancer Research to provide Travel Fellowships of up to €3,000 to enable early-career cancer researchers to gain new skills through a short-term visit to a lab or research group in another country.

You can read about other Travel Fellowship awardees and their experiences here.

Ausrine Nestarenkaite, Ronja Struck & Kamila Baltrukovic at the host lab

Name: Ronja Struck
Job title: PhD Student
Home institute: Royal College of Surgeons in Ireland, Ireland
Host institute: Vilnius University and the National Pathology Centre, Lithuania
Dates of visit: 18 July – 21 October 2022
Research: With the goal of improving our understanding of tumour-immune interactions in neuroblastoma and eventually creating a 3D cell culture model, immune cells (T cells, NK cells, macrophages) were stained in patient samples. These slides were then classified into tumour and stroma regions with the help of artificial intelligence software. Using hexagonal tiling, the tumour-stroma-interface zone was determined and immune cell density in this area extracted and analysed. Linking this data to clinical data about the patient samples provides potential biomarkers and an advances our knowledge of the tumour.

Why did you choose this host lab?

The choice of host lab was largely based on the technique that I was going to learn there. Prof. Laurinavicius and his team are at the top of their field in digital image analysis. The communication prior to the trip was simple and effective and lay the foundation for a highly beneficial collaborative atmosphere. The choice was proven to be the right one when I received great levels of support throughout my entire stay and my research was visibly improved by their inputs and capacity for automated lab work.

Can you shortly summarise the research you did and what you learned on your visit?

Ronja preparing to scan her slides and send the resulting images to the appropriate software.

Three months was a rather narrow window of time to achieve everything laid out in the original plan. While I had prepared a list of stains I was to use prior to coming to Lithuania, after a round of test staining and further discussions with the experts at the institution I had to reconsider a number of stains, find appropriate alternatives and in some cases acquire these before staining patient samples could proceed.

I then trained a classifier software to recognise tumour and stroma regions after extensive reconsiderations of what falls into which category, as neuroblastoma is an incredibly complex tumour. The classifier software was then used to determine the densities of the stained immune cells in each region and I passed on the data to Allan who performed hexagonal grid tiling to determine the densities around the tumour edge only and provided me with the results.

Finally, Ausrine taught me how to use SAS, a statistics software to link all this data to the clinical data, find correlations and potential biomarkers and run significance tests on these. In total almost 200GB of images were generated during the stay with more to come as the project continues.

“Having the opportunity to discuss the slides with pathologists taught me what some key features and subtypes of neuroblastoma look like and now will be exciting to relate to their immune response”

Did you take part in any interesting local or cultural activities?

I was hosted by a lovely local artist who was kind enough to share a lot of her culture with me. A specifically memorable part of my stay will be the numerous soups she prepared for me. Some of which very local, others from neighbouring countries. My favourite by far has to be the national soup Šaltibarščiai, a cold beet root soup. She showed me the best place to get cepilini, the national dish, a fist sized potato dumpling filled with meat that is served with a dollop of sour cream, like almost everything in Lithuania. A habit I believe I will carry with me from now on, too.

I was lucky enough to experience the capitol day in Vilnius during which the streets are filled with stalls of local artists and food vendors, entertainment is offered and competitions are held and the days ending with a free concert and a light show.

What was a personal highlight on your trip?

I used pretty much all my free time very well in my opinion, seeing Klaipeda and the curonian spit with its beautiful beaches, the castle on the lake in Trakai, the capitol day in Vilnius and the city’s birthday in Riga, a holocaust memorial, monastery and lots more in and around Kaunas. It still feels easy to pick a favourite thing that I did: the hot air balloon ride over Vilnius. The red roofs of the old town, the meandering river and the overwhelming green from all the parks provided a beautiful scenery, while the hot air balloon ride was an exciting event in itself!

Was the host institution very different from your own?

Ronja discussing the quality of the classifier she created with Renaldas Auglius, an expert user of the software.

While my home institution is a university I spent the majority of my time in Lithuania at the National Centre of Pathology. This means the average age of my colleagues was a fair bit higher than that of the people I interact with on a regular basis at my home lab. This was quite beneficial for giving me an idea how my work could look in the future and to see what I am working towards. There also were a good few people who had been working in their jobs for a number of years before starting their PhD alongside it, whereas at home the norm seems to be to do a PhD right after an undergrad or postgraduate degree. I really enjoyed the size of the institution, as in a smaller institution it was a lot easier to get to know everyone and find my way around when I only had three months available there.

Have you brought back any specific knowledge/technique that has benefited your home lab?

This was my first introduction to digital pathology and hexagonal tiling. Both of which will be crucial aspects of my work over the next year. I build skillsets in the use of HALO and SAS software from zero. In HALO I created classifiers that can discern between different tissue types. The one-on-one sessions with Ausrine to understand SAS and determine the most appropriate statistical tests helped deepen my general understanding of statistics. While visiting the histology and immunohistochemistry labs I also gained insights into how I could have improved the histology work I performed before the trip.

By far the most widely applicable and specific knowledge I gained on this trip was that of neuroblastoma histology. Neuroblastoma is a very complex tumour with widely variable appearances. Having the opportunity to discuss the slides with pathologists taught me what some key features and subtypes of neuroblastoma look like and now will be exciting to relate to their immune response. A deeper understanding of the microarchitecture of neuroblastoma will also allow me to appreciate the potential implications of high risk specific features. These include for example incredibly high cell density with barely any cytoplasm or extracellular matrix compared to lower risk subtypes.

How has this visit been beneficial to your research and your career?

The National Centre of Pathology is also a diagnostics laboratory. As such I had the opportunity to look behind all the lab doors and peek into the life of potential career paths for my future. This was not only beneficial for my career panning through, but also helped my lab skills despite my work focussing on computer-based analysis. Seeing lab technicians who spend their entire day perfecting one skill gave me the chance to pick up a couple of hints and tips for performing histology. And maybe most importantly, being able to talk to pathologists about neuroblastoma images advanced my understanding of not only the cancer, but histology as a whole more than I could have anticipated.

Want to find out more?

If you are interested in applying for the Travel Fellowship scheme, please click here for more information: EACR Travel Fellowships.