Oncogenetics and Oden pots

Emeli Pontén MD, PhD student at the Department of Molecular Medicine and Surgery recently visited University of Tokyo within the UTokyo-KI collaboration. She shares her experience and hopes she can inspire other PhD students to go abroad.

What is my area of research?

Shrine in Tokyo

I’m an MD and a PhD candidate in the research group Rare Diseases at the Department of Molecular Medicine and Surgery (MMK), conducting epidemiological research in oncogenetics. We are exploring the etiology of childhood cancers by identifying tumor groups and leukemias associated with acquired and constitutional genetic defects. The research project is based on registry data from Swedish patients diagnosed with various genetic conditions and/or cancer.

Although the cause of most childhood cancers remains unknown, it has been established that the risk is higher in children with congenital anomalies and some specific genetic syndromes. Recently, studies of genes known to cause genetic syndromes in the context of their involvement in neoplastic processes have led to a better understanding of both cancer and rare diseases. Many developmental defects associated with cancer can be grouped into clusters with common molecular pathways and overlapping clinical manifestations. Examples of these are overgrowth syndromes, RASopathies, PTENopathies and syndromes caused by somatic or germline AKT/PI3K/mTOR pathway mutations.

Genomic techniques such as CGH-arrays and massive parallel sequencing (MPS) have facilitated progress in the understanding and diagnosis of genetic syndromes and cancers. Together with the available cytogenetic and molecular genetic data, we are able to initiate a unique research platform with a combination of genetic and environmental information to investigate the etiology of different childhood cancers.

Why I chose the University of Tokyo?

The University of Tokyo is considered one of the most prestigious universities in Japan and the world. The Department of Biostatistics at UTokyo is the longest-established laboratory of biostatistics and theoretical epidemiology in Japan. Their expertise covers methodological research on biostatistics, clinical trial design, epidemiological theories, computational statistics and application of advanced statistical methods.

As a PhD candidate striving to comprehend advanced biostatistics and cancer epidemiology, I was curious what it would be like to be based at this acclaimed biostatistics lab for a couple of months.

For one of the studies in my PhD project we have been discussing the use of space-time clustering and Geographical Information Systems, but there is no course at KI teaching this type of analysis. I reached out to Dr. Matsuyama, a professor at this department, and asked if any of his colleagues possibly had experience working with space-time clustering analysis. I got the response that in fact he knew someone with expertise in spatial epidemiology at Nagoya University, Dr. Takahashi, and that he could invite him to visit UTokyo for a seminar. I corresponded with my acquaintance Dr. Fukushi, a professor at the UTokyo Hongo campus, who recommended me to take the chance to visit Tokyo through the KI-UTokyo collaboration.

What did you do during your lab visit at Department of Biostatistics at The University of Tokyo?

During my stay I was offered an office, a personal computer containing the licensed software Statistical Analysis System (SAS 9.4), and free access to a library consisting of literature and journals in biostatistics. I was able to discuss medical statistics with the professors and students at the department, and participated in UTokyo research seminars and symposiums. I gave talks on cancer genetics at the Faculty of Medicine and made substantial progress in programming skills.

What was the major differences between working at KI and The University of Tokyo?

The Dept of Biostatistics is located on the green Hongo campus grounds, a very lush area. During hot and humid days it felt like field work in the middle of a rainforest. By the end of November and autumn, the scenery changed dramatically as we were indulged in falling golden Ginkgo leaves.

The Edo residence of the Maeda Clan once stood on land that now belongs to the Hongo campus. On my way to the department walking through the campus area I would pass Japanese gardens, the magnificent red Akamon*, and sometimes Kendō* training sessions, immersing my mornings with great awe and reverence.

Also fascinating was how work colleagues at the University of Tokyo so elegantly integrated food with work. After office hours it was common that colleagues would go out for dinner together, and continue discussions at some local Izakaya* or to the itamae* artistry known as Omakase*. The dishes were never disturbing to conservations since they were served in a certain succession and in small pieces. I was invited to join for one of these evenings gathering around an Oden* while sharing research quandaries. This was something I really appreciated, and I hope we can nourish a similar trend at KI. I believe good food is the root to all great ideas and the fundament of team work.

What is your impression of Tokyo?

Tokyo is a city where you can stimulate any type of appetite, whether it be for food, games, science or art. Of all cities in the world, Tokyo harbors the most Michelin starred restaurants.

Tokyo is also a city dense in technical inventions, every corner you turn there is some AI robot or equipment accommodating needs you never knew you had. The range of creativity seems infinite. That, combined with the meticulous attention to detail, may explain the many famous designers, artists and countless galleries residing in Tokyo. Although you might feel lonely at times, there is always distraction.

Do you have any recommendations for doctoral students/researchers wanting to do a lab visit/research visit in Japan?

Do not hesitate. No matter what you’ll experience I can guarantee you that moving abroad will result in leaps for your personal as well as professional growth. Whatever niched interest you might have there is no doubt a group of individuals passionate about that specific activity or entity in Tokyo.

If you feel ambitious or are looking to return frequently, take a course in Japanese. As a scholar or researcher at University of Tokyo there are Japanese language courses offered for free, a great venue to connect with expats from all over the world.

What was a memorable experience from your stay?

About a week after I had arrived to Tokyo, the department organized a welcoming reception where I got to meet all the professors and students while sharing sake and an enormous platter of assorted sushi. In the midst of the umami high, I was very humbled to find myself among this group of exceptional researchers.

Also memorable was the annual earthquake evacuation rehearsal at the University with complementary dried emergency rice and tofu (quite delicious actually), and not to mention the violent typhoon Hagibis.

Alone and lost in translation it was a challenge to arrange with research commitments, three different housings and rental contracts in Japanese, while building a social network from scratch simultaneously.

Emeli Pontén MD, PhD student

To what extent have your impressions and experiences from your stay abroad affected you personally?

I have been traveling extensively my entire life, sometimes to dangerous places doing injury prone activities, but this trip is definitely the one that has made me a truly fearless traveler. Alone and lost in translation it was a challenge to arrange with research commitments, three different housings and rental contracts in Japanese, while building a social network from scratch simultaneously.

What will you bring back to KI?

I hope to motivate other PhD candidates to take the opportunity to travel and find inspiration for a research career on an international arena. Collaborations with researchers on a different continent is inevitably an eye-opening experience that will prepare you for future postdoc fellowships, or other types of interactions with external labs and researchers. I also hope to be able to spur courage in women who are tempted to get into coding and programming, a field traditionally dominated by men which can be intimidating when you’re fresh out of high school and just starting to navigate your path in academia. I know we can change this with just persistent encouragement and mentorship, particularly in early stages of education and career.

Explanations to Japanese words in the text ( *)

Akamon = famous gate (mon) built in 1827

Kendō = traditional Japanese martial art

Izakaya = Japanese bar serving small dishes

Itamae = chef title of high-end Japanese cuisine

Omakase = a selection of dishes composed by the chef depending on season and personal style

Oden = a type of nabemono (Japanese one-pot dishes) consisting of various ingredients stewed in dashi broth