prof. Katleen De Preter (PhD)

The common theme of the Translational Onco-genomics and Bio-informatics lab (UGent) headed by Katleen De Preter is the development of analytical and bio-informatic pipelines for diagnostic, prognostic and predictive analysis enabling a more precise cancer management. 
Previous research projects have led to new prognostic and predictive biomarkers for neuroblastoma which opened new perspectives on clinical management of these patients. This work was driven by the application of various bioinformatics tools exploring transcriptomic data from primary neuroblastoma samples. This resulted in the identification and dissection of oncogenic pathways to pinpoint new vulnerable nodes for therapy and the establishment of m(i)RNA expression signatures for a more accurate prognosis. At the genomics level, we succeeded in the identification of prognostic DNA copy number alterations for high-risk neuroblastoma by an extensive international collaborative study. 
The past years our research focus has shifted from neuroblastoma to a broad spectrum of cancer entities, including lung cancer, esophageal cancer, prostate cancer, triple negative breast cancer, various pediatric cancers as well as CUPs (cancers of unknown primary). Moreover, we embarked on the processing of liquid biopsies such as blood plasma for the analysis and interpretation of (epi-)genomic biomarkers. In this context, we also focus on the development of dedicated data mining pipelines that should accompany these new analytical tools and which are necessary to fully exploit the clinical application for the cancer patient. For instance, we established a new analytical and bioinformatics pipeline to identify the copy number profile for prognosis based on cfDNA (circulating cell-free DNA) isolated from blood plasma. In addition, we developed a method that measures the DNA methylation profile of cfDNA and that aids in diagnosis of both pediatric and adult cancers. At the moment, we are investigating the potential of circulating DNA molecules isolated from blood samples as marker for drug sensitivity and resistance. To allow the interpretation of bulk omics data of complex mixtures (such as in blood), we have built ample expertise in computational deconvolution of bulk omics data. This computational method allows to dissolve data from a complex mixture in its individual components and is also highly relevant in the context of tumor heterogeneity.  Since recently, we embarked on the analysis of tumor heterogeneity (more specifically at transcriptomic and epigenomic level) using single-cell and spatial omics tools, allowing to build a comprehensive reference atlas for the liquid biopsy assays.
In summary, our team has expertise in (single-cell and spatial) (epi-)genomics, bioinformatics and (liquid biopsy) biomarker research for pediatric and adult cancers. Importantly, our research is positioned at the interface between technological/bioinformatic development and clinical validation/implementation.
 

In 2000, Katleen De Preter obtained a Master in Bioscience Engineering (Cell and Gene Biotechnology) at Ghent University. During her PhD and post-doctoral fellowship in the team of prof. Frank Speleman, she was involved in genomics profiling of neuroblastoma tumors aiming to identify new vulnerable markers for therapy and better biomarkers for prognosis and prediction. Since 2011, Katleen became part-time professor at Ghent University and started the research lab of Translational Onco-genomics and Bio-informatics.
In 2019, she obtained a position as full professor with a BOF-ZAP grant. She is author of more than 130 scientific articles in international journals and has a H-index of 45 (Web of Science, August 2026).
In May 2019, her work on biomarkers for neuroblastoma was rewarded with the Antoine Faes price. Katleen was one of the CRIG co-founders and since end 2019 she is member of the CRIG steering committee. 
In 2022, Katleen obtained an ERC consolidator grant for the “EpiGuide” project. End of 2022, she joined the Center for Medical Biotechnology at VIB-UGent as group leader. 
 

• prof. dr. ir. Katleen De Preter - principal investigator, full professor
• prof. Celine Everaert (PhD)
• dr. Kathleen Schoofs (PhD) - post-doctoral fellow
• dr. Sam Kint (PhD) - post-doctoral fellow
• dr. Truong Nguyen (PhD) - post-doctoral fellow
• Lotte Cornelli - doctoral fellow
• dr. Eufra Van Damme (MD) - doctoral fellow
• Vittorio Zanzani - doctoral fellow
• Tamas Trombitas - doctoral fellow
• Seoyeon Oh - doctoral fellow
• Edoardo Giuili - doctoral fellow
• Areti Georgiadi - doctoral fellow
• Luca Visser - doctoral fellow
• Caro Bienstman - doctoral fellow
• Rita Leblans - doctoral fellow
• Toon Callens - doctoral fellow
• Renske Imschoot - doctoral fellow
• Sofie Roelandt - technician
• Robin Van Belle - wet lab technician
• Sofie Van de Velde - dry lab technician 
   

• NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors. CELL REPORTS 43(10):114804. (2024)
• Diagnosis of pediatric central nervous system tumors using methylation profiling of cfDNA from cerebrospinal fluid. CLINICAL EPIGENETICS 16(1):87. (2024)
• A fast, affordable and minimally-invasive diagnostic test for Cancer of Unknown Primary (CUP) using DNA methylation profiling. LABORATORY INVESTIGATION Jun 1:102091. (2024)
• SOX11 Regulates SWI/SNF Complex Components as Member of the Adrenergic Neuroblastoma Core Regulatory Circuitry. NATURE COMMUNICATIONS 14 (1). (2023)
• Benchmarking of Cell Type Deconvolution Pipelines for Transcriptomics Data. NATURE COMMUNICATIONS 11 (1). (2020)
   

• Lab address:  VIB Center for Medical Biotechnology
  UGent Department of Biomolecular Medicine
  Technologiepark-Zwijnaarde 75 - 9052 Gent – BELGIUM
• TOBI lab 
• CMB
• LinkedIn
• Google Scholar
• prof. De Preter is interested to receive invitations for presentations or talks