Computational Cancer Genomics and Tumour Evolution
Within this line of research, the 'Anatomy and Embryology Research Group' uses experimental and computational approaches to study human carcinogenesis.
Cancer is a disease of the genome. It is caused by the successive accumulation of DNA errors (somatic driver mutations). This carcinogenic process starts in normal cells and is an example of Darwinian evolution, where each driver event results in a fitness advantage, positive selection and clonal expansion of the affected cells.
The CCGG lab aims to understand tumor evolution better using state-of-the-art and newly developed wet lab and computational approaches. By gaining new insights into the key mechanisms underlying tumor evolution, the ultimate goal is to identify novel diagnostic and therapeutic strategies for cancer patients.
The lab's core expertise is in the analysis of somatic mutation patterns, spatial omics applications, machine learning, and interactive data visualization. Analyses are mostly performed on next-generation sequencing data, which are obtained from public repositories or newly sequenced tissues from cancer patients, whole-body donors (post-mortem tissues), or experimental model systems.
Research projects
Mutant clones in normal tissues
Recent evidence suggests that somatic mutations in cancer genes lead to microclone formation in multiple histologically normal epithelial tissues, likely forming the foundation of human carcinogenesis.
We aim to determine how these clones and their putative interactions eventually result in malignant tumor formation.
- researchers: Jimmy Van den Eynden, Tom Luijts, Sofie Hoogstoel, Eden Pappaert
- funding: Bijzonder onderzoeksfonds (BOF; Special Research Fund, Ghent University), CRIG partnership grant, Fonds Wetenschappelijk Onderzoek – Vlaanderen (FWO; Research Foundation – Flanders), Kom op Tegen Kanker (Stand up against Cancer)
Neuroblastoma
Neuroblastoma is the most frequent cancer during infancy and accounts for 15% of pediatric cancer-related death.
Based on the analysis of DNA and RNA sequencing data obtained from different experimental model systems (e.g., cell lines, mice models), this multidisciplinary and international project aims to identify novel therapeutic targets.
- researchers: Jimmy Van den Eynden, Peter Merseburger, Eden Pappaert
- funding: Barncancer Fonden, Fonds Wetenschappelijk Onderzoek – Vlaanderen (FWO; Research Foundation – Flanders), Stichting Tegen Kanker (Foundation against cancer), CRIG young investigator proof of concept (YIPOC) grant
Tumor evolution and immune selection
Tumor evolution is determined by interactions with the immune system, which eventually determine whether and how a patient will respond to cancer immunotherapy.
We develop novel computational approaches to study neoantigens and immune selection signals in large, publicly available genomic and transcriptomic datasets and evaluate those signals as putative biomarkers for immunotherapy responses.
- researchers: Jimmy Van den Eynden, Arne Claeys
- funding: Bijzonder onderzoeksfonds (BOF; Special Research Fund, Ghent University), Kom op Tegen Kanker (Stand up against Cancer)
Collaborations
- Mutant clones in post-mortem tissues: Wouter Willaert, Anne Vral, Tim Lammens
- Skin cancer: Isabelle Hoorens
- Development of novel spatial omics technologies: Jo Vandesompele
- Neuroblastoma: Frank Speleman, Kaat Durinck and Ruth Palmer (University of Gothenburg, Sweden)
- Thyroid cancer: Maxime Taribichi (Université Libre de Bruxelles)
- Peritoneal carcinomatosis: Wim Ceelen and Wouter Willaert
Publications
Questions?
- Jimmy Van den Eynden, researcher
+32 9 332 48 55