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Downregulation of ARID1B, a tumor-suppressor in the WNT subgroup medulloblastoma, activates multiple oncogenic signaling pathways

ABSTRACT: Downregulation of ARID1B, a tumor-suppressor in the WNT subgroup medulloblastoma, activates multiple oncogenic signaling pathways

PROVIDER: PRJNA687667 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13301891.fastq.gz	Fastqsanger.gz
	SRR13301892.fastq.gz	Fastqsanger.gz
	SRR13301893.fastq.gz	Fastqsanger.gz
	SRR13301894.fastq.gz	Fastqsanger.gz
	SRR13301895.fastq.gz	Fastqsanger.gz

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Downregulation of ARID1B, a tumor-suppressor in the WNT subgroup medulloblastoma, activates multiple oncogenic signaling pathways

Project description:About 85% of WNT subgroup medulloblastomas exhibit the loss of one copy of chromosome 6. Loss of function mutations were identified in the ARID1B gene located on chromosome 6 in WNT subgroup tumors suggesting tumor suppressor role for ARID1B in WNT medulloblastomas. The expression of ARID1B was downregulated in the medulloblastoma cell line Daoy using two independent shRNA sequences in a doxycycline-inducible lentiviral vector tet-pLKO-puro and the effect of its downregulation on the gene expression profile was studied by the RNA-seq analysis

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Identification of genes involved in SHH subgroup medulloblastoma using murine whole-body Sleeping Beauty insertional mutagenesis

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Identification of genes involved in SHH subgroup medulloblastoma using murine whole-body Sleeping Beauty insertional mutagenesis

Project description:Ptch+/- mice, which are predisposed to SHH subgroup medulloblastoma, were mutagenised using the Sleeping Beauty transposon to identify genes which increase the frequency of medulloblastoma formation. Gene expression in tumours was assessed both to investigate their relationship to human subgroup tumours, and to identify genes where expression was altered by mutagenesis. Total RNA isolated from tumours induced by SB mutagenesis were compared to normal cerebellum, tumours induced witout SB mutagenesis, and tumours from a distinct model of disease (GTML).

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Subgroup specific somatic copy number aberrations in the medulloblastoma genome

Project description:Medulloblastoma, the most common malignant pediatric brain tumour is currently treated with non-specific cytotoxic therapies including surgery, whole brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, prior attempts to identify targets for therapy have been underpowered due to small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1087 unique medulloblastomas. SCNAs are more common than SNVs in medulloblastoma, and are predominantly subgroup enriched. The most common region of focal copy number gain is a tandem duplication of the Parkinson's disease gene SNCAIP, which is exquisitely restricted to Subgroup 4alpha. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1 that arise through localized chromosomal shattering (topochromothripsis) are restricted to Group 3 tumours. Numerous actionable SCNAs, including recurrent events targeting TGFbeta signaling in Group 3, and NF-kappaB signaling in Group 4 suggest future avenues for rational, targeted therapy This SuperSeries is composed of the SubSeries listed below.

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ARID1B

Project description:ARID1B

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Novel mutations target distinct subgroups of medulloblastoma.

Project description:Medulloblastoma is a malignant childhood brain tumour comprising four discrete subgroups. To identify mutations that drive medulloblastoma we sequenced the entire genomes of 37 tumours and matched normal blood. One hundred and thirty-six genes harbouring somatic mutations in this discovery set were sequenced in an additional 56 medulloblastomas. Recurrent mutations were detected in 41 genes not yet implicated in medulloblastoma: several target distinct components of the epigenetic machinery in different disease subgroups, e.g., regulators of H3K27 and H3K4 trimethylation in subgroup-3 and 4 (e.g., KDM6A and ZMYM3), and CTNNB1-associated chromatin remodellers in WNT-subgroup tumours (e.g., SMARCA4 and CREBBP). Modelling of mutations in mouse lower rhombic lip progenitors that generate WNT-subgroup tumours, identified genes that maintain this cell lineage (DDX3X) as well as mutated genes that initiate (CDH1) or cooperate (PIK3CA) in tumourigenesis. These data provide important new insights into the pathogenesis of medulloblastoma subgroups and highlight targets for therapeutic development. A total of 76 pediatric medulloblastoma samples were analyzed, representing 4 expression classes

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Project description:The BAF complex modulates chromatin accessibility. Specific BAF configurations have functional consequences, and subunit switches are essential for cell differentiation. ARID1B and its paralog ARID1A encode for mutually exclusive BAF subunits. De novo ARID1B haploinsufficient mutations cause a neurodevelopmental disorder spectrum, including Coffin-Siris syndrome, which is characterized by neurological and craniofacial features. Here, we reprogrammed ARID1B+/- Coffin-Siris patient-derived skin fibroblasts into iPSCs, and modeled cranial neural crest cell (CNCC) formation. We discovered that ARID1B is active only during the first stage of this process, coinciding with neuroectoderm specification, where it is part of a lineage-specific BAF configuration (ARID1B-BAF), including SMARCA4, and nine additional subunits. ARID1B-BAF acts as a gate-keeper, ensuring exit from pluripotency and lineage commitment, by attenuating NANOG, SOX2 and the thousands of enhancers directly regulated by these two pluripotency factors at the iPSC stage. In iPSCs, these enhancers are maintained active by an ARID1A-containing BAF. At the onset of differentiation, cells transition from ARID1A-BAF to ARID1B-BAF, eliciting attenuation of the NANOG/SOX2 networks, and triggering pluripotency exit. Coffin-Siris patient cells fail to perform the ARID1A/ARID1B switch, and maintain ARID1A-BAF at pluripotency enhancers throughout all stages of CNCC formation. This leads to a persistent and aberrant SOX2 and NANOG activity, which impairs CNCC formation. In fact, despite showing the typical neural crest signature (TFAP2A+, SOX9+), the ARID1B-haploinsufficient CNCCs are also NANOG-positive, in stark contrast with the ARID1B-wt CNCCs, which are NANOG-negative. These findings suggest a connection between ARID1B mutations, neuroectoderm formation, and a pathogenic mechanism for Coffin-Siris syndrome.

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Integrative Genomic Analysis of Medulloblastoma Identiﬁes a Molecular Subgroup That Drives Poor Clinical Outcome

Project description:Medulloblastomas are heterogeneous tumors that collectively represent the most common malignant brain tumor in children. To understand the molecular characteristics underlying their heterogeneity and to identify whether such characteristics represent risk factors for patients with this disease, we performed an integrated genomic analysis of a large series of primary tumors. Identified are six molecular subgroups of medulloblastoma, each with a unique combination of numerical and structural chromosomal aberrations that globally influence mRNA and miRNA expression. We reveal the relative contribution of each subgroup to clinical outcome as a whole and show that a previously unidentified molecular subgroup, characterized genetically by c-MYC copy number gains and transcriptionally by enrichment of photoreceptor pathways and increased miR-183-96-182 expression, is associated with significantly lower rates of event-free and overall survivals. Our results detail the complex genomic heterogeneity of medulloblastomas and identify a previously unrecognized molecular subgroup with poor clinical outcome for which more effective therapeutic strategies should be developed.

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