In this position, you will integrate genomic and immunological data collected in innovative trials with combination immunotherapy in bladder and breast cancer patients. The main dataset you will work on in the first two years will come from the NABUCCO trial, in which bladder cancer patients received combination immunotherapy before surgical resection. Tumor tissue is available pre- and post-therapy, providing a unique opportunity to study the immunological effects of immunotherapy on bladder cancer. Next, your research will focus on the combination of chemotherapy and immunotherapy in triple negative breast cancer patients (triple B study, will include over 250 patients). The main goal of this project is to find biomarkers to predict therapy response and personalize treatment.
Your bioinformatic analyses will center around the prediction of response to therapy, a better understanding of the tumor-immune microenvironment and the development of novel therapeutic strategies. You will work with bulk RNA, TCR and exome sequencing data and multiplex tissue imaging technologies. Recently we started exploiting single cell RNA sequencing to get a more in-depth picture of the cancer-immune-interactions.

The Team
You will be a key player in a translational research team with clinicians, cancer researchers, immunologists and computational scientists. Your projects will be in close collaboration with clinical PhD students, cancer biologists and other computational scientists. For the first two years you will focus on bladder cancer research under supervision of Michiel van der Heijden (department of medical oncology and molecular carcinogenesis). The final two years, your projects will mainly be related to breast cancer in the group of Marleen Kok ( department of Tumor Biology & Immunology). During this PhD, you will be exposed to a broad spectrum of cancer immunology research. Throughout your project, Lodewyk Wessels (department of molecular carcinogenesis) will supervise the computation aspects of these projects.

• The breast cancer immunology group of Dr Marleen Kok has the mission to improve immunotherapy for breast cancer patients. Via better understanding of the cancer-immune-interactions using innovative clinical trials, state of the art technologies and team-science, we work in the forefront of translational immunotherapy.
• The bladder cancer group of Dr Michiel van der Heijden develops innovative immunotherapeutic approaches to treat bladder cancer. We mainly conduct our clinical trials in the pre-operative setting, which allows for extensive tissue collection pre- and on-therapy. This enables us to study the effect of systemic therapies on the tumor-immune microenvironment in detail.
• The Computational cancer biology group of Lodewyk Wessels is focused on quantifying and understanding treatment response in model systems and patients. To this end we develop and apply computational methods to data derived from clinical trials and experimental model systems. We actively collaborate with many research groups in the NKI and strongly believe in the power of ‘team science’.

You are an ambitious, creative computational biologist, with a strong interest in translational research. Candidates should hold a degree or have expertise in bioinformatics, computer science or a related discipline, have experience in statistics and/or machine learning and be proficient in bioinformatics programming languages (e.g. R, Python). We expect candidates to be team-players with strong communication skills. General background knowledge in biology and immunology is preferable, and experience with projects involving genomics to identifying candidate targets and biomarkers is a plus.

Fixed-term contract: 4 years.

The temporary employment will be for a period of 4 years. The gross salary per month for our PhD will range from € 2.882,- to a maximum of € 3.322,- according to the standard PhD scales. The terms of employment will be in accordance with the CAO Ziekenhuizen (Collective Labor Agreement for Hospitals). In addition you will receive a fixed end-of-year bonus in December (8,33%) and in May you will receive 8,33% holiday pay. For more information in regard to the secondary conditions please contact the recruiter via: c.de.santis@nki.nl.

Netherlands Cancer Institute

The NKI 
Approximately 750 persons are employed in the research laboratories. Discussions, lectures and seminars are all in English and a the multi-national community of postdocs, students and staff members contribute to the stimulating atmosphere of the Institute. We offer an inspiring and interactive research environment, state-of-the-art facilities, training, a competitive salary (including possibilities for tax-reduction) and housing facilities in the vicinity of the Institute. Amsterdam is a livable city with many cultural amenities. We are located within a 20 minute tram or bicycle ride from the center of Amsterdam and within 20 minutes from Schiphol airport by car, bus or bicycle.

Bladder cancer

Individualized therapy in bladder cancer: biomarkers and the tumor-immune microenvironment
Bladder cancer is a common cancer, with a worldwide prevalence of 2.7 million patients. Although bladder cancer is often superficial at diagnosis, 30-40% of patients present with more advanced disease or progress to more aggressive disease. For patients with locally advanced or metastatic bladder cancer, platinum-based chemotherapy is the mainstay of treatment. Most patients will eventually die of their disease. In recent years, immunotherapy has shown to be active in bladder cancer. Impressive responses are seen, however only a minority of patients benefits from these treatments and it is unclear which patients respond. We aim to advance the development of a personalized approach to bladder cancer by exploring and targeting the tumor-immune microenvironment and finding biomarkers that can guide systemic therapy. Our key focus is on the neoadjuvant setting, as we believe the highest gains in cure rates can be achieved here. Through the large number of bladder cancer patients, excellent multidisciplinary collaboration and broad availability of clinical trials with novel therapeutics at the NKI/AVL, discoveries can rapidly be translated into clinical trials.