Biology subjects

Van Roy, N.

Publications and source records attributed to Van Roy, N..

4 recordsLinked to original sources

bioRxiv2026

Benchmarking fragmentation-derived artificial cfDNA reference standards

An important step toward clinical implementation of (epi-)genomic assays on liquid biopsies is their validation on identical samples within and across laboratories. For these validation studies, there is a need for cell-free DNA (cfDNA) samples with defined tumor fractions and (epi-)genomic aberrations. However, the amount of circulating cfDNA isolated from patient samples is often limited, especially in pediatric cases. Additionally, patient samples contain a high degree of variability in cfDNA yield and tumor fraction. Several commercial artificial cfDNA products are available for validation studies, however their use is restricted to specific assays, aberrations and/or tumor entities. Alternatively, artificial cfDNA samples can be produced by fragmenting genomic DNA to mimic highly fragmented cfDNA derived from both tumor and healthy blood, followed by mixing artificial tumoral and healthy cfDNA at defined fractions. In this study, we compared native cfDNA with artificial cfDNA generated by three different fragmentation methods, including sonication and two enzymatic digestions using micrococcal nuclease and double-stranded deoxyribonuclease (dsDNase). We assessed fragment length profiles, end motifs and nucleosome occupancy patterns from shallow whole-genome sequencing data, as well as coverage profiles from targeted panel sequencing, together with a small-scale mixing experiment of tumor and healthy cell derived artificial cfDNA. Although sonication remains a convenient high-throughput approach to generate artificial cfDNA for certain downstream applications, enzymatic fragmentation, particularly the dsDNase-based method, more faithfully reproduced native cfDNA characteristics.

genomics↗

bioRxiv2025

Targeting replication stress in neuroblastoma by exploiting the synergistic potential of second generation RRM2 and CHK1 inhibitors

Tumor cells often cope with elevated levels of replication stress (RS) causing increased dependency on ATR-CHK1 signalling. We previously presented RRM2, the regulatory component of the ribonucleotide reductase (RNR) enzyme, as novel dependency in neuroblastoma, in keeping with its role in RS resistance. We identified strong synergism for combined RRM2-CHK1 inhibition using the iron chelator triapine and prexasertib respectively. To obtain direct RNR targeting, we evaluated a novel inhibitor, TAS1553, specifically disrupting the RNR complex in this study. Treatment with TAS1553 impedes cell growth and induces enhanced RS, DNA damage and apoptosis. We demonstrated strong synergism between TAS1553 the CHK1 inhibitors prexasertib and SRA737 in both NB and sarcoma cell lines, underscoring the broad clinical potential of combinatorial RRM2-CHK1 inhibition. Transcriptome profiling demonstrated strong overlap between the different RRM2-CHK1 treatments and revealed differential expression of RNA splicing components, opening new perspectives for combination treatments using splicing inhibitors. Altogether, this study paves the way for further preclinical testing of second generation RRM2 and CHK1 inhibitors such as TAS1553 and SRA737 in neuroblastoma and sarcomas.

cancer biology↗

bioRxiv2020

SOX11 is a lineage-dependency factor and master epigenetic regulator in neuroblastoma

The pediatric extra-cranial tumor neuroblastoma (NB) is characterised by a low mutation burden while copy number alterations are present in most high-risk cases. We identified SOX11 as a strong lineage dependency transcription factor in adrenergic NB based on recurrent chromosome 2p focal gains and amplifications, its specific expression in the normal sympatho-adrenal lineage and adrenergic NBs and its regulation by multiple adrenergic specific cis-interacting (super-)enhancers. Adrenergic NBs are strongly dependent on high SOX11 expression levels for growth and proliferation. Through genome-wide DNA-binding and transcriptome analysis, we identified and validated functional SOX11 target genes, several of which implicated in chromatin remodeling and epigenetic modification. SOX11 controls chromatin accessibility predominantly affecting distal adrenergic lineage-specific enhancers marked by binding sites of the adrenergic core regulatory circuitry. During normal sympathoblast differentiation we find expression of SOX11 prior to members of the adrenergic core regulatory circuitry. Given the broad control of SOX11 of multiple epigenetic regulatory complexes and its presumed pioneer factor function, we propose that adrenergic NB cells have co-opted the normal role of SOX11 as a crucial regulator of chromatin accessibility and cell identity.

cancer biology↗

bioRxiv2019

Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA: a proof-of-principle study

In the clinical management of pediatric solid tumors, histological examination of tumor tissue obtained by a biopsy remains the gold standard to establish a conclusive pathological diagnosis. The DNA methylation pattern of a tumor is known to correlate with the histopathological diagnosis across cancer types and is showing promise in the diagnostic workup of tumor samples. This methylation pattern can be detected in the cell-free DNA. Here, we provide proof-of-concept of histopathologic classification of pediatric tumors using cell-free reduced representation bisulfite sequencing (cf-RRBS) from retrospectively collected plasma and cerebrospinal fluid samples. We determined the correct tumor type in 49 out of 60 (81.6%) samples starting from minute amounts (less than 10 ng) of cell-free DNA. We demonstrate that the majority of misclassifications were associated with sample quality and not with the extent of disease. Our approach has the potential to help tackle some of the remaining diagnostic challenges in pediatric oncology in a cost-effective and minimally invasive manner. Translational relevanceObtaining a correct diagnosis in pediatric oncology can be challenging in some tumor types, especially in renal tumors or central nervous system tumors. Furthermore, the diagnostic odyssey can result in anxiety and discomfort for these children. By applying a novel technique, reduced representation bisulfite sequencing on cell-free DNA (cf-RRBS), we show the feasibility of obtaining the histopathological diagnosis with a minimally invasive test on either plasma or cerebrospinal fluid. Furthermore, we were able to derive the copy number profile or tumor subtype from the same assay. Given that primary tumor material might be difficult to obtain, in particular in critically ill children or depending on the tumor location, and might be limited in terms of quantity or quality, our assay could become complementary to the classical tissue biopsy in difficult cases.

genomics↗