Dr Freek van Eeden
Room: C13 Firth Court
Brief career history
Using the zebrafish as a genetic tool to study development and disease. We are interested in understanding the role of the patched genes in Hedgehog signaling. In addition, we have created a knockout for the von Hippel Lindau disease (VHL) gene and are interested in modeling VHL deficient cancers in zebrafish.
Disease modelling in zebrafish
Understanding VHL and hypoxic signalling in Cancer
The zebrafish provides a powerful organism to model human development and disease. We are exploiting and developing the zebrafish, e.g. by creating such disease models, by using knockout technology like CRISPR, or by looking for chemicals that can modify disease-relevant phenotypes.
One of our current projects, models the human Von Hippel Lindau disease, caused by mutation of the VHL gene. VHL is a negative regulator of the Hypoxia Inducible Factor (HIF) signalling pathway, which is vital for development and survival of many tumours. However, this is not the only function of VHL and over the years numerous others have been identified. We found that in zebrafish, the functions of human VHL have been split over two genes, which we named vhl and vhl-like (vll).
Interestingly, we found that the fish vhl gene has an important role in HIF regulation, as mutants we made by reverse genetics show all hallmarks of an inappropriate hypoxic response under normoxic conditions. The role of vll was initially enigmatic, null mutants that we created in this gene were viable and fertile. However, using a unique and novel in vivo reporter for genome stability that we created, we discovered that the vll gene is important for maintaining genome stability, which is a major driver for tumour initiation. This is what we are currently trying to understand better.
Current collaborations: Sherif El-Khamisy (genome stability), Albert Ong (pkd2 model), Jane McKeating (Birmingham), Francesco Argenton (Padua) (both glucocorticoid-HIF interaction).
Undergraduate and postgraduate taught modules
Genetic and Drug Screening in DNA Repair Deficient Zebrafish for Novel Targets in the Treatment of Neurological Disease and Cancer
Co-supervisor: Professor Sherif El-Khamisy
Funding status: Competition funded project European/UK students only
This project is eligible for a department scholarship. These scholarships are awarded on a competitive basis – find out more on our funding webpage.
BBSRC DTP funding available.
A cell can experience ~1 million DNA lesions per day from endogenous and exogenous genotoxins. A variety of lesions also result from aberrant replication, or DNA repair itself. DNA lesions threaten essential processes such as transcription and replication and can lead apoptosis and cancer. For example, accumulation of protein-linked DNA breaks (PDBs) cause various neurological diseases, and on the other hand, have been exploited to treat cancer.
Although we know much about DNA-repair pathways from studies in cultured cells, we know little about the extent of functional redundancy at the organismal level. This is important since harnessing this knowledge is rapidly emerging as a powerful approach to treat diseases such as neurodegeneration and cancer. For example, we recently reported, in Nature Neuroscience, a novel mechanism by which PDBs and DNA/RNA hybrids cause motor neuron disease.
Through BBSRC funding and a joint studentship, we established CRISPR mutants in tdp1, brca2, atm, rad52, rad51, which all act in DNA repair, but are mostly viable and often have only mild/no defects as embryos. The objective of the PhD project is to identify backup pathways that can protect the organism if the primary PDB repair pathway is absent. As DNA-repair pathways are often redundant, homozygous mutants provide an excellent background for chemical/genetic modifier screens.
Our primary focus will be on tdp1 mutants, these embryos are - surprisingly- as resistant to DNA damage, as their siblings. We will use CRISPR/CRISPRi technology, and have various chemical libraries available and will screen for defects after induction of DNA damage. We developed an in vivo GFP-reporter system, that uses destruction of a sentinel-repressor to show GFP activation after defective DNA repair. This provides a simple readout in embryos to quantify DNA repair. Importantly, identification of mechanisms behind redundancy may suggest clinical strategies to treat the human disease that results from mutation of tdp1, SCAN1. Moreover, it will provide a platform to stratify cancer patients receiving TDP1 inhibitors currently under development in our labs in collaboration with CRUK technology arm (CRT).
Keywords: Cancer / Oncology, Cell Biology / Development, Genetics, Molecular Biology, Neuroscience/Neurology
For informal enquiries about the project or application process, please feel free to contact:
For further information about these projects and how to apply, see our PhD Opportunities page:
- Wilkinson RN, Elworthy S, Ingham PW & van Eeden FJM (2017) Fin clipping and genotyping embryonic zebrafish at 3 days post-fertilization. BioTechniques, 62(1).
- Greenald D, Jeyakani J, Pelster B, Sealy I, Mathavan S & van Eeden FJ (2015) Genome-wide mapping of Hif-1α binding sites in zebrafish. BMC Genomics, 16(1). View this article in WRRO
- Wilkinson RN, Elworthy S, Ingham PW & van Eeden FJM (2013) A method for high-throughput PCR-based genotyping of larval zebrafish tail biopsies.. Biotechniques, 55(6), 314-316.
- Watson O, Novodvorsky P, Gray C, Rothman AMK, Lawrie A, Crossman DC, Haase A, McMahon K, Gering M, Van Eeden FJM & Chico TJA (2013) Blood flow suppresses vascular Notch signalling via dll4 and is required for angiogenesis in response to hypoxic signalling.. Cardiovasc Res, 100(2), 252-261. View this article in WRRO
- Kettleborough RN, Busch-Nentwich EM, Harvey SA, Dooley CM, de Bruijn E, van Eeden F, Sealy I, White RJ, Herd C, Nijman IJ, Fényes F, Mehroke S, Scahill C, Gibbons R, Wali N, Carruthers S, Hall A, Yen J, Cuppen E & Stemple DL (2013) A systematic genome-wide analysis of zebrafish protein-coding gene function.. Nature, 496, 494-497. View this article in WRRO
- Santhakumar K, Judson EC, Elks PM, McKee S, Elworthy S, van Rooijen E, Walmsley SS, Renshaw SA, Cross SS & van Eeden FJM (2012) A zebrafish model to study and therapeutically manipulate hypoxia signaling in tumorigenesis.. Cancer Res, 72(16), 4017-4027.
- Elks PM, van Eeden FJ, Dixon G, Wang X, Reyes-Aldasoro CC, Ingham PW, Whyte MKB, Walmsley SR & Renshaw SA (2011) Activation of hypoxia-inducible factor-1α (Hif-1α) delays inflammation resolution by reducing neutrophil apoptosis and reverse migration in a zebrafish inflammation model.. Blood, 118(3), 712-722.
- van Eeden FJ, Granato M, Schach U, Brand M, Furutani-Seiki M, Haffter P, Hammerschmidt M, Heisenberg CP, Jiang YJ, Kane DA, Kelsh RN, Mullins MC, Odenthal J, Warga RM, Allende ML, Weinberg ES & Nüsslein-Volhard C (1996) Mutations affecting somite formation and patterning in the zebrafish, Danio rerio.. Development, 123, 153-164.