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RNA-seq of four tissue samples of dedifferentiated liposarcoma and corresponding matched well-differentiated liposarcoma

ABSTRACT: RNA-seq of four tissue samples of dedifferentiated liposarcoma and corresponding matched well-differentiated liposarcoma

PROVIDER: PRJNA763563 | ENA |

REPOSITORIES: ENA

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RNA-seq of four tissue samples of dedifferentiated liposarcoma and corresponding matched well-differentiated liposarcoma

Project description:Dedifferentiated liposarcoma (DDL) has the same cellular and molecular genetics features as well-differentiated liposarcoma (WDL), and there is still no ideal biomarker for the prediction of DDL patient prognosis in clinical practice. In order to explore the genes that cause WDL to obtain local invasion and distant metastasis capacities and transform it into DDL, The four DDL tissue specimens in this study were matched with four WDL tissue specimens according to baseline characteristics, such as gender, age, and recurrence, before high-throughput sequencing was conducted. Then total RNAs were subjected to RNA isolation and RNA-seq analyses were generated by deep sequencing using Illumina Hiseq.

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Genomic characterization of well differentiated/dedifferentiated retroperitoneal liposarcoma

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Project description:Genomic characterization of well differentiated/dedifferentiated retroperitoneal liposarcoma

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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 (expression)

Project description: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 dedifferentiated liposarcoma (DDLPS) and well differentiated liposarcoma (WDLPS) cell lines using the Affymetrix U133A GeneChip array

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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)

Project description: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.

2015-08-04 | E-GEOD-57749 | biostudies-arrayexpress

Novel dedifferentiated liposarcoma xenograft models reveal PTEN down regulation as a malignant signature and response to PI3K pathway inhibition

Project description:Liposarcoma is a type of soft tissue sarcoma, exhibiting poor survival and a high recurrence rate. Treatment is generally limited to surgery and radiation, emphasizing the need to understand this disease. Because very few in vivo and in vitro models can reproducibly recapitulate the human disease, we generated several xenograft models from surgically resected human dedifferentiated liposarcoma. Our study demonstrates that all xenografts recapitulate morphologic and gene expression characteristics of the patient tumors after continuous in vivo passages. Importantly, xenograftability is directly correlated with disease specific survival of liposarcoma patients. When treated with the PI3K/AKT/mTOR pathway inhibitor rapamycin alone or in combination with the multi-kinase inhibitor sorafenib, all xenografts responded with increased lipid content and a more differentiated gene expression profile. One-color arrays: Vehicle vs combination (rapamycin & sorafenib) treatment for 2 separate dedifferentiated liposarcoma xenografts. Two-color arrays: Comparison of patient tumor, several passages of xenograft generated from that tumor, and cells cultured from xenografted tumors.

2012-12-19 | E-GEOD-42975 | biostudies-arrayexpress

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

2015-08-04 | GSE57750 | GEO

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

2015-08-04 | GSE57749 | GEO

Novel dedifferentiated liposarcoma xenograft models reveal PTEN down regulation as a malignant signature and response to PI3K pathway inhibition

2012-12-19 | GSE42975 | GEO

Differentiating liposarcoma from lipoma using a simple blood test: A miRNA signature

Project description:Background: Liposarcoma constitute about 13% of all soft tissue sarcoma and are associated with a high risk of metastases. As the preoperative differentiation between benign and malign lipomatous tumors is restricted to magnetic resonance imaging, computed tomography and biopsy, we performed a miRNA array to distinguish liposarcoma patients from healthy controls and lipoma patients. Workflow: Blood samples of patients with dedifferentiated liposarcoma, healthy controls and lipoma patients were collected. Whole blood RNA was extracted and samples of patients with dedifferentiated liposarcoma (n=6) and of healthy donors (n=4) were analyzed using an Affymetrix GeneChip miRNA Array v. 4.0. qRT-PCR was carried out to confirm the most differentially expressed miRNA; being further analyzed in an independent cohort of healthy controls as well as in lipoma patients. Results: As shown by the microarray, two miRNAs (miR-4668-5p and miR-3613-3p) were shown to be significantly upregulated (fold change: >2.5; p<0.05) in patients with dedifferentiated liposarcoma (n=6) as compared to healthy controls (n=4). miR-4668-5p was further validated by qRT-PCR to be significantly upregulated in liposarcoma patients compared to an independent cohort of healthy controls (n=3) and lipoma patients (n=6). Conclusion: We identified a specific whole blood miRNA (miR-4668-5p) that may serve to distinguish between lipoma and liosarcoma patients, thus potentially serving as a specific biomarker for dedifferentiated liposarcoma.

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