Katleen De Preter
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View article: Defining the optimal setting for transcriptomic analyses on blood samples for response prediction in immunotherapy-treated NSCLC patients
Defining the optimal setting for transcriptomic analyses on blood samples for response prediction in immunotherapy-treated NSCLC patients Open
View article: Blood collection tube and RNA purification method recommendations for extracellular RNA transcriptome profiling: A large-scale pre-analytical variable performance evaluation
Blood collection tube and RNA purification method recommendations for extracellular RNA transcriptome profiling: A large-scale pre-analytical variable performance evaluation Open
Using blood-based extracellular RNA (circulating cell-free RNA; exRNA) as a clinical biomarker requires validated procedures for sample collection and processing and RNA quantification. No study to date has systematically tested pre-analyt…
View article: Dramatic impact of blood collection tube and RNA purification method on extracellular RNA transcriptomes
Dramatic impact of blood collection tube and RNA purification method on extracellular RNA transcriptomes Open
The use of blood-based extracellular RNA (cell-free RNA; exRNA) as clinical biomarker requires the implementation of a validated procedure for sample collection, processing, and profiling. So far, no study has systematically addressed the …
View article: Diagnosis of pediatric central nervous system tumors using methylation profiling of cfDNA from cerebrospinal fluid
Diagnosis of pediatric central nervous system tumors using methylation profiling of cfDNA from cerebrospinal fluid Open
View article: miR-99b-5p, miR-380-3p, and miR-485-3p are novel chemosensitizing miRNAs in high-risk neuroblastoma
miR-99b-5p, miR-380-3p, and miR-485-3p are novel chemosensitizing miRNAs in high-risk neuroblastoma Open
View article: Diagnosis of pediatric central nervous system tumors using methylation profiling of cfDNA from cerebrospinal fluid
Diagnosis of pediatric central nervous system tumors using methylation profiling of cfDNA from cerebrospinal fluid Open
Pediatric central nervous system tumors remain challenging to diagnose. Imaging approaches do not provide sufficient detail to discriminate between different tumor types, while the histopathological examination of tumor tissue shows high i…
View article: Computational deconvolution of DNA methylation data from mixed DNA samples
Computational deconvolution of DNA methylation data from mixed DNA samples Open
In this review, we provide a comprehensive overview of the different computational tools that have been published for the deconvolution of bulk DNA methylation (DNAm) data. Here, deconvolution refers to the estimation of cell-type proporti…
View article: Evaluation of single-sample network inference methods for precision oncology
Evaluation of single-sample network inference methods for precision oncology Open
A major challenge in precision oncology is to detect targetable cancer vulnerabilities in individual patients. Modeling high-throughput omics data in biological networks allows identifying key molecules and processes of tumorigenesis. Trad…
View article: MYCN and SNRPD3 cooperate to maintain a balance of alternative splicing events that drives neuroblastoma progression
MYCN and SNRPD3 cooperate to maintain a balance of alternative splicing events that drives neuroblastoma progression Open
Many of the pro-tumorigenic functions of the oncogene MYCN are attributed to its regulation of global gene expression programs. Alternative splicing is another important regulator of gene expression and has been implicated in neuroblastoma…
View article: Mitotic Dysregulation at Tumor Initiation Creates a Therapeutic Vulnerability to Combination Anti-Mitotic and Pro-Apoptotic Agents for MYCN-Driven Neuroblastoma
Mitotic Dysregulation at Tumor Initiation Creates a Therapeutic Vulnerability to Combination Anti-Mitotic and Pro-Apoptotic Agents for MYCN-Driven Neuroblastoma Open
MYCN amplification occurs in approximately 20–30% of neuroblastoma patients and correlates with poor prognosis. The TH-MYCN transgenic mouse model mimics the development of human high-risk neuroblastoma and provides strong evidence for the…
View article: Human iPSC modeling recapitulates in vivo sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma
Human iPSC modeling recapitulates in vivo sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma Open
Studies defining normal and disrupted human neural crest cell development have been challenging given its early timing and intricacy of development. Consequently, insight into the early disruptive events causing a neural crest related dise…
View article: Case series on clinical applications of liquid biopsy in pediatric solid tumors: towards improved diagnostics and disease monitoring
Case series on clinical applications of liquid biopsy in pediatric solid tumors: towards improved diagnostics and disease monitoring Open
Background and aims Solid tumors account for about 30% of all pediatric cancers. The diagnosis is typically based on histological and molecular analysis of a primary tumor biopsy. Liquid biopsies carry several advantages over conventional …
View article: Circulating immune cell dynamics as outcome predictors for immunotherapy in non-small cell lung cancer
Circulating immune cell dynamics as outcome predictors for immunotherapy in non-small cell lung cancer Open
The use of immune checkpoint inhibitors (ICIs) continues to transform the therapeutic landscape of non-small cell lung cancer (NSCLC), with these drugs now being evaluated at every stage of the disease. In contrast to these advances, littl…
View article: Evaluation of single-sample network inference methods for precision oncology
Evaluation of single-sample network inference methods for precision oncology Open
A major challenge in precision oncology is to identify targetable cancer vulnerabilities in individual patients. Modelling high-throughput omics data in biological networks allows identifying key molecules and processes of tumorigenesis. T…
View article: Table S6 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Table S6 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
TEAD4 ChIP-seq results
View article: Table S1 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Table S1 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
Neuroblastoma Molecular subtypes and clinical information.
View article: Table S3 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Table S3 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
ARACNe-AP transcriptional network from gene expression profiles
View article: Table S3 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Table S3 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
ARACNe-AP transcriptional network from gene expression profiles
View article: Supplementary Data from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Supplementary Data from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
Supplementary Experimental Procedures; Supplementary Figures S1-S10; Supplementary Table Legends S1-S9; Supplementary Tables S8-S9; Additional References
View article: Table S5 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Table S5 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
RNAi screening to identify MYCNA subtype specific MRs
View article: Table S4 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Table S4 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
Master Regulator Analysis results from msVIPER
View article: Data from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Data from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
High-risk neuroblastomas show a paucity of recurrent somatic mutations at diagnosis. As a result, the molecular basis for this aggressive phenotype remains elusive. Recent progress in regulatory network analysis helped us elucidate disease…
View article: Table S1 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Table S1 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
Neuroblastoma Molecular subtypes and clinical information.
View article: Table S7 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Table S7 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
RNA-seq derived signatures and pathway analysis from shTEAD4, shMYCN ans shWWTR1
View article: Data from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Data from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
High-risk neuroblastomas show a paucity of recurrent somatic mutations at diagnosis. As a result, the molecular basis for this aggressive phenotype remains elusive. Recent progress in regulatory network analysis helped us elucidate disease…
View article: Table S6 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Table S6 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
TEAD4 ChIP-seq results
View article: Table S4 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Table S4 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
Master Regulator Analysis results from msVIPER
View article: Supplementary Data from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Supplementary Data from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
Supplementary Experimental Procedures; Supplementary Figures S1-S10; Supplementary Table Legends S1-S9; Supplementary Tables S8-S9; Additional References
View article: Table S2 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Table S2 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
Differential expression and biological pathway enrichment analysis of neuroblastoma molecular subtypes
View article: Table S2 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Table S2 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma Open
Differential expression and biological pathway enrichment analysis of neuroblastoma molecular subtypes