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CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION [RNA-seq]

ABSTRACT: CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION [RNA-seq]

PROVIDER: PRJNA779412 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16905094_1.fastq.gz	Fastqsanger.gz
	SRR16905094_2.fastq.gz	Fastqsanger.gz
	SRR16905095_1.fastq.gz	Fastqsanger.gz
	SRR16905095_2.fastq.gz	Fastqsanger.gz

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CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION

Project description:CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION

| PRJNA779408 | ENA

CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION [methylation]

Project description:CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION [methylation]

| PRJNA779411 | ENA

CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION [miRNA-seq]

Project description:CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION [miRNA-seq]

| PRJNA779413 | ENA

CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION [methylation]

Project description:Undifferentiated soft tissue sarcomas (UDSTS ) are a group of mesenchymal tumors that remain a diagnostic challenge due to their morphologic heterogeneity and unclear histologic origin (Pe-ters et al. 2015b). In this case report, we present the first multi-omics molecular signature for BCOR-CCNB3 sarcomas (BCS) that includes mutation analysis, gene expression, DNA methyla-tion, and mi-RNA expression. We identify a paucity of additonal mutations in this tumor and de-tail that there is significant dysregulation of gene expression of epigeneic remodeling agents in-cluding key members of the PRC, Sin3A/3b, NuRD, and NcoR/SMRT complexes and the DNA methyltransferases DNMT1, DNMT3a, and DNMT3b. This is accompanied by significant DNA methylation changes and dysregulation of multiple miRNA with known links to tumorigenesis. This study significantly increases our understanding of the BCOR effects on fusion positive un-differentiated sarcomas at both the genomic and epigenomic level, and suggests that as better-tailored and more refined treatment algorithms continue to evolve, epigenetic modifying agents should be further evaluated for their efficacy against these tumors.

2021-11-12 | GSE188552 | GEO

CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION [RNA-seq]

2021-11-12 | GSE188554 | GEO

CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION [miRNA-seq]

2021-11-12 | GSE188553 | GEO

A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion

Project description:The identification of subtype-specific translocations has revolutionized diagnostics of sarcoma and provided new insight into oncogenesis. We used RNA-Seq to investigate samples diagnosed as small round cell tumors of bone, possibly Ewing sarcoma, but lacking the canonical EWSR1-ETS translocation. A new fusion was observed between the BCL6 co-repressor (BCOR) and the testis specific cyclin B3 (CCNB3) genes on chromosome X. RNA-Seq results were confirmed by RT-PCR and cloning the tumor-specific genomic translocation breakpoints. 24 BCOR-CCNB3-positive tumors were identified among a series of 594 sarcomas. Gene profiling experiments indicate that BCOR-CCNB3-positive cases are biologically distinct from other sarcomas, particularly EwingM-bM-^@M-^Ys sarcoma. Finally, we show that CCNB3 immunohistochemistry is a powerful diagnostic marker for this group of sarcoma and that over-expression of BCOR-CCNB3 or of a truncated CCNB3 activates S-phase in NIH3T3 cells. Thus the intrachromosomal X fusion described here represents a new subtype of bone sarcoma caused by a novel gene fusion mechanism. Comparison of expression profiles of 10 BCOR-CCNB3 samples (plus 4 EWS-FLI1 Ewing sarcomas samples as control) with publicly available profiles of other tumor types.

2012-03-03 | E-GEOD-34800 | biostudies-arrayexpress

A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion

Project description:The identification of subtype-specific translocations has revolutionized diagnostics of sarcoma and provided new insight into oncogenesis. We used RNA-Seq to investigate samples diagnosed as small round cell tumors of bone, possibly Ewing sarcoma, but lacking the canonical EWSR1-ETS translocation. A new fusion was observed between the BCL6 co-repressor (BCOR) and the testis specific cyclin B3 (CCNB3) genes on chromosome X. RNA-Seq results were confirmed by RT-PCR and cloning the tumor-specific genomic translocation breakpoints. 24 BCOR-CCNB3-positive tumors were identified among a series of 594 sarcomas. Gene profiling experiments indicate that BCOR-CCNB3-positive cases are biologically distinct from other sarcomas, particularly Ewing’s sarcoma. Finally, we show that CCNB3 immunohistochemistry is a powerful diagnostic marker for this group of sarcoma and that over-expression of BCOR-CCNB3 or of a truncated CCNB3 activates S-phase in NIH3T3 cells. Thus the intrachromosomal X fusion described here represents a new subtype of bone sarcoma caused by a novel gene fusion mechanism.

2012-03-03 | GSE34800 | GEO

CLINICOPATHOLOGIC AND MOLECULAR ANALYSIS OF A BCOR-CCNB3+ UNDIFFERENTIATED SARCOMA OF THE KIDNEY REVEALS SIGNIFICANT EPI-GENETIC ALTERATION

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-11-12 | GSE188555 | GEO

Molecular and clinicopathologic characteristics of CNS tumors with BCOR::EP300 gene fusions

Project description:Genomewide DNA methylation array profiling of 37 BCOR altered tumors and 37 non-BCOR altered tumors to study the rare tumor entity of EP300::BCOR fusion in central nervous system. The raw methylation idat files and processed beta values were provided here.

2022-10-09 | GSE211156 | GEO

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