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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Cross-species genomics identifies postanatal CPE as novel choroid plexus carcinoma oncogenes.

ABSTRACT: Choroid plexus carcinomas (CPC) are poorly understood and frequently lethal brain tumors with minimal treatment options. Using a new mouse model of the disease and a large cohort of human CPCs [GSE60892; GSE60899], we performed a cross-species, genome-wide search for novel oncogenes within syntenic regions of chromosome gain. TAF12, NFYC and RAD54L, co-located on human chromosome 1p32-35.3 and mouse chromosome 4qD1-D3, were identified as oncogenes that are gained in tumors in both species and required to initiate and progress the disease in mice. TAF12 and NFYC are transcription factors that regulate the epigenome, while RAD54L plays a central role in DNA repair. Our data identify a group of concurrently gained, novel oncogenes that cooperate in the formation of CPC and unmask potential new avenues for therapy. CPC mouse model samples of tumors derived from choroid plexus epithelium (CPE) cells that are Tp53/RB/Pten null in FVB mice. Female CD1 nude (host) mice were transfected with postanatal CPE and compared with a medulloblastoma normal mouse embryonic, postnatal and adult controls (loxP TP53/RB/PTEN (no Cre)) Implanted and reimplanted are from the orthotropic transplants of the primary tumor or later tumors

ORGANISM(S): Mus musculus

SUBMITTER: David Finkelstein

PROVIDER: E-GEOD-61659 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cross-species genomics identifies postanatal CPE as novel choroid plexus carcinoma oncogenes.

Project description:Choroid plexus carcinomas (CPC) are poorly understood and frequently lethal brain tumors with minimal treatment options. Using a new mouse model of the disease and a large cohort of human CPCs [GSE60892; GSE60899], we performed a cross-species, genome-wide search for novel oncogenes within syntenic regions of chromosome gain. TAF12, NFYC and RAD54L, co-located on human chromosome 1p32-35.3 and mouse chromosome 4qD1-D3, were identified as oncogenes that are gained in tumors in both species and required to initiate and progress the disease in mice. TAF12 and NFYC are transcription factors that regulate the epigenome, while RAD54L plays a central role in DNA repair. Our data identify a group of concurrently gained, novel oncogenes that cooperate in the formation of CPC and unmask potential new avenues for therapy.

2015-05-01 | GSE61659 | GEO

Cross-species genomics identifies TAF12, NFYC and RAD54L as novel choroid plexus carcinoma oncogenes

Project description:Choroid plexus carcinomas (CPC) are poorly understood and frequently lethal brain tumors with minimal treatment options. Using a new mouse model of the disease and a large cohort of human CPCs, we performed a cross-species, genome-wide search for novel oncogenes within syntenic regions of chromosome gain. TAF12, NFYC and RAD54L, co-located on human chromosome 1p32-35.3 and mouse chromosome 4qD1-D3, were identified as oncogenes that are gained in tumors in both species and required to initiate and progress the disease in mice. TAF12 and NFYC are transcription factors that regulate the epigenome, while RAD54L plays a central role in DNA repair. Our data identify a group of concurrently gained, novel oncogenes that cooperate in the formation of CPC and unmask potential new avenues for therapy.

| EGAS00001000961 | EGA

Proteomics profiling of pediatric choroid plexus tumors

Project description:Aggresome is a para nuclear inclusion body that functions as a storage compartment for misfolded proteins. Our previous work revealed the presence of aggresomes in pediatric choroid plexus tumors (CPT). CPTs are rare neoplasms comprised of three pathological subgroups; choroid plexus carcinoma (CPC), a grade III tumor, atypical choroid plexus papilloma (ACPP), a grade II tumor, and choroid plexus papilloma (CPP), a grade I tumor. In the current study, we aimed to investigate the prognostic value of aggresomes-positivity and its correlation to the pathological and molecular subtypes. The proteomics profiling of 21 CPT pediatric samples was investigated using ABSciex Triple TOF 5600+ mass spectrometer.

2021-02-11 | PXD021076 | Pride

Gene expression and functional annotation of choroid plexus epithelium failure in Alzheimer disease

Project description:We investigated the gene expression of the human CPE in Braak stadia 0, 3 and 6.We isolated CPE cells with laser dissection microscopy from healthy human donor choroid plexus tissues and from human choroid plexus tissue from brains that were post-mortem staged in Braak 3 and Braak 6 Alzheimer disease stages . Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays.

2014-12-31 | GSE61196 | GEO

Methylation profiling of pediatric choroid plexus tumors

Project description:Aggresome is a para nuclear inclusion body that functions as a storage compartment for misfolded proteins. Our previous work revealed the presence of aggresomes in pediatric choroid plexus tumors (CPT). CPTs are rare neoplasms comprised of three pathological subgroups; choroid plexus carcinoma (CPC), a grade III tumor, atypical choroid plexus papilloma (ACPP), a grade II tumor, and choroid plexus papilloma (CPP), a grade I tumor. In the current study, we aimed to investigate the prognostic value of aggresomes-positivity and its correlation to the pathological and molecular subtypes. The genome-wide methylation profile of 42 CPT pediatric samples was investigated using Illumina Infinium Methylation EPIC BeadChip array.

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Gene expression of the human choroid plexus epithelium (CPE)

Project description:We investigated the gene expression of the human CPE.We isolated CPE cells from healthy human donor choroid plexus tissues with laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays. We performed the microarrays against a common reference sample, namely human RPE/choroid RNA. We performed 7 replicates of human CPE samples from 7 different donors.

2013-09-27 | E-GEOD-49969 | biostudies-arrayexpress

Myc and loss of p53 cooperate to drive formation of choroid plexus carcinoma

Project description:Choroid plexus carcinoma (CPC) is a rare brain tumor that occurs most commonly in very young children, and has a dismal prognosis despite intensive therapy. Improved outcomes for CPC patients depend on a deeper understanding of the mechanisms underlying the disease. We developed transgenic models of CPCs by activating the Myc oncogene and deleting the Trp53 tumor suppressor gene in murine neural stem cells or progenitors. Murine CPCs resemble their human counterparts at a histological level, and like the hypodiploid subset of human CPCs, exhibit multiple whole-chromosome losses, particularly of chromosomes 8, 12 and 19. Analysis of murine and human CPC gene expression profiles and copy number changes reveals altered expression of genes involved in cell cycle, DNA damage response and cilium function. Finally, high throughput drug screening identifies small molecule inhibitors that decrease the viability of CPCs. These models will be valuable tools for understanding the biology of choroid plexus tumors and for testing novel approaches to therapy.

2020-01-28 | GSE126408 | GEO

Gene expression profiles obtained from laser-microdissected human choroid plexus papilloma cells

Project description:Gene expression profiles generated from human tumor cells laser-microdissected from surgical samples of seven choroid plexus papillomas (Grade I WHO) as eight samples of epithelial cells lasermicrodissected from normal choroid plexus obtained at autopsy. Choroid plexus tumors are rare pediatric brain tumors derrived from the choroid plexus epithelium. Gene expression profiles of lasermicrodissected tumor cells from 7 individual choroid plexus tumor samples obtained at surgery were compared to gene expression profiles from non-neoplastic choroid plexus epithelial cells lasermicrodissected from normal non-neoplastic choroid plexus obtained at autopsy (Am J Surg Pathol. 2006 Jan;30(1):66-74.) in order to identfy genes differentially expressed in choroid plexus tumor cells.

2009-02-01 | E-GEOD-14098 | biostudies-arrayexpress

Mus musculus

Project description:Cross-species genomics identifies postanatal CPE as novel choroid plexus carcinoma oncogenes.

| PRJNA261821 | ENA

Gene expression data from normal mouse choroid plexus, choroid plexus papilloma and choroid plexus carcinoma

Project description:Atoh1-Cre; Myc/Myc mice developed choroid plexus papilloma and Atoh1-Cre; Myc/Myc; p53fl/fl mice developed choroid plexus carcinoma. By studying the gene expression profiles of normal choroid plexus, choroid plexus papilloma and choroid plexus carcinoma in mice, we aim to gain a better understanding of the biology of choroid plexus tumors

2019-05-01 | GSE126327 | GEO

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