1ede31df-7cf5-45d6-9dcd-8a881d8cc389 - samples
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ABSTRACT:
PROVIDER: EGAD00001009973 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Autopsy-derived, later snap-frozen tissue fragments from a 5-year-old female with recurrent metastatic fusion-negative embryonal rhabdomyosarcoma (RMS) primary tumor of the left thigh were analyzed. No quality matched tissue was available. Prior panel analysis identified 2 prominent genetic changes: NRAS Q61K, PIK3CA H1047R, CDKN2A/B loss, and ERBB3 overexpression.
| EGAS00001006946 | EGA
Project description:We measured the expression profiles of a series of 30 Rhabdomyosarcoma biopsy samples (15 embryonal RMS, 10 translocation-positive alveolar RMS and 5 translocation-negative alveolar RMS). Expression data was used for unsupervised hierarchical clustering as well as supervised analysis to find gene expression signatures characteristic for the different histological RMS subgroups.
2004-06-30 | E-MEXP-121 | biostudies-arrayexpress
Project description:Rhabdomyosarcoma (RMS) is a highly malignant tumour accounting for nearly half of soft tissue sarcomas in children. Altered miRNA levels have been reported in human cancers, including RMS. Using deep sequencing technology, a total of 685 miRNAs were investigated in a group of alveolar RMSs (ARMSs), embryonal RMSs (ERMSs) as well as in normal skeletal muscle (NSM). Bioinformatics pipelines were used for miRNA target prediction and clustering analysis. Ninety-seven miRNAs were significantly deregulated in ARMS and ERMS when compared to NSM. MiR-378 family members were dramatically decreased in RMS tumour tissue and cell lines. Interestingly, members of the miR-378 family presented as a possible target the insulin-like growth factor receptor 1 (IGF1R), a key signalling molecule in RMS.
2015-01-28 | E-MTAB-3246 | biostudies-arrayexpress
Project description:Rhabdomyosarcoma (RMS) is the most common paediatric soft-tissue sarcoma and resembles developing skeletal muscle. Specific genomic alterations including translocations, deletions and amplification events have been associated with the alveolar and embryonal subtypes of RMS. Characterizing these changes has led to increased understanding of the underlying molecular biology. However, further aberrations and their significance remain to be defined. Genomic copy number variations have been shown to affect the level of transcription in several tumor types. In this study, we have combined array comparative genomic hybridization analysis of 13 RMS cell lines, supported by confirmatory PCR analyses, with their corresponding expression profiles. This identified sets of genes that are altered in their level of expression by genomic imbalances. We also show that the effect on gene expression was proportional to the level of genomic gain or loss. Keywords: Rhabdomyosarcoma cell lines will be added later on
2009-06-04 | E-GEOD-8840 | biostudies-arrayexpress
Project description:Rhabdomyosarcoma (RMS) is the most common paediatric soft-tissue sarcoma and resembles developing skeletal muscle. Specific genomic alterations including translocations, deletions and amplification events have been associated with the alveolar and embryonal subtypes of RMS. Characterizing these changes has led to increased understanding of the underlying molecular biology. However, further aberrations and their significance remain to be defined. Genomic copy number variations have been shown to affect the level of transcription in several tumor types. In this study, we have combined array comparative genomic hybridization analysis of 13 RMS cell lines, supported by confirmatory PCR analyses, with their corresponding expression profiles. This identified sets of genes that are altered in their level of expression by genomic imbalances. We also show that the effect on gene expression was proportional to the level of genomic gain or loss. Keywords: Rhabdomyosarcoma cell lines
2009-06-04 | GSE8840 | GEO
Project description: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. Comprehensive genomic analysis has previously defined the mutational and copy number spectrum for the more common ERMS and ARMS, as well as revealed corresponding methylation signatures. In contrast, genetic and epigenetic correlates have not been defined for the rare SC/SRMS or PRMS histologic subtypes. Herein, we present genomic sequencing, copy number analysis, and methylation profiling of the largest cohort of molecularly characterized RMS samples to date. We identified two novel methylation subtypes, one having SC/SRMS histology and defined by MYOD1 p. L122R mutations and the other matching adult type PRMS. Selected tumors from adolescent patients grouped with the PRMS methylation class, expanding the age range of these rare tumors. Pediatric patients in the MYOD1-mutant group, as well as those clustering with PRMS, appear to have poor overall survival.
2021-11-24 | GSE167059 | GEO
Project description:Exosomes were isolated by differential centrifugation from the fusion negative human embryonal rhabdomyosarcoma (ERMS) cell lines (JR1, Rh36, and RD) and fusion positive alveolar RMS (ARMS) cell lines (Rh30 and Rh41) and characterized by western blot for exosomal markers. miRNA content of the RMS-derived exosomes was determined using the Affymetrix GeneChip miRNA 3.0 array and analyzed to specify differentially deregulated (either enriched or depleted) miRNA relative to cellular miRNA from the respective ERMS and ARMS cell lines. Characterization of the miRNA content of RMS exosome is needed to better understand the mechanism by which these particles exert their physiologic effects, notably on proliferation, migration, invasion, and metastasis.
2016-12-01 | E-MTAB-5321 | biostudies-arrayexpress
Project description:Fusion-positive rhabdomyosarcoma (FP-RMS) driven by the expression of the PAX3-FOXO1 (P3F) fusion oncoprotein is an aggressive subtype of pediatric rhabdomyosarcoma. FP-RMS histologically resembles developing muscle yet occurs throughout the body in areas devoid of skeletal muscle highlighting that FP-RMS is not derived from an exclusively myogenic cell of origin. Here we demonstrate that P3F reprograms mouse and human endothelial progenitors to FP-RMS. We show that P3F expression in aP2-Cre expressing cells reprograms endothelial progenitors to functional myogenic stem cells capable of regenerating injured muscle fibers. Further, we describe a novel FP-RMS mouse model driven by P3F expression and CDKN2A loss in endothelial cells. Additionally, we show that P3F expression in p53 null human iPSCs blocks endothelial directed differentiation and guides cells to become myogenic cells that form FP-RMS tumors in immunocompromised mice. Together these findings demonstrate that FP-RMS can originate from aberrant development of non-myogenic cells driven by P3F.
2023-09-30 | GSE218265 | GEO
Project description:Fusion-positive rhabdomyosarcoma (FP-RMS) driven by the expression of the PAX3-FOXO1 (P3F) fusion oncoprotein is an aggressive subtype of pediatric rhabdomyosarcoma. FP-RMS histologically resembles developing muscle yet occurs throughout the body in areas devoid of skeletal muscle highlighting that FP-RMS is not derived from an exclusively myogenic cell of origin. Here we demonstrate that P3F reprograms mouse and human endothelial progenitors to FP-RMS. We show that P3F expression in aP2-Cre expressing cells reprograms endothelial progenitors to functional myogenic stem cells capable of regenerating injured muscle fibers. Further, we describe a novel FP-RMS mouse model driven by P3F expression and CDKN2A loss in endothelial cells. Additionally, we show that P3F expression in p53 null human iPSCs blocks endothelial directed differentiation and guides cells to become myogenic cells that form FP-RMS tumors in immunocompromised mice. Together these findings demonstrate that FP-RMS can originate from aberrant development of non-myogenic cells driven by P3F.
2023-09-30 | GSE218254 | GEO
Project description:Fusion-positive rhabdomyosarcoma (FP-RMS) driven by the expression of the PAX3-FOXO1 (P3F) fusion oncoprotein is an aggressive subtype of pediatric rhabdomyosarcoma. FP-RMS histologically resembles developing muscle yet occurs throughout the body in areas devoid of skeletal muscle highlighting that FP-RMS is not derived from an exclusively myogenic cell of origin. Here we demonstrate that P3F reprograms mouse and human endothelial progenitors to FP-RMS. We show that P3F expression in aP2-Cre expressing cells reprograms endothelial progenitors to functional myogenic stem cells capable of regenerating injured muscle fibers. Further, we describe a FP-RMS mouse model driven by P3F expression and Cdkn2a loss in endothelial cells. Additionally, we show that P3F expression in TP53-null human iPSCs blocks endothelial-directed differentiation and guides cells to become myogenic cells that form FP-RMS tumors in immunocompromised mice. Together these findings demonstrate that FP-RMS can originate from aberrant development of non-myogenic cells driven by P3F.
2023-09-30 | GSE241645 | GEO