Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes

Background: Transgenic zebrafish lines with the expression of a fluorescent reporter under the control of a cell-type specific promoter, enable transcriptome analysis of FACS sorted cell populations. RNA quality and yield are key determinant factors for accurate expression profiling. Limited cell number and FACS induced cellular stress make RNA isolation of sorted zebrafish cells a delicate process. We aimed to optimize a workflow to extract sufficient amounts of high-quality RNA from a limited number of FACS sorted cells from Tg(fli1a:GFP) zebrafish embryos, which can be used for accurate gene expression analysis. Results: We evaluated two suitable RNA isolation kits (theRNAqueous micro and the RNeasy plus micro kit) and determined that sorting cells directly into lysis buffer is a critical step for success. For low cell numbers, this ensures direct cell lysis, protects RNA from degradation and results in a higher RNA quality and yield. We showed that this works well up to 0.5x dilution of the lysis buffer with sorted cells. In our sort settings, this corresponded to 30,000 and 75,000 cells for the RNAqueous micro kit and RNeasy plus micro kit respectively. Sorting more cells dilutes the lysis buffer too much and requires the use of a collection buffer. We also demonstrated that an additional genomic DNA removal step after RNA isolation is required to completely clear the RNA from any contaminating genomic DNA. For cDNA synthesis and library preparation, we combined SmartSeq v4 full length cDNA library amplification, Nextera XT tagmentation and sample barcoding. Using this workflow, we were able to generate highly reproducible RNA sequencing results. Conclusions: The presented optimized workflow enables to generate high quality RNA and allows accurate transcriptome profiling of small populations of sorted zebrafish cells

RRM2 enhances MYCN-driven neuroblastoma formation and acts as a synergistic target with CHK1 inhibition

High-risk neuroblastoma, a pediatric tumor originating from the sympathetic nervous system, has a low mutation load but highly recurrent somatic DNA copy number variants. Previously, segmental gains and/or amplifications allowed identification of drivers for neuroblastoma development. Using this approach, combined with gene dosage impact on expression and survival, we identified ribonucleotide reductase subunit M2 (RRM2) as a candidate dependency factor further supported by growth inhibition upon in vitro knockdown and accelerated tumor formation in a neuroblastoma zebrafish model coexpressing human RRM2 with MYCN. Forced RRM2 induction alleviates excessive replicative stress induced by CHK1 inhibition, while high RRM2 expression in human neuroblastomas correlates with high CHK1 activity. MYCN-driven zebrafish tumors with RRM2 co-overexpression exhibit differentially expressed DNA repair genes in keeping with enhanced ATR-CHK1 signaling activity. In vitro, RRM2 inhibition enhances intrinsic replication stress checkpoint addiction. Last, combinatorial RRM2-CHK1 inhibition acts synergistic in high-risk neuroblastoma cell lines and patient-derived xenograft models, illustrating the therapeutic potential

SOX11 as guardian of epigenetic plasticity in neuroblastoma

Background/Introduction: Normal human development is controlled through the complex interplay of multiple transcription factors and the reshaping of epigenetic landscapes. Tumor cells can co-opt normal developmental pathways for functions that are linked to tumor progression and may become addicted to survival mechanisms controlled by developmental master regulators. Neuroblastoma (NB), the most common extra-cranial tumor in childhood, arises from the sympatho-adrenergic lineage during normal embryonic development. The genomic landscape of NB is characterized by a low mutational burden and highly recurrent copy number changes. Consequently, these copy number alterations affecting lineage-dependency factors in the sympatho-adrenal lineage might be strong candidates for NB cell addiction. The study of such oncogenic lineage-dependency factors is considered of strong translational value as they could represent highly selective drug targets compared to conventional cytotoxic therapy.Aims: We aimed to scrutinize DNA copy number profiles for gains or amplifications of putative lineage-dependency transcription factors involved in the epigenetic landscape and development of NB.Methods/Materials: Using high resolution copy number analysis of NB tumors we sought for candidate lineage-dependency transcription factors. In vitrofunctional assays were performed upon SOX11knockdown and overexpression. Tumor acceleration was evaluated upon SOX11overexpression in a MYCN-driven zebrafish model. ChIP-seq, ATAC-seq and RNA-sequencing was performed to evaluate the transcriptome and epigenetic landscape, which consequently resulted in the execution of drugging assays for strong candidate targets.Results: We identified recurrent focal gains and amplifications encompassing the SOX11locus and selected this transcription factor as a strong candidate based on (1) its expression in the normal sympatho-adrenal lineage and adrenergic NBs and (2) its control by multiple adrenergic specific distal (super-) enhancers, amongst others. Both in vitroSOX11 knockdown in NB cells and data from the Cancer Dependency Map are indicative for strong dependency of NB cell lines to elevated SOX11expression levels. Furthermore, SOX11 overexpression in a MYCN-driven NB zebrafish model showed accelerated tumor formation. ChIP-sequencing revealed SOX11 controlled transcription of multiple components of major epigenetic modulating protein complexes implicated in chromatin remodeling and enhancer activation (SWI/SNF), chromatin modification (PRC1 and PRC2), DNA methylation as well as several pioneer transcription factors including MYB. Furthermore, ATAC-sequencing indicated SOX11 controlled chromatin opening, predominantly affecting distal enhancers 71marked by SMARCC1 and MYB binding motifs. In addition to the strong co-regulation of MYBand SOX11, SOX11high expressing NB cells showed increased sensitivity for peptidomimetic blockade of MYB.Summary/Conclusions: Our data suggest a key role for SOX11 in the activation of multiple epigenetic modulators in NB leading to an impact on maintenance of adrenergic NB chromatin accessibility and cell identity and contributing to the proliferative MYCNdriven NB phenotype