The objective of our Infrastructure & Technologies (I&T) Programme is to support the Oncode research community with access to state-of-the-art research facilities. The programme specifically targets larger equipment and infrastructure projects that are more cost-effective when shared by more than one research group or institute. Oncode has allocated €10M of its funding to support the setting up, expansion and/or upgrade of large-scale equipment, facilities and infrastructures that offer the Oncode community broad access to key scientific capabilities.

In 2018, we funded the purchase of ten high-end pieces of equipment with a total budget of €4M through a non-competitive call. In early 2019, the goals and conditions for a new call were evaluated and re-formulated. In this new call, funding would be allocated to initiatives that are widely supported by the Oncode research community and cover the setting up of technologies that were not previously available to the community or initiatives that propose making unique technologies currently restricted to one or a few groups widely available to the community.

In 2019, we funded five out of nine submitted proposals, totalling almost €4M. The proposals were peer reviewed for their uniqueness in the Oncode community, their usefulness for multiple Oncode researchers from various institutes, and their expected longer-term value. The successful proposals include infrastructure or technology initiatives in genomics, proteomics, Artificial Intelligence and Deep Learning, molecular imaging, and biobanking.

We expect these infrastructures and technologies to be installed and become available to the research community in 2020. During the coming year, we will focus on informing both the Oncode community and the wider Dutch research community about their availability as well as the availability of other Oncode equipment and facilities. At the same time, we will invest the remaining funds in the Infrastructure & Technologies Programme to further strengthen our research community.

In 2019, a total of 463 peer-reviewed papers were published by Oncode Researchers. Of these, 72 were written in collaboration with industrial partners and 70% were published in open access journals. Highlights of these papers are listed below.

In collaboration with the labs of Ton Schumacher, Lodewyk Wessels and Wilbert Zwart, the groups of Jos Jonkers and Karin de Visser published their research into the role of the p53 gene in systemic inflammation in breast cancer patients. Systemic inflammation is associated with poor overall survival in different cancers. The current work shows that loss of p53 leads to increased secretion of signalling molecules from tumour cells. This induces systemic inflammation, which leads to higher rates of metastasis. Their research further paves the way for personalized approaches in treating breast cancer. Read the paper in Nature.

The Kops, Snippert, Clevers and van Oudenaarden labs published a paper in Nature Genetics. In it, they looked into chromosomal instability in colorectal carcinomas. Using patient derived organoids in combination with single cell analysis, they show that chromosomal instability is widespread in colorectal carcinomas and that these mitotic errors are quite well tolerated. This may be an important factor in tumour heterogeneity.

Oncode strives to create an environment in which Oncode researchers can reach their maximum innovation potential. To that end, we use our base fund to enable each of our investigators to pursue innovative research in uncharted areas of cancer biology. Each year, our 42 Senior Oncode Investigators receive €250k, and our 19 Junior Oncode Researchers receive €150k from our base fund.

These funds provide them with the opportunity to pursue leads that are typically outside their own scientific expertise, initiate research that may be difficult to finance due to the lack of preliminary data, or conduct research that requires access to specialized and expensive technologies. In this way, Oncode offers its investigators the financial capability and flexibility to accelerate research lines, change the scope of existing research programmes, or terminate unsuccessful projects.

The approach is valued by our scientific community and has led to several tangible results in 2019:

“I initiated a new research line in which we aim to investigate how inherited mutations in the LKB1 gene mediate predisposition to the development of gastrointestinal cancer in Peutz-Jeghers Syndrome (PJS) patients. Without Oncode support, it would be difficult to obtain funding for this research line because the work is entirely new to my lab and funding schemes commonly require a track record in the field.”

Madelon Maurice, UMCU

“Oncode base funding allowed me to hire a chemist with whom we are developing novel probes. These probes could potentially act as inhibitors of a family of enzymes for which inhibition might benefit (current) treatment of cancers like breast cancer and multiple myeloma. This collaboration allowed us to apply for TKI-Public Private Partnership funding which was awarded. The model for jumpstarting this industry collaboration was very useful.”

 Titia Sixma, NKI

“We use single molecule imaging to study virus replication in mammalian cells. Oncode funding gave me the opportunity to start studying oncolytic viruses, but since my lab has no previous experience in this area, and we have no preliminary data to support this project, traditional grant applications would not have been successful. However, using my Oncode base-funding, I have been able to initiate this highly successful project, and using the preliminary data generated as a result of the Oncode base funding, I have now submitted a grant proposal for traditional funding.”

Marvin Tanenbaum, Hubrecht Institute

The Oncode Training Programme provides our researchers with tailored training to help them with the use of research tools, as well as extending their network. In 2019, Oncode organized four science-driven technical masterclasses that were co-created with Oncode Investigators and researchers. These technical masterclasses were customized to the needs of the research community and addressed the following topics: gene editing, macro molecular structures in cancer research, drug repurposing, and the application of organoids.

“The technology workshops organized by Oncode have been very useful for my group, including the technicians. After hearing back from one of my technicians who attended a workshop on CRISPR-technology, what I found important was that he not only learned new things that he could implement, but that he was also able to bring something to the community by sharing his technical experiences and expertise.”

Susanne Lens, UMCU

In addition to its technical masterclasses, Oncode organizes mentoring sessions for Junior Oncode Investigators. The goal of these sessions is to foster their creativity, independence and well-being, enabling them to establish their careers in today’s complex and dynamic professional environment. We collaborate with an external party to moderate peer-to-peer discussions between Junior Oncode Investigators, and we also provide Junior Oncode Investigators with the opportunity to be linked to a Senior Investigator.

“The Oncode mentoring programme provides me with valuable training on group leader skills. The training days with fellow young Oncode Investigators are inspiring, useful and a great way to share experiences.”

Sylvie Noordermeer, LUMC 

Oncode brings basic research and clinical practice closer together to enable the effective translation of promising research into novel clinical treatment strategies. To support this goal, Oncode created its Clinical Proof-of-Concept (CPoC) Programme, with an earmarked budget of €10M for pre-clinical and early clinical studies based on findings from Oncode research labs.

Via a rolling call, Oncode Investigators, together with clinicians, can submit proposals to start (pre-)clinical projects. To support the development of proposals, Oncode installed the Oncode Exploratory Development Expert Support (OEDES) Team. The team comprises experts in pre-clinical and clinical development with experience in academic, industry and clinical settings.

In 2019, three projects were approved with a total budget of ~€1.8M. A team led by Roland Kanaar will investigate the use of a functional repair capacity test in the selection of advanced breast cancer patients who may benefit from carboplatin treatment, Jan Paul Medema will lead a project investigating stromal activation to guide gastrointestinal cancer therapy, and Sjoerd van der burg has started a project into TEIPP-targeting immunotherapy to potentially overcome immune escape in tumours.

Clinical workshops
To facilitate connections between the basic science, clinical researcher and clinician communities, we organize regular clinical workshops each dealing with a specific tumour type. Two workshops were organized in 2019, one on Colorectal Cancer (CRC) and the other on Glioblastoma. Each of these workshops included between 50-60 attendees and stimulated fruitful discussions about unmet clinical needs, trends in basic research and challenges in the clinic. 

“For me, the CRC workshop showcased not only the clinical challenges but also the available material and ongoing studies that researchers could use to help attack those challenges. After the CRC workshop, we started collaborating with a clinical research group at NKI on the origins and impact of chromosomal instability in early adenomas.”

Geert Kops, Hubrecht Institute