GEO DataSets

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

42 Samples

Download data: IDAT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL21145

40 Samples

Download data: IDAT, TXT

(Submitter supplied) The SWI/SNF-family chromatin remodeling protein ATRX is a tumor suppressor in sarcomas, gliomas and other malignancies. Its loss of function facilitates the alternative lengthening of telomeres (ALT) pathway in tumor cells, while it also affects Polycomb repressive complex 2 (PRC2) silencing of its target genes. To further define the role of inactivating ATRX mutations in carcinogenesis, we knocked out atrx in our previously published p53/nf1-deficient zebrafish line that develops malignant peripheral nerve sheath tumors and gliomas. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

10 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) 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-GGFβ3 mice) develop MPNSTs. more...

Organism:

Mus musculus

Type:

Genome variation profiling by array

Platform:

GPL11288

12 Samples

Download data: TXT

(Submitter supplied) Comparison of copy number changes in MPNST samples against benign neurofibromas in NF1 patients

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL6088

27 Samples

Download data: GPR

(Submitter supplied) 7 MPNSTs from 7 neurofibromatosis-type 1 patients were screened with a high resolution array-CGH. Each MPNST DNA (somatic tumor DNA) was individually hybridized on Agilent whole human genome 244K microarrays (Platform GPL4091) using the pooled genomic constitutional DNA (lymphocytes DNA) from the normal control patients as reference, in order to detect tumor-specific aberrations.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4091

7 Samples

Download data: TXT

(Submitter supplied) We have performed gene expression analyses as part of a European multicentre study on MPNST. The data was used for transcriptomic subtyping, gene set enrichment analyses and integration with DNA copy number data.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

79 Samples

Download data: CEL, CHP

(Submitter supplied) Rhabdomyosarcomas (RMS) represent a family of aggressive soft tissue sarcomas that present in both the pediatric and adult setting. Pathologic risk stratification for RMS has been based on histologic subtype, with poor outcomes observed in alveolar rhabdomyosarcoma (ARMS) and adult-type pleomorphic rhabdomyosarcoma (PRMS) compared to embryonal rhabdomyosarcoma (ERMS). Recent genomic sequencing studies have expanded the spectrum of RMS, with several new molecularly defined entities, including fusion-driven spindle cell/sclerosing rhabdomyosarcoma (SC/SRMS) and MYOD1-mutant SC/SRMS. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL23976

158 Samples

Download data: IDAT

(Submitter supplied) To investigate the function of p53 in regulating response to MET inhibition in MPNST cells we established NF1-MET;sgP53 cells in which Trp53 was knocked out using CRISPR-Cas9. As a control, the parental NF1-MET was transduced with CRISPR-Cas9 in the absence of sgRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of the 2 different cells treated with either capmatinib or vehicle in duplicate.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms

50 Samples

Download data: CSV, H5, TAR, TBI, TSV, TXT

(Submitter supplied) We used single-cell RNAseq to profile early and advanced mouse MPNST tumors, as well as human neurofibroma and MPNST. Our work defines the stage-specific kinetics of transcriptomics, cellular heterogeneity, and tumor cell fate decisions in murine and human MPNSTs.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

16 Samples

Download data: TXT

(Submitter supplied) We used single-cell RNAseq to profile early and advanced mouse MPNST tumors, as well as human neurofibroma and MPNST. Our work defines the stage-specific kinetics of transcriptomics, cellular heterogeneity, and tumor cell fate decisions in murine and human MPNSTs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

14 Samples

Download data: TAR

(Submitter supplied) We used single-cell RNAseq to profile early and advanced mouse MPNST tumors, as well as human neurofibroma and MPNST. Our work defines the stage-specific kinetics of transcriptomics, cellular heterogeneity, and tumor cell fate decisions in murine and human MPNSTs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23227

17 Samples

Download data: TXT

(Submitter supplied) We used single-cell RNAseq to profile early and advanced mouse MPNST tumors, as well as human neurofibroma and MPNST. Our work defines the stage-specific kinetics of transcriptomics, cellular heterogeneity, and tumor cell fate decisions in murine and human MPNSTs.

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676

3 Samples

Download data: CSV, H5, TBI, TSV

(Submitter supplied) We established a new genetically engineered mouse (GEM) model of malignant peripheral nerve sheath tumors (MPNST) based on postnatal deletion of a Nf1;Trp53 cis-conditional allele by the tamoxifen-inducible Plp-CreER (NP-Plp). We also generated two Lats1;2 conditional knockout models by using Nestin-Cre (Lats-Nes) and Plp-CreER (Lats-Plp), both of which also develop tumors similar to MPNST (GEM-PNST). more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676

44 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Conditionally replicative adenoviruses (CRAds) preferentially infect and lyse tumor cells. While CRAds have been clinically applied, their potential for neurofibromatosis type-1 associated malignant peripheral nerve sheath tumors (MPNSTs) remains unexplored. This study evaluates Cyclooxygenase 2 (COX2)-driven CRAds as a therapy for MPNST. METHODS: Viruses with wild type (WT) and modified fiber-knob domains were assessed for binding efficiency to the MPNST models. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21103 GPL24247

51 Samples

Download data: TXT, VCF

(Submitter supplied) EGFR aberrations are reported in a subset of myofibroblastic lesions with kinase domain duplication (EGFR-KDD) and exon 20 mutations being assigned to infantile fibrosarcomas (IFS), mesoblastic nephroma and fibrous hamartoma of infancy (FHI), respectively. In this retrospective study, we correlated molecular findings with histomorphology of 14 myofibroblastic lesions harboring such genetic changes identified by NGS. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

14 Samples

Download data: IDAT

(Submitter supplied) Cavitating ultrasonic aspirator devices are frequently used in pediatric neurosurgery for efficient microsurgical resection of brain tumours while minimizing tissue damage to surrounding healthy brain. Within this study molecular diagnostics using methylation-based classification of ultrasonic aspirated samples was performed and performance against routine microarray diagnostics was assessed.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24106

21 Samples

Download data: CSV, TXT

(Submitter supplied) In vitro models of pediatric brain tumors (pBT) are tools instrumental for better understanding the mechanisms contributing to oncogenesis and testing new therapies; and thus, ideally, they should recapitulate the original tumor. We applied DNA methylation (DNAm) and copy number variation (CNV) profiling to characterize 241 pBT samples, including 155 tumors and 86 pBT-derived cell cultures, and considering serum vs serum-free conditions, late vs early passages, and dimensionality (2D vs 3D cultures). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL23976

241 Samples

Download data: IDAT, TXT