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 (including ALK and FOXM1 pathway) to pinpoint new vulnerable nodes for therapy (ref 1 and 2) 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 (ref 3). 

The past years our research focus has shifted from neuroblastoma to a broad spectrum of cancer entities, including lung cancer, esophageal cancer, prostate 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 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 (ref 4). 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 (ref 5 and 6). At the moment, we are investigating the potential of circulating RNA and DNA from blood cells as marker for drugs sensitivity including immunotherapy. 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 which is an emerging new area in bioinformatics. 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 (ref 7 and 8).  Since recently, we embarked on the analysis of tumor heterogeneity using also single-cell omics tools.

In summary, our team has expertise in (single-cell) 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 100 scientific articles in international journals and has a H-index of 42 (Web of Science, May 2020).
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) - post-doctoral fellow
• dr. Gert Van Peer (PhD) - post-doctoral fellow
• dr. Jilke De Wilde (MD) - doctoral fellow
• dr. Kathleen Schoofs (PhD) - post-doctoral fellow
• Jan Pieter Vanwelkenhuyzen - doctoral fellow
• Alvaro Marcos Rubio - doctoral fellow 
• Bikash Ranjan Samal - doctoral fellow 
• Lotte Cornelli - doctoral fellow 
• dr. Eufra Van Damme (MD) - doctoral fellow
• Noah Bonine - doctoral fellow
• Vittorio Zanzani - doctoral fellow 
• Maísa Renata Ferro dos Santos - doctoral fellow
• Tamas Trombitas - doctoral fellow
• Tine D’hamers - doctoral fellow (focus: immunodeficiency disease)
• Seoyeon Oh - doctoral fellow
• Edoardo Giuili - doctoral fellow
• Sofie Roelandt - technician
• Sofie Van de Velde - dry lab technician 
   

• SOX11 regulates SWI/SNF complex components as member of the adrenergic neuro- blastoma core regulatory circuitry. Nat Commun. 2023 Mar 7;14(1):1267. doi:10.1038/s41467-023-36735-2. PMID: 36882421; PMCID: PMC9992472.
• Benchmarking of cell type deconvolution pipelines for transcriptomics data. Nat Commun. 2020 Nov 6;11(1):5650. doi: 10.1038/s41467-020-19015-1. Erratum in: Nat Commun. 2020 Dec 2;11(1):6291. PMID: 33159064; PMCID: PMC7648640.
• Minimally invasive classification of paediatric solid tumours using reduced representation bisulphite sequencing of cell-free DNA: a proof-of-principle study. Epigenetics. 2021 Jan-Feb;16(2):196-208. doi: 10.1080/15592294.2020.1790950. Epub 2020 Jul 14. PMID: 32662719; PMCID: PMC7889189.
• In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors. Sci Rep. 2018 Nov 30;8(1):17468. doi: 10.1038/s41598-018-35868-5. Erratum in: Sci Rep. 2019 Jun 4;9(1):8360. PMID: 30504901; PMCID: PMC6269481.
• TBX2 is a neuroblastoma core regulatory circuitry component enhancing MYCN/FOXM1 reactivation of DREAM targets. Nat Commun. 2018 Nov 19;9(1):4866. doi: 10.1038/s41467-018-06699-9. PMID: 30451831; PMCID: PMC6242972.
• Genomic Amplifications and Distal 6q Loss: Novel Markers for Poor Survival in High-risk Neuroblastoma Patients. J Natl Cancer Inst. 2018 Oct 1;110(10):1084-1093. doi: 10.1093/jnci/djy022. PMID: 29514301; PMCID: PMC6186524.
• Shallow Whole Genome Sequencing on Circulating Cell-Free DNA Allows Reliable Noninvasive Copy-Number Profiling in Neuroblastoma Patients. Clin Cancer Res. 2017 Oct 15;23(20):6305-6314. doi: 10.1158/1078-0432.CCR-17-0675. Epub 2017 Jul 14. PMID: 28710315.
• Circulating immune cell dynamics as outcome predictors for immunotherapy in non-small cell lung cancer. J Immunother Cancer. 2023 Aug;11(8):e007023. doi: 10.1136/jitc-2023-007023. PMID: 37536935; PMCID: PMC10401220.
• Opportunities and challenges in interpretable deep learning for drug sensitivity prediction of cancer cells. Front Bioinform. 2022 Nov 17;2:1036963. doi: 10.3389/fbinf.2022.1036963. PMID: 36466148; PMCID: PMC9714662.
   

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