Genomics

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Epigenetic profiling of well differentiated and dedifferentiated liposarcoma identifies H3K9me3 and Kruppel-like factor 6 (KLF6) as determinants of aggressiveness in sarcoma (ChIP-seq)


ABSTRACT: Little is known about the epigenomics of liposarcoma (LPS). Here, we profiled the global expression of 9 epigenetic marks in well differentiated (WD) and dedifferentiated (DD) LPS from 151 patients and found increased H3K9me3 among DDLPS tumors. We performed ChIP-seq and gene expression profiling of patient derived cell lines to discover functionally significant regions of differential H3K9me3 enrichment between WDLPS and DDLPS associated with concomitant gene expression changes. We performed genome-wide transcriptional profiling of H3K9me3 in dedifferentiated liposarcoma DDLPS and well differentiated liposarcoma WDLPS cell lines.

ORGANISM(S): Homo sapiens  

SUBMITTER: Lynda Chin   Kadir C Akdemir  Emily Z Keung  Kadir Caner Akdemir 

PROVIDER: E-GEOD-57749 | ArrayExpress | 2015-08-04

SECONDARY ACCESSION(S): SRP042051GSE57749PRJNA248009

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Increased H3K9me3 drives dedifferentiated phenotype via KLF6 repression in liposarcoma.

Keung Emily Z EZ   Akdemir Kadir C KC   Al Sannaa Ghadah A GA   Garnett Jeannine J   Lev Dina D   Torres Keila E KE   Lazar Alexander J AJ   Rai Kunal K   Chin Lynda L  

The Journal of clinical investigation 20150720 8


Liposarcoma (LPS) can be divided into 4 different subtypes, of which well-differentiated LPS (WDLPS) and dedifferentiated LPS (DDLPS) are the most common. WDLPS is typically low grade, whereas DDLPS is high grade, aggressive, and carries a worse prognosis. WDLPS and DDLPS frequently co-occur in patients. However, it is not clear whether DDLPS arises independently from WDLPS, or whether epigenomic alterations underly the histopathological differences of these subtypes. Here, we profiled 9 epigene  ...[more]

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