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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Deep Sequencing Identifies IDH1 R132S Mutation in Adult Medulloblastoma (Nanostring)

ABSTRACT: Here we present the case of adult medulloblastoma with minimal chromosomal rearrangements but Shh expression profile and IDH1 mutation. Data presented here are NanoString analyses of two biopsies of adult patient with a medulloblastoma which was classified as a Shh subtype Analyses were performed on 2 archival specimens of medulloblastoma, WHO Grade IV, seen at the Department of Pathology, Massachusetts General Hospital in 2007.

ORGANISM(S): Homo sapiens

SUBMITTER: Matija Snuderl

PROVIDER: E-GEOD-43123 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Deep Sequencing Identifies IDH1 R132S Mutation in Adult Medulloblastoma (CGH)

Project description:Here we present the case of adult medulloblastoma with minimal chromosomal rearrangements. Data presented here are aCGH analyses of two biopsies of adult patient with a medulloblastoma which was classified as a Shh subgroup. Analyses were performed on 2 archival specimens of medulloblastoma, WHO Grade IV, seen at the Department of Pathology, Massachusetts General Hospital from 2007. This Series represents the CGH part of the study.

2013-01-01 | E-GEOD-41990 | biostudies-arrayexpress

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Gene expression analysis of human heart valves

Project description:Semilunar valve leaflets have a well-described trilaminar histoarchitecture with a sophisticated elastic fiber network. It was previously proposed that elastin-containing fibers play a subordinate role in early human cardiac valve development; however, this assumption was based on data obtained from mouse models and human second and third trimester tissues. Here, we systematically analyzed tissues from human fetal first (4-12 weeks) and second (13-18 weeks) trimester, adolescent (14-19 years) and adult (50-55 years) hearts to monitor the temporal and spatial distribution of elastic fibers, focusing on semilunar valves. Global gene expression analyses revealed that the transcription of genes essential for elastic fiber formation starts early within the first trimester. These data were confirmed by quantitative PCR and immunohistochemistry employing antibodies that recognize fibronectin, fibrilin-1, -2 and -3, EMILIN-1, fibulin-4 and fibulin-5, which were all expressed at the onset of cardiac cushion formation (~week 4 of development). Tropoelastin/ elastin protein expression was first detectable in leaflets of 7-week hearts. We revealed that immature elastic fibers are organized in early human cardiovascular development, and mature elastin-containing fibers first evolve in semilunar valves when blood pressure and heartbeat accelerate. Our findings provide a conceptual framework with the potential to lead to novel hypotheses in human cardiac valve development and disease. Total RNA obtained from fetal cardiac valve cushions, developed fetal heart valves, adolescent heart valves, and adult heart valves.

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Project description:Medulloblastoma could be classified into four subtypes: Wnt, Shh, Group 3, and Group 4. Subtypes of medulloblastoma have distinct epigenetic properties. We report that a chromatin regulator SMARCA4/Brg1 controls a transcriptional program that specifically required for Shh-type medulloblastoma identity and proliferation. We show that Brg1 deletion significantly inhibited tumor formation and progression in a mouse medulloblastoma model. Genomic experiments indicate that Brg1 specifically coordinates with key transcription factors including Gli1, Atoh1, and REST to regulate the expression of both oncogenes and tumor suppressors. Shh-type medulloblastoma displays distinct H3K27me3 properties. We demonstrate that Brg1 modulates activities of H3K27me3 modifiers to regulate expression of medulloblastoma genes. Brg1 is important for the growth of a human medulloblastoma cell line and Brg1-regulated pathways are conserved in human Shh-type medulloblastoma. This study reveals a novel epigenetic mechanism that controls medulloblastoma development and provides a rationale for developing subtype-specific treatment strategies.

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SMARCA4/Brg1 Coordinates Genetic and Epigenetic Networks Underlying Shh-type Medulloblastoma Development [gene expression]

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Gene expression data from medulloblastoma tumor samples

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2014-06-02 | E-GEOD-49243 | biostudies-arrayexpress

The miR-17/92 Polycistron Is Up-regulated in Sonic Hedgehog-Driven Medulloblastomas and Induced by N-myc in Sonic Hedgehogâ??Treated Cerebellar Neural Precursors

Project description:Medulloblastoma is the most common malignant pediatric brain tumor, and mechanisms underlying its development are poorly understood. We identified recurrent amplification of the miR-17/92 polycistron proto-oncogene in 6% of pediatric medulloblastomas by high-resolution single-nucleotide polymorphism genotyping arrays and subsequent interphase fluorescence in situ hybridization on a human medulloblastoma tissue microarray. Profiling the expression of 427 mature microRNAs (miRNA) in a series of 90 primary human medulloblastomas revealed that components of the miR-17/92 polycistron are the most highly up-regulated miRNAs in medulloblastoma. Expression of miR-17/92 was highest in the subgroup of medulloblastomas associated with activation of the sonic hedgehog (Shh) signaling pathway compared with other subgroups of medulloblastoma. Medulloblastomas in which miR-17/92 was up-regulated also had elevated levels of MYC/MYCN expression. Consistent with its regulation by Shh, we observed that Shh treatment of primary cerebellar granule neuron precursors (CGNP), proposed cells of origin for the Shh-associated medulloblastomas, resulted in increased miR-17/92 expression. In CGNPs, the Shh effector N-myc, but not Gli1, induced miR-17/92 expression. Ectopic miR-17/92 expression in CGNPs synergized with exogenous Shh to increase proliferation and also enabled them to proliferate in the absence of Shh. We conclude that miR-17/92 is a positive effector of Shh-mediated proliferation and that aberrant expression/amplification of this miR confers a growth advantage to medulloblastomas. A total of 90 primary medulloblastoma specimens were profiled by Affymetrix exon array and gene-level analysis was performed.

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