PhD student – Immune landscape and immunotherapy ependymoma

We are seeking an enthusiastic, highly motivated PhD candidate to join our group. The project aims to characterize ependymoma tumor cells and its tumor microenvironment (TME) on a single cell level. The goal of the project is to use this knowledge of the immune landscape to develop better immunotherapy approaches. You will be working in a stimulating, multi-disciplinary research environment with international collaborations.

Are you willing to take on the challenge?

Ependymomas are brain tumors that primarily affect children. Despite intense treatments like surgery, radiation, and sometimes chemotherapy, the survival rates remain low because some cancer cells survive treatment and cause the tumor to relapse. Furthermore, these therapies lead to long‑term problems for children, including difficulties with memory, learning, and daily activities. Hence, there is an urgent need for more effective and less harmful treatments.

Novel immunotherapies, such as CAR‑T cell–based approaches, show promise in various tumor types, such as leukemia, due to low toxicity and sustained efficacy. However, thus far they remain ineffective in ependymoma and other pediatric brain tumors, most likely due to the immunosuppressive TME and suboptimal targeting of tumor cells by therapy.

This project will use state‑of‑the‑art single‑cell and spatial transcriptomics to characterize ependymoma and its immune TME. You will perform these experiments and analyze the composition, differentiation, and activation states within the TME and tumor cells. By comparing samples from different stages of disease, from different molecular ependymoma subtypes, and from other pediatric brain tumors, you will characterize the myeloid (resident micro phages and bone marrow‑derived macrophages) and lymphoid compartment to find commonalities and differences in cellular composition, spatial organization and cell state.

Furthermore, you will investigate potential alternative targets for immunotherapies or for reprogramming of the immune TME. Overall, the goal is to reveal the molecular underpinnings of TME heterogeneity and identify potential targets for therapeutic intervention.

The project is part of a larger international programme funded by the Brain Tumour Charity. There will be complementary data for inclusion in the analyses that is being generated with the Máxima or by our international collaborators. These include, for instance, in‑vitro and in‑vivo experiments, proteomic analyses (spectral‑flow cytometry and cyclic immunofluorescence), and additional transcriptomic data. Within the Kool group, you will work closely together with a Bioinformatic Postdoc and will be supported by research technicians.

Furthermore, you are expected to actively collaborate within the international programmes, as well as the collaborating research group and physicians in the Máxima.

We are looking for an enthusiastic and highly motivated PhD candidate, who is eager to spearhead this project, with the following qualifications and skills:

• A Master of Science degree or equivalent in bioinformatics, (molecular) biology, biomedical sciences, immunology, or related disciplines.
• Demonstrated experience with coding and bioinformatic analyses of transcriptomic and/or imaging data is essential. Knowledge of Python or R is preferred.
• Demonstrated wet lab experience is essential. NGS experiments or advanced imaging, such as single‑cell or spatial transcriptomic experiments, is preferred.
• Knowledge about immunology and/or (pediatric) brain tumour is preferred but not required.
• A strong motivation, attention to detail, flexibility, well‑organised and good data management skills are critical.
• The ability to work independently as well as collaboratively in multidisciplinary and multicultural research teams.
• Excellent English written and verbal communication skills.

We offer you a temporary, full‑time PhD‑position for a total duration of 4 years (36 hours / 5 days a week) in our group. You will also collaborate with various research groups at the Princess Máxima Center and abroad. You will initially be contracted for a period of 1 year,…