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Series GSE53844 Query DataSets for GSE53844
Status Public on May 19, 2015
Title Undifferentiated pleomorphic sarcoma recapitulates the expressional profile of Subtype II Leiomyosarcoma
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Overall design In this study, 3’ end RNA Sequencing (3SEQ) was used to expression profile 6 UPS and 99 LMS cases. In order to explore the molecular differences between UPS and LMS, We analyzed the expression data by SAMseq to identify the genes which were significantly differently expressed between UPS and LMS, between UPS and each LMS subtype.
Contributor(s) Guo X, Zhu SX, Varma S, Kwok S, West RB, van de Rijn M
Citation(s) 25896974
Submission date Jan 06, 2014
Last update date May 15, 2019
Contact name Xiangqian Guo
Phone 650 725 7742
Organization name Stanford University
Department Department of Pathology
Lab vanderijn-west Lab
Street address 300 Pasteur Dr.
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (6)
GSM1302027 STT6619_UPS
GSM1302028 STT6622_UPS
GSM1302029 STT6623_UPS
BioProject PRJNA233524
SRA SRP034953

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE53844_6UPS.transcriptome_TPM_round.txt.gz 389.9 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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