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Fusion Negative Rhabdomyosarcoma Cell Lines

ABSTRACT: Fusion Negative Rhabdomyosarcoma Cell Lines

PROVIDER: PRJNA330685 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3932771.fastq.gz	Fastqsanger.gz
	SRR3932772.fastq.gz	Fastqsanger.gz
	SRR3932773.fastq.gz	Fastqsanger.gz
	SRR3932774.fastq.gz	Fastqsanger.gz
	SRR3932775.fastq.gz	Fastqsanger.gz

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Gene Expression Profiling of Fusion Negative Rhabdomyosarcoma Cell Lines

Project description:We analyzed the expression of two fusion-negative established Rhabdomyosarcoma cell lines. Together with Chip-seq, we were able to identify transcribed loci bound by myogenic regulatory transcription factors (MYF5 and MYOD) that pertain to embryonic muscle development and cell cycle regulation pathways. Keywords: rhabdomyosarcoma, gene expression profiling, RD, Rh18

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Expression Profiling of human Fusion-Positive and Fusion-Negative Rhabdomyosarcoma

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Transcriptome analysis of genetically engineered murine fusion-negative rhabdomyosarcoma model-derived cell lines

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Expression Profiling of human Fusion-Positive and Fusion-Negative Rhabdomyosarcoma

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Transcriptome analysis of genetically engineered murine fusion-negative rhabdomyosarcoma model-derived cell lines

Project description:Fusion-negative rhabdomyosarcoma (FN-RMS) is the most common soft tissue sarcoma of childhood arising from undifferentiated skeletal muscle cells. Tumor cells derived from genetically engineered murine models are a valid tool to study cancer biology. In order to investigate the poor myogenic commitment of FN-RMS, we performed RNA sequencing of two cell lines derived from a previously described genetically engineered murine model of FN-RMS. We then performed bioinformatics analysis to compare the transcriptome with murine satellite cells, and identify the key factors that distinguish FN-RMS from skeletal muscle cells.

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Project description:Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. Prognosis for patients with high grade and metastatic disease is still very poor, and survivors are burdened with long-lasting side effects. Therefore, more effective and less toxic therapies are needed. Surface proteins are ideal targets for antibody-based therapies, like bispecific antibodies, antibody drug conjugates, or chimeric antigen receptor (CAR) T cell. Specific surface targets for RMS are scarce. Here, we performed a surfaceome profiling based on differential centrifugation enrichment of surface/membrane proteins and detection by LC-MS on six fusion-positive (FP) RMS cell lines, five fusion-negative (FN) RMS cell lines, and three RMS patient-derived xenografts (PDXs). 699 proteins were detected in the three RMS groups. Ranking based on expression levels and comparison to expression in normal MRC-5 fibroblasts and myoblasts, followed by statistical analysis, highlighted known RMS targets such as FGFR4, NCAM1, and CD276/B7-H3, and revealed AGRL2, JAM3, MEGF10, GPC4, CADM2, as potential targets for immunotherapies of RMS. L1CAM expression was investigated in RMS tissues and strong L1CAM expression was observed in more than 80% of alveolar RMS tumors, making it a practicable target for antibody-based therapies of alveolar RMS.

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Clinical Application of Prognostic Gene Expression Signature in Fusion Gene-Negative Rhabdomyosarcoma

Project description:To date, there are no known prognostic markers identified in patients with fusion gene-negative rhabdomyosarcoma. This study validates the 5-gene (MG5) signature as a prognostic marker in patients with fusion negative intermediate-risk rhabdomyosarcoma clearly stratifying this otherwise clinically homogenous population of patients into two risk groups based on outcome. In addition, this analysis was performed using nCounter assay on paraffin embedded tissues and the results were concordant to previously published results using frozen tissues in a different patient cohort. Therefore, this work holds tremendous translational relevance as the MG5 signature can be reliably assessed in readily available paraffin embedded tissues of fusion gene-negative rhabdomyosarcoma patients in prospective clinical trials to stratify them into prognostic risk groups as well as to potentially tailor future therapy based on these risk groups.

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ChIP-seq of Active Histone Mark (H3K27ac) and Myogenic Regulatory Factors (MYF5 and MYOD) in Fusion Negative Rhabdomyosarcoma Cell Lines

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