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Genomic signatures predict poor outcome in Undifferentiated Pleomorphic Sarcomas and Leiomyosarcomas

ABSTRACT: Array-based comparative genomic hybridization (array CGH) analyses was used to analyze 20 UPS and 17 LMS samples from untreated patients. The data were validated using quantitative PCR.

ORGANISM(S): Homo sapiens

PROVIDER: GSE45573 | GEO | 2013/05/20

SECONDARY ACCESSION(S): PRJNA194609

REPOSITORIES: GEO

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Genomic signatures predict poor outcome in Undifferentiated Pleomorphic Sarcomas and Leiomyosarcomas

Project description:Array-based comparative genomic hybridization (array CGH) analyses was used to analyze 20 UPS and 17 LMS samples from untreated patients. The data were validated using quantitative PCR. Experiment condition, 20 UPS and 17 LMS DNA samples obtained from untreated patients were laleled with Cy5 and commercial reference samples (Promega) were labled with Cy3. Samples Cy3 and Cy5 were mixed and hybridized at slide glasses Agilent 4x44 platform.

2013-05-20 | E-GEOD-45573 | biostudies-arrayexpress

Genomic signatures predict poor outcome in undifferentiated pleomorphic sarcomas and leiomyosarcomas.

Project description: Not available

| S-EPMC3692486 | biostudies-literature

Gene expression profiling in leiomyosarcomas and undifferentiated pleomorphic sarcomas: SRC as a new diagnostic marker

2013-09-15 | GSE49941 | GEO

Gene expression profiling in leiomyosarcomas and undifferentiated pleomorphic sarcomas: SRC as a new diagnostic marker

Project description:Transcriptional profiling of leiomyosarcomas (LMS) and undifferentiated pleomorphic sarcomas (UPS) aiming to identify molecular biomarkers. Data were validated using RT-qPCR. To assess the relevance of the gene signature, a meta-analysis was performed using five published studies. SRC protein immunolabeling was performed for 38 UPS and 52 LMS. Experiment condition, 22 LMS vs. 22 UPS. Total RNA extracted from tumors was labeled with Cy5, while a custom reference sample (combination of equal amounts of total RNA obtained from 15 different human cell lines) was labeled with Cy3. Samples Cy3 and Cy5 were mixed and hybridized on a two-Color Human GE 4X44K Microarray platform (Agilent Technologies, Palo Alto, CA, USA).

2013-09-15 | E-GEOD-49941 | biostudies-arrayexpress

Undifferentiated pleomorphic sarcoma recapitulates the expressional profile of Subtype II Leiomyosarcoma

Project description:Background: Undifferentiated pleomorphic sarcoma (UPS), used to be called malignant fibrous histiocytoma (MFH), is a malignant soft tissue tumor of uncertain origin, and is characterized by morphology. UPS often share similar morphological characters with other sarcomas, especially Leiomyosarcoma. Leiomyosarcoma (LMS) is another malignant soft tissue sarcoma with complex genomic abnormalities, origin from smooth muscle. As a result, development of gene signature and/or biomarkers distinguishing UPS and LMS will definitely help the pathologist to precisely diagnose those patients. However, in the past, UPS was reported to be indistinguishable with LMS by genomic profiles. Methods and Results: In this study, 3’ end RNA Sequencing (3SEQ) was used to expression profile 6 UPS and 99 LMS cases. Overall, UPS was undistinguished with LMS by 3SEQ data, however, when we stratified LMS into three subtypes, UPS was shown to share similar expression pattern with Subtype II LMS, but had distinct molecular expression patterns with Subtype I and Subtype III LMS. Additional Immunohistochemistry staining by using LMS Subtype I and Subtype II markers validated that UPSs were positive for Subtype II marker ARL4C, but negative for Subtype I marker LMOD1. Furthermore, CD4 was shown to be significantly more highly expressed in UPS than LMS in both mRNA and protein levels. Conclusion: This study first reported that UPS shared similar gene expression pattern with subtype II LMS and UPS recapitulated the expression profiles of subtype II LMS.

2015-05-19 | GSE53844 | GEO

Undifferentiated pleomorphic sarcoma recapitulates the expressional profile of Subtype II Leiomyosarcoma

2015-05-19 | E-GEOD-53844 | biostudies-arrayexpress

Shared prognostic markers in undifferentiated pleomorphic sarcoma and leiomyosarcoma of the extremities

Project description:Soft tissue sarcoma diagnostics and prognostics are challenging, particularly in highly malignant and pleomorphic subtypes such as undifferentiated pleomorphic sarcoma (UPS) and leiomyosarcoma (LMS). We applied 32K BAC-arrays and gene expression profiling to 18 extremity soft tissue LMS and 31 extremity soft tissue UPS with the aim to identify molecular subtype signatures and genomic prognostic markers. Both the gains/losses and gene expression signatures revealed striking similarities between UPS and LMS, which were indistinguishable using unsupervised hierarchical cluster analysis and significance analysis for microarrays. Gene expression analysis revealed just 9 genes, among them Tropomyosin beta, that were differentially expressed. Loss of 4q31 (encompassing the SMAD1 locus), loss of 18q22 and tumor necrosis were identified as independent predictors of metastasis in multivariate stepwise Cox regression analysis. Combined analysis applying loss of 4q31 and 18q22 and presence of necrosis improved the area under receiver operating characteristic curve for metastasis prediction from 0.64 to 0.86. The extensive genetic similarities between extremity soft tissue UPS and LMS suggest a shared lineage of these STS subtypes and the new and independent genetic prognosticators identified hold promise for refined prognostic determination in high-grade, genetically complex STS. Genomic DNA was extracted from a total of 49 samples, 31 Undifferentiated pleomorphic Sarcomas and 18 Leiomyosarcomas. The DNA was labeled using Bioprime array CGH labeling kit (Invitrogen). Promega pooled male DNA was used as reference. Labeled DNA was hybridized onto BAC arrays containing ~32 000 BAC clones printed in singlets. BAC arrays were produced at the SWEGENE DNA Microarray Facility at Lund University.

2010-10-08 | E-GEOD-13775 | biostudies-arrayexpress

Shared prognostic markers in undifferentiated pleomorphic sarcoma and leiomyosarcoma of the extremities

2009-03-24 | GSE13775 | GEO

Gene expression profiling in leiomyosarcomas and undifferentiated pleomorphic sarcomas: SRC as a new diagnostic marker.

Project description: Not available

| S-EPMC4100821 | biostudies-literature

Single cell RNA-sequencing of undifferentiated pleomorphic sarcomas and leiomyosarcomas.

Project description:The tumor microenvironment plays a crucial role in soft tissue sarcoma development and response to therapy. We used single cell RNA sequencing to analyze the malignant, immune, and other stromal cells present within soft tissue sarcomas.

2023-12-12 | GSE212527 | GEO

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