Biology subjects

van Hooff, S. R.

Publications and source records attributed to van Hooff, S. R..

5 recordsLinked to original sources

bioRxiv2026

Sensitivity profiling reveals consistent drug responses across preclinical neuroblastoma models

Despite intensive treatment, overall survival for high-risk and relapse neuroblastoma patients remains below 50%. Even though comprehensive molecular profiling enables treatment stratification, druggable alterations have been identified for only a subset of patients. In vitro drug screening offers a complementary approach. Here, we compare the translational potential of three preclinical drug screening methods: ex vivo short-term, in vitro patient-derived organoid and in vivo patient-derived xenograft (PDX) drug testing. In total, 55 screens were performed from 38 neuroblastoma samples and five pediatric non-malignant samples, testing 77-224 drugs per screen. Ex vivo short-term drug screens achieved higher success rates than organoid screens (65% versus 23%) and shorter turnaround times (14 days versus 3-12 months). Matched samples showed consistent drug sensitivities across sample origin (patient versus PDX-derived; mean r = 0.84) and method (ex vivo short-term versus organoids; mean r = 0.87), demonstrating that ex vivo short-term screens recapitulate drug sensitivities found in long-term organoid models. In parallel, as part of the ITCC-P4 consortium, ten compounds were tested in vivo in eight PDX models, with samples matching the ex vivo screens. For seven out of ten clinically available compounds, ex vivo drug responses were comparable with in vivo responses in matched PDX models. These results demonstrate that, while organoids and PDX models remain essential for drug discovery, ex vivo short-term drug screening provides a rapid alternative for functional precision oncology in neuroblastoma.

cell biology↗

bioRxiv2026

Apc truncation enforces optimal Wnt signalling during early intestinal tumourigenesis

Colorectal cancer (CRC) development is frequently initiated by inactivation of tumour suppressor gene adenomatous polyposis coli (APC), resulting in hyperactivation of the Wnt/ {beta}-catenin signalling pathway. The level of Wnt pathway activation is determined by the number of functional {beta}-catenin binding site repeats retained within the truncated APC protein. Accumulating evidence indicates that acquisition of the second APC mutational event is non-random and selects for mutations that confer a just right level of Wnt activity, suggesting that tumour initiation requires Wnt signalling to be maintained within a specific range. In this study, we investigated how specific Apc mutations modulate Wnt pathway activity and downstream cellular programs. Using CRISPR/Cas9 technology, we generated mouse intestinal organoid cultures harbouring distinct alterations in the number of {beta}-catenin binding repeats. We demonstrate a direct correlation between the number of retained repeats and Wnt signalling activity. Notably, organoids retaining higher numbers of functional repeats were subjected to selective pressure, resulting in the acquisition of additional mutations that lead to increased Wnt activity, consistent with the just right model. Transcriptomic analysis by RNA sequencing revealed that clones with distinct {beta}-catenin binding capacity exhibit differential transcriptional programs, including graded changes in cell cycle activity and a metabolic shift associated with progressive loss of {beta}-catenin binding repeats. Together, these findings reveal functional and metabolic heterogeneity among Apc- mutant cells, support the existence of selective pressures for optimal Wnt signalling during tumor initiation, and identify potential metabolic vulnerabilities that may be exploited for therapeutic intervention including interception of premalignant lesions.

cancer biology↗

bioRxiv2022

Two opposing gene expression patterns within ATRX aberrant neuroblastoma

Neuroblastoma is the most common extracranial solid tumor in children. A subgroup of high-risk patients is characterized by aberrations in the chromatin remodeller ATRX that is encoded by 35 exons. In contrast to other pediatric cancer where ATRX point mutations are most frequent, multi-exon deletions (MEDs) are the most frequent type of ATRX aberrations in neuroblastoma. Of these MEDs 75% are predicted to produce in-frame fusion proteins, suggesting a potential gain-of-function effect compared to nonsense mutations. For neuroblastoma there are only a few patient-derived ATRX aberrant models. Therefore, we created isogenic ATRX aberrant models using CRISPR-Cas9 in several neuroblastoma cell lines and one tumoroid and performed total RNA-sequencing on these and on the patient-derived model. Gene set enrichment analysis (GSEA) showed decreased expression of genes related to both ribosome biogenesis and several metabolic process in our isogenic ATRX exon 2-10 MED model systems, the patient-derived MED models and in tumor data containing two patients with an ATRX exon 2-10 MED. Interestingly, for our isogenic ATRX knock-out and exon 2-13 MED models GSEA revealed an opposite expression pattern characterized by increased expression of genes related to ribosome biogenesis and several metabolic process. Our validations confirmed a potential role of ATRX in the regulation of ribosome homeostasis. In this manner we identified two distinct molecular expression patterns within ATRX aberrant neuroblastomas with important implications for the need of distinct treatment regimens.

cancer biology↗

bioRxiv2021

Loss of p16INK4a in neuroblastoma cells induces shift to an immature state with mesenchymal characteristics and increases sensitivity to EGFR inhibitors

Homozygous inactivation of the CDKN2A locus is one of the most common genomic aberrations in human cancer. The locus codes for two unrelated and distinctly regulated proteins: p14ARF and p16INK4a, which inhibit MDM2 and CDK4/6, respectively. Loss of CDKN2A is also a recurrent event in relapsed neuroblastoma, a childhood tumour that arises from neural crest cells. To examine the consequences of the loss of the two distinct gene transcripts in neuroblastoma, we used the CRISPR-Cas9 system to knockout p14, p16 and p14+p16 in SY5Y cells. RNA sequencing of the transcriptome revealed a striking shift towards an immature Schwann cell precursor-like phenotype with mesenchymal characteristics, specifically in the p16 and p14+p16 knockouts. High-throughput drug screening of p16 and p14+p16 knockout clones identified a large increase in sensitivity to EGFR inhibitors. On protein level, we were able to confirm that EGFR pathway activation is higher in p14+p16 knockout cells and that treatment with the EGFR inhibitor afatinib resulted in higher levels of apoptosis. Afatinib also reduced tumour growth in vivo in xenografts transplanted with p14+p16 knockout SY5Y cells. Overall, our study suggests that CDKN2A deletion in neuroblastoma relates to a phenotypic shift towards a more progenitor like state and increases sensitivity to EGFR inhibitors.

cancer biology↗

bioRxiv2020

Tumor to normal single cell mRNA comparisons reveal a pan-neuroblastoma cancer cell

Neuroblastoma is an embryonal childhood cancer that arises from aberrant development of the neural crest, mostly within the fetal adrenal medulla. It is not established what developmental processes neuroblastoma cancer cells represent. Here, we sought to reveal the phenotype of neuroblastoma cancer cells by comparing cancer (n=16,591) with fetal adrenal single cell transcriptomes (n=57,972). Our principal finding was that the neuroblastoma cancer cell resembled fetal sympathoblasts, but no other fetal adrenal cell type. The sympathoblastic state was a universal feature of neuroblastoma cells, transcending cell cluster diversity, individual patients and clinical phenotypes. We substantiated our findings in 652 neuroblastoma bulk transcriptomes and by integrating canonical features of the neuroblastoma genome with transcriptional signals. Overall, our observations indicate that there exists a pan-neuroblastoma cancer cell state which may be an attractive target for novel therapeutic avenues.

cancer biology↗