A5034282785- Neuroblastoma Research and Treatments
- Cancer, Hypoxia, and Metabolism
- Protein Degradation and Inhibitors
- Cancer Genomics and Diagnostics
- Ubiquitin and proteasome pathways
- Cancer-related molecular mechanisms research
- Lung Cancer Research Studies
- Signaling Pathways in Disease
- Glioma Diagnosis and Treatment
- Molecular Biology Techniques and Applications
- Virus-based gene therapy research
- Chromatin Remodeling and Cancer
- CAR-T cell therapy research
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- Cancer therapeutics and mechanisms
- MicroRNA in disease regulation
- Genomic variations and chromosomal abnormalities
- RNA modifications and cancer
- CRISPR and Genetic Engineering
- Receptor Mechanisms and Signaling
- Single-cell and spatial transcriptomics
- Microtubule and mitosis dynamics
- Renal and related cancers
- interferon and immune responses
Ghent University Hospital
2015-2024
Cancer Research Institute Ghent
2015-2024
Ghent University
2015-2024
VIB-UGent Center for Medical Biotechnology
2023-2024
Vlaams Instituut voor Biotechnologie
2023
Bioinformatics Institute
2016
Inserm
2010-2014
Institut Curie
2014
German Cancer Research Center
2011-2013
Heidelberg University
2005-2013
Many computational methods have been developed to infer cell type proportions from bulk transcriptomics data. However, an evaluation of the impact data transformation, pre-processing, marker selection, composition and choice methodology on deconvolution results is still lacking. Using five single-cell RNA-sequencing (scRNA-seq) datasets, we generate pseudo-bulk mixtures evaluate combined these factors. Both methodologies those that use scRNA-seq as reference perform best when applied in...
Compromised RNA quality is suggested to lead unreliable results in gene expression studies. Therefore, assessment of integrity and purity deemed essential prior including samples the analytical pipeline. This may be particular importance when diagnostic, prognostic or therapeutic conclusions depend on such analyses. In this study, comparative value six parameters was determined using a large panel 740 primary tumour for which real-time quantitative PCR were available. The tested comprise...
Purpose Neuroblastoma is a genetically heterogeneous pediatric tumor with remarkably variable clinical behavior ranging from widely disseminated disease to spontaneous regression. In this study, we aimed for comprehensive genetic subgroup discovery and assessment of independent prognostic markers based on genome-wide aberrations detected by comparative genomic hybridization (CGH). Materials Methods Published CGH data 231 primary untreated neuroblastomas were converted digitized format...
ALK inhibitors induce complete tumor regression in a mouse model of ALK-driven neuroblastoma.
Targeting BET proteins was previously shown to have specific antitumoral efficacy against MYCN-amplified neuroblastoma. We here assess the therapeutic of inhibitor, OTX015, in preclinical neuroblastoma models and extend knowledge on role BRD4 MYCN-driven neuroblastoma.The OTX015 assessed vitro vivo human murine To study effects inhibition context high MYCN levels, ectopically expressed cells. The effect BRD4-regulated transcriptional pause release analyzed using H3K27Ac chromatin...
1 Summary Recent advances in RNA sequencing enable the generation of genome-wide expression data at single-cell level, opening up new avenues for transcriptomics and systems biology. A application whole-transcriptomics is unbiased ordering cells according to their progression along a dynamic process interest. We introduce SCORPIUS, method which can effectively reconstruct an individual without any prior information about process. Comprehensive evaluation using ten scRNA-seq datasets shows...
Abstract High-risk neuroblastomas show a paucity of recurrent somatic mutations at diagnosis. As result, the molecular basis for this aggressive phenotype remains elusive. Recent progress in regulatory network analysis helped us elucidate disease-driving mechanisms downstream genomic alterations, including chromosomal alterations. Our identified three subtypes high-risk neuroblastomas, consistent with and subtype-specific master regulator proteins that were conserved across independent...
Histone chaperone FACT acts in a positive feedback loop with MYCN and is therapeutic target neuroblastoma.
Neuroblastoma, a childhood cancer that originates from neural crest-derived cells, is the most common deadly solid tumor of infancy. Amplification MYCN oncogene, which occurs in approximately 20–25% human neuroblastomas, prominent genetic marker high-stage disease. The availability valid preclinical vivo models prerequisite to develop novel targeted therapies. We here report on generation transgenic mice with Cre-conditional induction dopamine β-hydroxylase-expressing termed...
Purpose: Neuroblastoma (NB) is a heterogeneous disease characterized by distinct clinical features and the presence of typical copy-number alterations (CNAs). Given strong association these CNA profiles with prognosis, analysis profile at diagnosis mandatory. Therefore, we tested whether circulating cell-free DNA (cfDNA) present in plasma samples patients NB could offer valuable alternative to primary tumor for profiling.Experimental Design: In 37 NB, cfDNA using shallow whole genome...
// Alex Cazes 1,2 , Lucille Lopez-Delisle Konstantina Tsarovina 3 Cécile Pierre-Eugène Katleen De Preter 4 Michel Peuchmaur 5,6 André Nicolas 7 Claire Provost 8 Caroline Louis-Brennetot Romain Daveau Candy Kumps Ilaria Cascone 9 Gudrun Schleiermacher 1,2,10 Aurélie Prignon Frank Speleman Hermann Rohrer Olivier Delattre and Isabelle Janoueix-Lerosey 1 Inserm U830, 26 rue d'Ulm, 75005 Paris, France. 2 Institut Curie, Centre de Recherche, Research Group Developmental Neurobiology, Max Planck...
Abstract Chromosome 17q gains are almost invariably present in high-risk neuroblastoma cases. Here, we perform an integrative epigenomics search for dosage-sensitive transcription factors on marked by H3K27ac defined super-enhancers and identify TBX2 as top candidate gene. We show that is a constituent of the recently established core regulatory circuitry with features cell identity factor, driving proliferation through activation p21-DREAM repressed FOXM1 target genes. Combined MYCN/TBX2...
Neuroblastoma is characterized by substantial clinical heterogeneity. Despite intensive treatment, the survival rates of high-risk neuroblastoma patients are still disappointingly low. Somatic chromosomal copy number aberrations have been shown to be associated with patient outcome, particularly in low- and intermediate-risk patients. To improve outcome prediction neuroblastoma, we aimed design a prognostic classification method based on aberrations.In an international collaboration,...
Abstract Background Neuroblastoma tumor cells are assumed to originate from primitive neuroblasts giving rise the sympathetic nervous system. Because these precursor not detectable in postnatal life, their transcription profile has remained inaccessible for comparative data mining strategies neuroblastoma. This study provides first genome-wide mRNA expression of human fetal neuroblasts. To this purpose, small islets normal were isolated by laser microdissection adrenal glands. Results...