Transcriptome analysis in shNull and shSETD8 medulloblastoma cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA496472 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8055324.fastq.gz | Fastqsanger.gz | |||
| SRR8055325.fastq.gz | Fastqsanger.gz | |||
| SRR8055326.fastq.gz | Fastqsanger.gz | |||
| SRR8055327.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptome analysis in siNC and siSMO medulloblastoma cells
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Project description:Embryonal tumors of the central nervous system (CNS) represent a highly malignant tumor group of medulloblastoma (MB), atypical teratoid/rhabdoid tumor (AT/RT), and primitive neuroectodermal tumor (PNET) that frequently afflict children. In this study, we report transcriptome traits in MB by using gene expression microarray analyses. We also compare MB dataset with AT/RT cases and AT/RT-like cases. 22 MB cases are subjected to transcriptome analysis
2015-04-15 | E-GEOD-67850 | biostudies-arrayexpress
Project description:Purpose: Medulloblastoma (MB) is the most common malignant brain tumor in children. About 30% MB isreleated to the abnormally activation of the Hedgehog signaling pathway. Smoothened(SMO) is a G protein-coupled receptor that interacts with the patched protein(PTCH) to transduce the hedgehog's proteins signal.This study analyzed the differential expression gene and obtained GO(Gene Ontology) terms and KEGG of these genes after SMO knockdown in Daoy medulloblastoma cells by transcriptome profiling (RNA-seq) .This study aims to provide the basis for subsequent study on medulloblastoma's driven genes. Methods: Cultured Daoy medulloblastoma cells were transfected with 50nM SMO small interference RNA(siRNA) or negtive control siRNA using Lipofectamine 2000 for 48 hours, and transfection efficiency was analyzed by reverse transcription polymerase chain reaction (qRT–PCR) and Western Blot. Then the transriptome profiles of siNC and siSMO cell were sequenced with high-throughput sequencing technology. Results: Using a standardized data analysis workflow, we mapped about 45 million sequence reads per sample. With comparative analysis of transcriptome of siNC and siSMO samples that each repeated three times, 216 differentially expressed genes (DEGs) were found, including 79 up-regulated and 137 down-regulated genes.Genes with q≤0.05 and |log2_ratio|≥1 are identified as DEGs. The ratio that sequence data mapping into reference genome is above 97%. Gene sequences were aligned to public datases such as GO, KEGG(kyoto Encyclopedia of Genes and Genomes) and STRING (Protein-Protein Interaction Networks Functional Enrichment Analysis). 47 genes were matched to GO database. 158 genes were up regulate in 114 pathways and 306 genes were down regulate in 179 pathways in KEGG database. Conclusions: In cancer research, cancer cell lines are important for examining and manipulating molecular and cellular process. DAOY cell line is grouped in the TP53 mutant SHH subgroup MB.Our study represents the first detailed analysis of SMO transcriptomes in Daoy medulloblastoma cells, with biologic replicates, generated by RNA-seq technology. We conclude that knockdown of SMO could participate in transcriptional regulation of many genes and lead to changes in many signaling pathways, witch provises important basis for further investigation of molecular mechanism in SHH subtype MS.
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Project description:Proteogenomic Analysis of Medulloblastoma
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Project description:DDX3X is an ATP-dependent RNA helicase. Missense mutations in DDX3X gene are known to occur in WNT, SHH subgroup medulloblastomas. The role of DDX3X in medulloblastoma biology was studied by downregulating its expression in a SHH subgroup Daoy medulloblastoma cell line. DDX3X knockdown resulted in considerable reduction in proliferation, clonogenic potential and anchorage-independent growth of the medulloblastoma cells. Transcriptome analysis was performed to delineate the molecular mechanism underlying reduction in the malignant potential of the medulloblastoma cells upon DDX3X knockdown. Exogenous expression of three DDX3X missense mutants in the DDX3X knockdown cells could restore the malignant potential of the medulloblastoma cells.
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Project description:Extensive high-throughput sequencing led to the characterization of four main medulloblastoma subgroups. However, to date these analyses have not attained a global comprehension of their dynamic network complexity. Wishing to get a comprehensive view of all medulloblastoma subgroups, we employed a proteomic analysis to integrate accurate protein activity. In this study we present the first analysis regrouping genomic and methylation status, whole-transcriptome sequencing and quantitative proteomics. First, our proteomic analysis clarified medulloblastoma subgroup identity. Second, analysis of proteome and phosphoproteome highlighted disregulated signalling pathways that have not been predicted by transcriptomic analysis. Altogether, combined multi-scale analyses of medulloblastoma have allowed us to identify and prioritize novel molecular drivers involved in human medulloblastoma.
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Project description:The proto-oncogene MYCN is mis-expressed in various types of human brain tumors. To clarify how developmental and regional differences influence transformation, we transduced wild-type or mutationally-stabilized murine N-mycT58A into neural stem cells (NSCs) from perinatal murine cerebellum, brain stem and forebrain. Transplantation of Nmyc WT NSCs was insufficient for tumor formation. N-mycT58A cerebellar and brain stem NSCs generated medulloblastoma/primitive neuroectodermal tumors, whereas forebrain NSCs developed diffuse glioma. Expression analyses distinguished tumors generated from these different regions, with tumors from embryonic versus postnatal cerebellar NSCs demonstrating SHH-dependence and SHH-independence, respectively. These differences were regulated in-part by the transcription factor SOX9, activated in the SHH subclass of human medulloblastoma. Our results demonstrate context-dependent transformation of NSCs in response to a common oncogenic signal. 9 (total) orthotopic tumors generated from E16C, P0C, and P0F NSCs transduced with a mutation-stabilized N-Myc were compared to transduced (but not transplanted) NSCs, NSCs transduced with GFP, and cells derived from the orthotopic tumors. These were also compared to 5 normal P7 cerebella, and 32 medulloblastoma tumors from the GTML mouse model. A cell line derived from a tumor from the GTML mouse model is also included in the comparison.
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