ESR6 – Deep Learning for TNBC Arriving to Stavanger, Norway

What I take back home apart of the knowledge that I acquired is the vast number of friends and professionals that I met and that I will keep forever with me.

Hello everyone! This is Claudio Fernandez Martín, ESR6 at CLARIFY. Today I am going to tell you all about my experience during my three-month Secondment at the Stavanger University Hospital (SUH) in Norway.

When I was reviewing the pictures from my time in Norway to include in this blog post I could not avoid getting a bit nostalgic. I had a great time during my three-month Secondment at the Stavanger University Hospital (SUH) in Norway. This stay was my first in-person Secondment within the CLARIFY network and it could not have been any better. I learnt very valuable insights about pathology from Emiel Janssen, one of the best TNBC researchers in the world, and I have shared unforgettable experiences with people that I met in Stavanger, and that now I am lucky to consider my friends.

During the first days of my Secondment I met Umay Kiraz (ESR6) and since the very first minute she offered herself to help me in all possible ways, both academic and personal. The first two weeks with her I learnt how pathologists examine and evaluate the biopsies in order to come up with the final grading and the report. This was a crucial point not only from my Secondment but for my PhD in general, as it really helped me to understand what were the most important features to look at when facing a breast biopsy (or in my case a Whole-Slide Image). Thanks to Umay I learnt about the mitotic cycle and how to determine whether a nucleus is mitotic or not and to obtain the Mitotic Activity Index (MAI), I learnt to distinguish tumor cells from other nuclei and I learnt how to count and evaluate the Tumor Infiltrating Lymphocytes (TILs). Also, she taught me the importance of immunohistochemistry for pathologists, as thanks to different antibodies and a special staining applied to a biopsy it is possible, for instance, to observe only the cells that are in a particular phase of the cell cycle, like Ki-67 or PPH-3. This is particularly interesting for my project, as I am currently dealing with mitoses detection and these staining can mark as positive cells that are in a mitotic state, and therefore, they are used as proliferation markers that help to stratify between good and poor prognostic categories in invasive breast cancer.

In my first days in SUH I learnt the whole Whole-Slide Image (WSI) digitalization workflow from the extraction of the biopsy, the paraffin block creation, cutting and scanning. Also, throughout my three months I received several lectures from Emiel about Digital Pathology and learnt about its history, advances and challenges. He also taught me about Quantitative Pathology and the biomarkers used for diagnosis and prognosis of Breast Cancer, specifically about the histopathology of Triple Negative Breast Cancer (TNBC). I also learnt about the latest technologies and techniques in cancer research such as the Hyperion and the Nanostring geoMx together with an introduction about molecular pathology.

In the Secondment I had the chance to attend the research meetings from both the SUH and the BMDLab at the University of Stavanger (UiS) directed by Kjersti Engan. In these meetings I presented my work regularly and I received feedback from both medical personnel at the hospital and from AI and data science researchers at the university. Both perspectives helped me gain a much deeper understanding about the needs and possibilities in both aspects of my project, while I gained a lot of confidence and presentation skills as I had to present my progress to two completely different audience groups.

Overall, in this Secondment I learnt very important medical aspects of TNBC and Digital Pathology at SUH while also benefitting from the technical insight from the BMDLab PhD students and researchers. Nonetheless, what I take back home apart of the knowledge that I acquired is the vast number of friends and professionals that I met and that I will keep forever with me.

Figure 1. ESR6, Claudio Fernandez and ESR11, Umay Kiraz, together with the WSI scanner.

Figure 2. Picture with Emiel Jansseen, ESR5 (Saul Fuster), ESR6 (Claudio Fernandez), ESR9 (Zahra Tabatabaei), ESR 11 (Umay Kiraz) and Fernando Perez Bueno.