dr. Thomas Naert (PhD)

My research centers on the use of CRISPR/Cas9 genome engineering for cancer modeling and drug discovery, with a particular emphasis on Xenopus as an innovative in vivo system. During my Ph.D., I pioneered the first CRISPR/Cas9-mediated cancer model in Xenopus for retinoblastoma, laying the groundwork for extending this approach to other cancer types, including glioblastoma, neuroendocrine pancreatic tumors, and especially desmoid tumors. A notable outcome of this work was the identification of EZH2 as a novel therapeutic target for desmoid tumors using CRISPR-SID, a method I developed for in vivo genetic dependency mapping.
During my Marie Skłodowska-Curie fellowship at the University of Zurich, I developed a strong interest in light-sheet microscopy (LSM). There, I contributed to the design of novel imaging platforms and gained expertise in large-tissue staining, optical clearing, and deep learning-based analysis of complex, high-dimensional LSM datasets.
Currently, my research integrates these domains by using LSM to explore the 3D tumor microenvironment in desmoid tumors, providing new spatial and functional insights. This multidisciplinary approaches bridges biology, chemistry, optics, engineering, and computational science.
In parallel, I lead a project focused on modeling chromosomal translocation-driven cancers using cutting-edge, AI-optimized CRISPR/Cas9 strategies (Pythia – patent WO2025040617A1). My current focus is on using Pythia to model Ewing sarcoma, with the goal of identifying novel therapeutic vulnerabilities in this aggressive pediatric malignancy.
 

Thomas Naert obtained his Ph.D. in Biochemistry and Biotechnology from Ghent University (Belgium) in 2019, supported by a strategic basic research fellowship from the IWT (now FWO). From 2020 to 2023, he conducted research as a Marie Skłodowska-Curie postdoctoral fellow at the University of Zurich (Institute of Anatomy) under the mentorship of Prof. Dr. Soeren Lienkamp. In late 2023, he returned to Belgium with a BOF postdoctoral fellowship from Ghent University, followed by the award of an FWO senior postdoctoral fellowship in 2024. That same year, he also received young investigator proof-of-concept projects (YIPOC) seed funding from CRIG to investigate the desmoid tumor immune microenvironment in 3D using light-sheet microscopy (LSM).
Dr. Naert currently conducts independent research at the Department of Biomedical Molecular Biology at Ghent University, where he leads projects at the intersection of advanced imaging, genome engineering, and cancer biology. Throughout his career, he has been recognized with several awards, including the International Xenopus Board John Gurdon Award and the Belgian Society for Cell and Developmental Biology PhD Excellence Award.

 

• "CRISPR-SID: Identifying EZH2 as a druggable target for desmoid tumors via in vivo dependency mapping”. PNAS, 2021. (PMID: 34789568)
• "RBL1 (p107) functions as tumor suppressor in glioblastoma and small-cell pancreatic neuroendocrine carcinoma in Xenopus tropicalis". Oncogene, 2019. (PMID: 32001819)
• "CRISPR/Cas9 mediated knockout of rb1 and rbl1 leads to rapid and penetrant retinoblastoma development in Xenopus tropicalis". Scientific Reports, 2016. (PMID: 27739525)
• ”Mutations in the histone methyltransferase Ezh2 drive context-dependent leukemia in Xenopus tropicalis”. Leukemia, 2023. (PMID: 37794102)
• "The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples". Under Revision Nat. Comm., BioRxiv, 2023 pre-print (indexed on pubmed at PMID: 38168219)
• "Reflective multi-immersion microscope objectives inspired by the Schmidt telescope". Nature Biotechnology, 2023. (PMID: 36997681)
• "Maximizing CRISPR/Cas9 phenotype penetrance using predictive modeling of editing outcomes in Xenopus and zebrafish embryos". Scientific Reports 2020. (PMID: 32887910)
• "R-spondin2 inhibition of rnf43/znrf3 governs limb development independently of lgr4/5/6. ". Nature, 2018. (PMID: 29769720)
• "TALEN-mediated apc mutation in Xenopus tropicalis phenocopies familial adenomatous polyposis.”. Oncoscience, 2015. (PMID: 26097888)
   

• VIB-IRC, Lab of Developmental Biology, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052 Ghent
• Vleminckx lab - Lab of Developmental Biology & Human Disease Modeling, Department of Biomedical Molecular Biology (UGent)
• member of the consortium for sarcoma research Ghent, ConSarGhent
• Google Scholar
• Wordpress
• X (former Twitter)
• Thomas Naert is interested to receive invitations for presentations or talks