biostudies-arrayexpressOlivier GandrillonHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16741Neuroblastoma (NB), a pediatric cancer arising from disrupted sympathetic neuron differentiation, exhibits marked heterogeneity and limited therapeutic options. To better understand its molecular circuitry dynamics, we applied CARDAMOM, a novel Gene Regulatory Network (GRN) inference framework to single-cell RNA-seq data from patient-derived tumoroids. This approach models gene regulation via piecewise deterministic Markov processes, capturing transcriptional bursting and protein-mediated feedback, overcoming limitations of RNA velocity (e.g., gene independence and lack of biological time). We identified a continuous chromaffin-to-sympathoblast differentiation trajectory, validated by RNA velocity and scFates. Using velocity pseudotime, we selected 85 dynamically relevant genes enriched in cell cycle and DNA replication functions. Notably, 9 genes overlapped with those driving normal sympathoadrenal differentiation, underscoring tumor-normal similarity. The inferred 85-genes network reproduced quite well experimental gene expression patterns in silico, and allowed to predict protein-level dynamics. Furthermore, it allowed to assess the effect of in silico perturbations (both knock-out and overexpression) of hub genes (e.g., TCF4 and PLK1). We show that those perturbations significantly altered cell fate proportions, with TCF4 knockout increasing chromaffin-like cells and reducing proliferative late sympathoblasts — suggesting a therapeutic strategy to promote differentiation. Our work therefore demonstrates that NB tumoroids retain a dynamic, differentiation-like architecture amenable to GRN modeling. Predicted druggable targets (e.g., PLK1, TCF4) offer testable therapeutic avenues, including repurposing BET inhibitors (JQ1) or PLK1 inhibitors (BI2536), potentially in combination.biostudies-arrayexpressSample Collection - PDTs were derived as described in : "Nguyen, T. N. T., et al. (2025). Multiscale modeling of the spatial structure of stem cells in neuroblastoma patient-derived tumoroids reveals a critical role for a short range diffusive process. BioRXiv\Sequencing - Sequenced at tthe IGFL sequencing PSI platform: https://igfl.ens-lyon.fr/offres-et-technologies/platforms/sequencing-platform on an ILLUMINA NEXTSEQ500Nucleic Acid Extraction - Single-cell RNA sequencing was performed using RevGel-seq (Komatsu, 2023), adapted by Scipio Bioscience. PDTs were trypsinized into a single-cell suspension and chemically labeled with a bifunctional linker (polyA and hydrophobic moiety) in DPBS for 5 minutes. Labeled cells (300 cells/µL, 15,000 total) were mixed with barcoded beads (50 µL each) and homogenized to form cell-bead complexes via collisions. The mixture was diluted in 2.4 mL hydrogel, gelated on ice for 20 minutes, and lysed to release RNA, which hybridized to bead-bound poly-T oligos.Library Construction - After degelation, bead-bound RNA underwent reverse transcription (Maxima H Minus RT kit) and second-strand synthesis (S3 Supermix). cDNA was PCR-amplified (KAPA HiFi), purified with SPRIselect, and quality-checked via TapeStation and Qubit. Libraries were prepared using the Illumina Nextera XT Kit (5-minute fragmentation, 10 PCR cycles) and sequenced on the NextSeq500 platform (paired-end, 25/0/0/67).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - median count depth normalization with log1p transformationMetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNA from single cellsHomo sapiensOlivier GandrillonfalsescRNAseq dataset from neuroblastomas tumoroidsNeuroblastoma (NB), a pediatric cancer arising from disrupted sympathetic neuron differentiation, exhibits marked heterogeneity and limited therapeutic options. To better understand its molecular circuitry dynamics, we applied CARDAMOM, a novel Gene Regulatory Network (GRN) inference framework to single-cell RNA-seq data from patient-derived tumoroids. This approach models gene regulation via piecewise deterministic Markov processes, capturing transcriptional bursting and protein-mediated feedback, overcoming limitations of RNA velocity (e.g., gene independence and lack of biological time). We identified a continuous chromaffin-to-sympathoblast differentiation trajectory, validated by RNA velocity and scFates. Using velocity pseudotime, we selected 85 dynamically relevant genes enriched in cell cycle and DNA replication functions. Notably, 9 genes overlapped with those driving normal sympathoadrenal differentiation, underscoring tumor-normal similarity. The inferred 85-genes network reproduced quite well experimental gene expression patterns in silico, and allowed to predict protein-level dynamics. Furthermore, it allowed to assess the effect of in silico perturbations (both knock-out and overexpression) of hub genes (e.g., TCF4 and PLK1). We show that those perturbations significantly altered cell fate proportions, with TCF4 knockout increasing chromaffin-like cells and reducing proliferative late sympathoblasts — suggesting a therapeutic strategy to promote differentiation. Our work therefore demonstrates that NB tumoroids retain a dynamic, differentiation-like architecture amenable to GRN modeling. Predicted druggable targets (e.g., PLK1, TCF4) offer testable therapeutic avenues, including repurposing BET inhibitors (JQ1) or PLK1 inhibitors (BI2536), potentially in combination.2026-07-07T00:00:00Z2026-07-07T05:25:37.518Z2026-03-11T22:24:34.72ZE-MTAB-16741ERP190690EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184