Whole transcriptome analysis of sinonasal sarcoma with translocation t(2;4)(q37.1;q31.3)
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE52257 | GEO | 2014/04/17
SECONDARY ACCESSION(S): PRJNA227288
REPOSITORIES: GEO
Similar Datasets
Project description:Conventioal cytogenetic on 2 sinonasal sarcoma (SNS) cases showed t(2;4)(q37.1;q31.3) translocation previously. The aim of this whole transcriptome analysis is to determine potential candidate genes involved in this translocation. Total RNA extracted from frozen cultured primary tumor cells from a SNS characterized at the cytogenetics level was subjected to Illumina whole transcriptome RNA-sequencing anslysis.
2014-04-17 | E-GEOD-52257 | biostudies-arrayexpress
Project description:Analyses of gene expression profiling in sinonasal sarcoma (SNS) harboring PAX3-MAML3 fusion gene or PAX3 rearrangement and other types of tumors without having such fusion or rearrangement. The results provide important information for further investigations of the PAX3-MAML3 fusion functions in SNS. Total RNA was obtained from FFPE tissues of 41 tumors including 8 SNS (6 with PAX3-MAML3 fusion and 2 with PAX3 rearrangement only) and 33 cases from other 10 different types of tumors. Gene expression profiling of fusion group including 8 SNA vs.non-fusion group including 33 control tumors were analyszed.
2014-04-17 | E-GEOD-52252 | biostudies-arrayexpress
Project description:Analyses of gene expression profiling in sinonasal sarcoma (SNS) harboring PAX3-MAML3 fusion gene or PAX3 rearrangement and other types of tumors without having such fusion or rearrangement. The results provide important information for further investigations of the PAX3-MAML3 fusion functions in SNS.
2014-04-17 | GSE52252 | GEO
Project description:The diagnosis of sinonasal tumors is challenging due to a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we apply machine learning algorithm based on DNA methylation patterns to classify sinonasal tumors with clinical-grade reliability. We further show that sinonasal tumors with SNUC morphology are not as undifferentiated as their current terminology suggests but rather reassigned to four distinct molecular classes defined by epigenetic, mutational and proteomic profiles. This includes two classes with neuroendocrine differentiation, characterized by IDH2 or SMARCA4/ARID1A mutations with an overall favorable clinical course, whereas tumors that are driven by SMARCB1-deficiency and tumors that represent previously misclassified adenoid cystic carcinomas are highly aggressive. Our findings have the potential to dramatically improve the diagnostic classification of sinonasal tumors and will fundamentally change the current perception of SNUCs.
2022-09-25 | GSE196227 | GEO
Project description:Comparative analysis of gene expression in murine sinonasal mucosa in wild-type and CC10-knockout littermates with allergic eosinophilic chronic rhinosinusitis. The data provide a comprehensive overview of genes expressed in the mouse sinonasal mucosa and show that the expression of several known and unidentified genes is modified by disruption of the CC10 gene. Total RNA isolated from sinonasal mucosae of 6- to 8-week-old mice, C57BL/6 strain, was used for this comparison. Three groups: wild-type control, wild-type with allergic eosinophilic chronic rhinosinusitis, and CC10-knockout with allergic eosinophilic chronic rhinosinusitis.
2010-12-01 | E-GEOD-20969 | biostudies-arrayexpress
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
Project description:The histopathological diagnosis of sinonasal tumors is challenging as it encompasses a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we show that a machine learning algorithm based on DNA methylation is able to classify sinonasal tumors with clinical-grade reliability. We further show that tumors with SNUC morphology are not as undifferentiated as their current terminology suggests, but can be assigned to four molecular classes defined by distinct epigenic, mutational and proteomic profiles. This includes two classes with neuroendocrine differentiation, characterized by IDH2 or SWI/SNF chromatin remodeling complex mutations and overall favorable clinical course, highly aggressive tumors that are driven by SMARCB1-deficiency and tumors that represent previously misclassified adenoid-cystic carcinomas. Our findings have the potential to dramatically improve the diagnostic of challenging sinonasal tumors and could fundamentally change the current perception of SNUCs.
2022-09-25 | GSE189778 | GEO
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
Project description:Human sinonasal cavity Targeted loci environmental
| PRJNA407725 | ENA
Project description:Comparative analysis of gene expression in murine sinonasal mucosa in wild-type and CC10-knockout littermates with allergic eosinophilic chronic rhinosinusitis. The data provide a comprehensive overview of genes expressed in the mouse sinonasal mucosa and show that the expression of several known and unidentified genes is modified by disruption of the CC10 gene.
2010-12-01 | GSE20969 | GEO