Authors: Valeria Ariotta, Heidi Rausio, Erdogan Pekcan Erkan

In this blog post fairly recent recruits to the HERCULES project, a Master’s degree student, a doctoral student, and a postdoctoral researcher from three different research groups in Finland tell a bit about themselves and what it is like to do research on ovarian cancer.


valeriaMy name is Valeria and I am studying for a Master’s degree in Biomedical engineering at Politecnico di Torino, Italy.  Just over two months ago I started an internship for my Master’s thesis project at the Hautaniemi Lab, University of Helsinki. In particular, I work with samples of histological images from High-Grade Serious Ovarian Cancer (HGSOC), meaning pictures of the tumor samples that have been processed with certain dyes to identify different cells and tissues in the samples.  My research focuses on developing an automated image analysis technique to predict which patients can benefit from platinum-taxane treatment, which is the most common chemotherapy for HGSOC.

For the first month I have studied histology, ovarian cancer, and previous studies in order to gain a better understanding of the state of the art; during this first phase, I have discovered and developed a strong interest in histological images. At present, I am implementing code and sharing ideas with other researchers to further investigate a way to construct such an automated system. For me, this is the most challenging and interesting research topic.

I am grateful to participate in such a big and important project as this; it is very interesting, not only because it is challenging to work with these kinds of samples, but I also believe that the outcomes could be very useful for some patients if we can eventually suggest other treatments to try, thus increasing their likelihood of survival. I think that the possibility to combine image and genetic data could be an important step in making further discoveries.


Heidi

I am Heidi, a newcomer at the lab of Professor Olli Carpén and Docent Kaisa Huhtinen at the University of Turku, Finland. In 2016, I graduated with a Master`s Degree, with Drug Discovery and Development as my major, from the University of Turku. Now, I´m a PhD student in Drug Research Doctoral Program and I have been taking part in the HERCULES project for four months. My doctoral thesis project focuses on characterization of novel fusion genes in HGSOC. A fusion gene is caused by DNA damage which results in parts from two separate genes to merge together. I also evaluate if the potential fusion proteins made from those genes could be targeted by drugs.

My thesis project is still at an early stage. The fusion genes have been detected by deep sequencing and, currently, we are validating the best fusion candidates for further studies to verify that the fusions really are present in the cancer cells. The detection and validation is performed in close collaboration with the group of Professor Sampsa Hautaniemi at the University of Helsinki. The main aim of my thesis is to study the role of the fusion genes in ovarian cancer.

Days at work do not repeat themselves and can include, for example, getting acquainted with new methods, tools and softwares, culturing cells, preparing samples for next-generation sequencing and for the coming functional studies, visualization of fusion genes, and going to classes. Familiarizing myself with a new field, bioinformatics, has been challenging to me. Despite the challenges, now and in the future, the possibility of new findings that could be of help to future HGSOC patients keeps me very motivated to work hard.


erdogan

Hi, I am Erdogan. I completed my doctoral studies in Clinical Experimental Oncology at the Medical University of Vienna. Just a few years ago, I decided to leave the charming city of Izmir, Turkey, and join the Single-Cell Transcriptomics laboratory in Helsinki (and needless to say, embrace the perfect weather in Finland). Since November 2016, I am working as a postdoctoral researcher in the HERCULES project.

What do we do? We ensnare high-grade serous ovarian cancer tumors — or more precisely, we isolat E si N gle cell S a N d A nalyze t R anscriptom E s. With the help of single-cell sequencing, we strive to discover why and how ovarian cancer tumors become resistant to drug treatment.

Friday, typically hailed as the last working day of the week, is my first day for processing single-cell samples. My work starts when I receive the samples from Turku around noon. First, I examine cells under a microscope to check their quality. Second, I carry out a series of filtering and washing steps to remove impurities. Then, I bring the samples to another laboratory, where single cell capture and processing takes place inside an automated microfluidic device. In seven minutes, thousands of cells are partitioned to tiny vesicles and receive unique barcodes. The resulting gems (pun intended) are pooled together and, after some more processing and quality control steps, sent to a sequencing facility.

Since day one, the HERCULES project has not only provided the continuous challenge I seek as a scientist, but also made it possible to make an impact on a global health problem. Therefore, it is a privilege for me to be part of the HERCULES team.