Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Malignant peripheral nerve sheath tumor (MPNST) and MPNST-like entities defined by DNA methylation profile in pediatric and juvenile population

ABSTRACT: Malignant peripheral nerve sheath tumor (MPNST) and MPNST-like entities defined by DNA methylation profile in pediatric and juvenile population

PROVIDER: PRJNA1034033 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Malignant peripheral nerve sheath tumor (MPNST) and MPNST-like entities defined by DNA methylation profile in pediatric and juvenile population

Project description:The diagnosis of Malignant peripheral nerve sheath tumors (MPNSTs) can be challenging, but is aided by their characteristic DNA methylation profile (DMP). An MPNST-like group, characterized by retained H3K27me3 expression, was recently recognized. To evaluate the diagnostic usefulness of DMP in pediatric/juvenile MPNSTs, we selected pediatric/juvenile malignancies from the Bambino Gesù Children's Hospital DMP database. DMP revealed unexpected molecular heterogeneity in histologically homogenous MPNSTs/Atypical neurofibromas, while samples with MPNST-like DMP manifested histological diversity. In conclusion, DMP is useful in diagnosing MPNST, discriminating morphologic mimics classified as MPNST in premolecular era, and investigating the MPNST-like ‘hybrid’ group in pediatrics.

2024-01-29 | GSE246644 | GEO

Malignant peripheral nerve sheath tumor (MPNST) tumor samples

Project description:Malignant peripheral nerve sheath tumor (MPNST) is an aggressive sarcoma. Comprehensive proteomic profiles of 23 MPNST tumor specimens were obtained using LC-MS/MS. Among 23 tumor specimens, 13 patients showed favorable prognosis and 10 did local recurrence/distant metastasis.

2022-12-22 | PXD030585 | JPOST Repository

BCAT1 and miR-2504: novel methylome signature distinguishes spindle/desmoplastic melanoma from superficial malignant peripheral nerve sheath tumor

Project description:Genome wide methylation of superficial malignant peripheral nerve sheath tumors and spindle cell melanomas. EPIC HD 850K array is used to identifiy differentally methylated promoter region probes and unique methyome signatures. Superficial/cutaneous malignant peripheral nerve sheath tumor (c-MPNST) is a rare, soft tissue neoplasm that shares morphological, immunohistochemical and molecular with spindle and desmoplastic melanoma (SDM). Herein we investigate a methylome signature distinguishing between both entities. DNA from formalin-fixed, paraffin-embedded (FFPE) tissues was extracted and processed using the Illumina Infinium epic array interrogating 866,562 CpG sites. Using a home grown informatics pipeline we identify differentially methylated regions (DMR) between both entities. Functional network analysis for enrichment signatures was performed using DAVID tools. Identified DMR’s are compared with TCGA skin cutaneous melanoma (SKCM) data and a recently published set of MPNST in order to assess specifity of the identified signature. Thirty patients are included (SDM= 15 and c-MPNST=15) including 23 males and 7 females. Unsupervised hierarchical clustering probes showed a distinct pattern of methylation between c-MPNST and SDM. Two probes cg20783223 and cg13332552 co-localized in the promoter region of BCAT1 and MIR2504. Pathway analysis highlighted an enrichment in s subset of genes involved in breast and gastric cancer centered on BCAT1 and downstream activated genes in the mTORC pathway. Our study identifies BCAT1 as a unique marker distinguishing between SDM and MPNST. Further immunohistochemical studies are underway to investigate the role of BCAT expression in that regard.

2018-09-10 | GSE112308 | GEO

Atypical Neurofibromas reveal distinct epigenetic features with proximity to benign peripheral nerve sheath tumor entities

Project description:Unsupervised hierarchical clustering and t-SNE analysis indicated that 36/40 ANF cluster separately from MPNST and instead close to the benign tumor entities. Of these 36 tumors, 23 ANF formed a molecularly distinct cluster in proximity to schwannomas. Tumors from this cluster had frequent heterozygous or homozygous loss of CDKN2A/B and significantly more lymphocyte infiltration than MPNST, schwannomas, and NF. Few ANF clustered closely with neurofibromas, schwannomas, or MPNST, raising the question, whether diagnosis based on histological features alone might pose a risk to both over- and underestimate the aggressiveness of these lesions.

2023-03-01 | GSE216262 | GEO

PRC2 is a tumor suppressor in malignant peripheral nerve sheath tumor (MPNST)

Project description:PRC2 is a tumor suppressor in malignant peripheral nerve sheath tumor (MPNST)

| PRJNA942516 | ENA

Genomic characterization of the MPNST

Project description:Malignant peripheral nerve sheath tumor (MPNST) is a rare sarcoma that lacks effective therapeutic strategies. By characterizing recurrent gene copy number aberrations, we gain insight into the most altered pathways with the purpose of scanning possible therapeutic targets. We conducted a microarray-based comparative genomic hybridization profiling of two cohorts of primary MPNST tissue samples including 25 patients treated at The University of Texas MD Anderson Cancer Center and 26 patients from Tianjin Cancer Hospital. All samples had at least 90% tumor content. Commercially available normal genomic DNAs were used as control.

2011-11-26 | E-GEOD-33881 | biostudies-arrayexpress

Transgenic mice overexpressing Neuregulin-1 model neurofibroma-malignant peripheral nerve sheath tumor progression and implicate specific chromosomal copy number variations in tumorigenesis.

Project description:Patients with neurofibromatosis type 1 (NF1) develop benign plexiform neurofibromas that frequently progress to become malignant peripheral nerve sheath tumors (MPNSTs). A genetically engineered mouse model that accurately models plexiform neurofibroma-MPNST progression would facilitate the identification of somatic mutations driving this process. We have previously reported that transgenic mice overexpressing the growth factor neuregulin-1 in Schwann cells (P0-GGF?3 mice) develop MPNSTs. To determine whether P0-GGF?3 mice accurately model neurofibroma-MPNST progression, cohorts of these animals were followed to death and necropsied. 94% of the mice developed multiple neurofibromas, with 70% carrying smaller numbers of MPNSTs; nascent MPNSTs were identified within neurofibromas, suggesting that these sarcomas arise from neurofibromas. Although neurofibromin expression was maintained, P0-GGF?3 MPNSTs, like human NF1-associated MPNSTs, demonstrated Ras hyperactivation. P0-GGF?3 MPNSTs also showed abnormalities in the p16INK4A-cyclin D/CDK4-Rb and p19ARF-Mdm-p53 pathways analogous to their human counterparts. Array comparative genomic hybridization (CGH) demonstrated reproducible chromosomal alterations in P0-GGF?3 MPNST cells (including universal chromosome 11 gains) and focal gains and losses affecting 39 genes previously implicated in neoplasia (e.g., Pten, Tpd52, Myc , Gli1, Xiap, Bbc3/PUMA). Array CGH also identified recurrent focal copy number variations affecting genes not previously linked to neurofibroma or MPNST pathogenesis. We conclude that P0-GGF?3 mice represent a robust model of neurofibroma-MPNST progression that can be used to identify novel genes driving neurofibroma and MPNST pathogenesis. Array CGH comparison of malignant peripheral nerve sheath tumor (MPNST) cells vs non-neoplastic Schwann cells

2012-12-31 | E-GEOD-40212 | biostudies-arrayexpress

Array-CGH of malignant peripheral nerve sheath tumors (MPNST)

Project description:Comparison of copy number changes in MPNST samples against benign neurofibromas in NF1 patients 24 MPNSTs and 3 NF samples were hybridised to the human 32K BAC tiling path array

2010-05-18 | E-GEOD-16041 | biostudies-arrayexpress

Genomic characterization of the MPNST

2011-11-26 | GSE33881 | GEO

Targeting RABL6A-RB1 signaling suppresses malignant peripheral nerve sheath tumors

Project description:Malignant peripheral nerve sheath tumors (MPNSTs) are deadly sarcomas that lack effective therapies. In most MPNSTs, the retinoblastoma (RB1) tumor suppressor is disabled by hyperactivation of cyclin dependent kinases (CDKs), commonly through loss of CDK inhibitory proteins such as p27(Kip1). RABL6A is an inhibitor of RB1 whose role in MPNSTs is unknown. To gain insight into MPNST development and establish new treatment options, we investigated RABL6A-RB1 signaling and CDK inhibitor-based therapy in MPNSTs.

2020-02-11 | GSE145064 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data