Project description:Neuroblastoma (NB) is the most common malignant solid tumor in the abdomen of children, with high degree of malignancy, poor prognosis and unknown pathogenesis. So we aim to investigate intra-tumor heterogeneity of neuroblastoma at single cell resolution.
Project description:WGBS was performed on: 1) untreated SH-SY5Y human neuroblastoma cells (day 0) 2) vincristine-treated SH-SY5Y human neuroblastoma cells (7 days of treatment - day 7) 3) vincristine-treated SH-SY5Y human neuroblastoma cells (7 days of treatment followed by 7 days of recovery - day 14)
Project description:Minichromosome maintenance complex component 6 (MCM6), as an important replication permission factor, is involved in the pathogenesis of various tumors. we studied the expression of MCM6 in neuroblastoma and its influence on tumor characteristics and prognosis, and we found MCM6 has significant effect on tumor growth promotion. To investigate the underlying mechanism that MCM6 in neuroblastoma, we compared the transcriptomes of siRNA interfered MCM6 and negative control neuroblastoma cells.
Project description:The specific genes that influence neuroblastoma biology and are targeted by genomic alterations remain largely unknown. We quantified mRNA expression in a highly annotated series of 101 prospectively collected diagnostic neuroblastoma primary tumors and the expression profiles were determined using Affymetrix U95Av2 arrays. Comparisons between the sample groups allow the identification of genes with localized expression patterns. This study demonstrates that the genomic data can be used to subcategorize the disease into molecular subsets and the regional copy number alterations are correlated with a broad number of transcriptional alterations genome wide. This data also suggests that multiple genes from several discrete regions of the human genome co-operate to supress neuroblastoma tumorigenesis and progression. Experiment Overall Design: A highly annotated series of 101 prospectively collected diagnostic neuroblastoma primary tumors were selected to quantify mRNA expression using an oligonucleotide based microarray. Genomic copy number status at the prognostically relevant loci 1p36,2p24(MYCN), 11q23 and 17q23 was determined by PCR and was aberrant in 26, 20, 40 and 38 cases, respectively. Fetal brain RNA was used as a control sample.
Project description:Following DPST crosslinking of human neuroblastoma cells, nuclear-cytoplasmic fractionation was performed using hypotonic lysis to obtain cytoplasmic and nuclear protein compartments. Through systematic analysis of crosslinking mass spectrometry data, we elucidated how subcellular compartmentalized microenvironments regulate spatial distribution of protein conformations and topological architecture of interaction networks. This study reveals the heterogeneous principles governing dynamic protein assembly between nuclear and cytoplasmic compartments in neuroblastoma cells.
Project description:Previous studies have reported that metastatic tumor cells acquire genomic aberrations compared to those present in the primary due to an unstable genome. However, it is not clear if all malignancies follow a similar pattern. Neuroblastoma is the most common extra-cranial solid tumor of childhood. To examine how the neuroblastoma genome changes during tumor progression, we investigated chromosomal structural alterations across three tumors from a patient with hisg-risk neuroblastoma. The tumors included the primary tumor, one metastatis collected at diagnosis before any treatment, and a second metastatis collected during post mortem investigation. The recapitulated chromosomal structural alterations demonstrated that all three tumors had extensive chromosomal alterations involving virtually every chromosome. All tumors were aneuploid and shared many chromosomal alterations often seen in neuroblastoma. Despite some tumor to tumor structural variability, approximately 81-91% of the altered regions were shared among the three tumor genomes with primary tumor and pre-treamment metastatis being the most similar. Three samples from one patient with high-risk neuroblastoma. Primary tumor plus two metastatic tumors. One of metastasis sampled at diagnosis, before any treatment, and second metastasis taken at autopsy.
Project description:Previous studies have reported that metastatic tumor cells acquire genomic aberrations compared to those present in the primary due to an unstable genome. However, it is not clear if all malignancies follow a similar pattern. Neuroblastoma is the most common extra-cranial solid tumor of childhood. To examine how the neuroblastoma genome changes during tumor progression, we investigated chromosomal structural alterations across three tumors from a patient with hisg-risk neuroblastoma. The tumors included the primary tumor, one metastatis collected at diagnosis before any treatment, and a second metastatis collected during post mortem investigation. The recapitulated chromosomal structural alterations demonstrated that all three tumors had extensive chromosomal alterations involving virtually every chromosome. All tumors were aneuploid and shared many chromosomal alterations often seen in neuroblastoma. Despite some tumor to tumor structural variability, approximately 81-91% of the altered regions were shared among the three tumor genomes with primary tumor and pre-treamment metastatis being the most similar.
Project description:RNA-sequencing was performed on the following human neuroblastoma cell lines: Kelly, NBL-S, CHP-212, SH-SY5Y, SH-SY5Y LDK-resistant and SH-EP.
Project description:This study was undertaken to assess transcriptional and epigenetic heterogeneity a the level of individual cells within neuroblastoma cell lines, and to compare cell lines with MYCN amplificaion to cell lines without MYCN amplification. Methods: We used 10X Genomics multiome sequencing technology to perform joint gene expression and ATAC profiling on thousands of nuclei isolated from the following human neuoblastoma cell lines: SHSY5Y, SK-N-AS, SK-N-SH, SK-N-DZ, Be-2c, and CHP134. Results: We found considerable gene expression and epigeneic heterogeneity both within and between neuroblastoma cell lines. Conclusion: Joint single-nucleus RNA sequencing and single-nucleus ATAC sequencing has demonsrated that neuroblastoma cell lines are heterogeneous, which may have implications for therapeutic strategies.
