Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

MiRNA expression profiles from Ewing sarcoma samples, Ewing sarcoma cell lines and mesenchymal stem cells

ABSTRACT: For the identification of differentially expressed miRNA relevant for ES pathogenesis and clinical behaviour miRNA expression profiling of 377 miRNAs for 40 fresh-frozen ES samples, including primary cases and metastases and cases with different translocation types and 6 ES cell lines and compared these to those of MSCs from 6 healthy donors as the potential cells of origin were generated

ORGANISM(S): Homo sapiens

SUBMITTER: Bianca Karnuth

PROVIDER: E-MTAB-1337 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Differentially expressed miRNAs in Ewing sarcoma compared to mesenchymal stem cells: low miR-31 expression with effects on proliferation and invasion.

Karnuth Bianca B Dedy Nicolas N Spieker Tilmann T Lawlor Elizabeth R ER Gattenlöhner Stefan S Ranft Andreas A Dirksen Uta U Jürgens Heribert H Bräuninger Andreas A

PloS one 20140325 3

Ewing sarcoma, the second most common bone tumor in children and young adults, is an aggressive malignancy with a strong potential to metastasize. Ewing sarcoma is characterised by translocations encoding fusion transcription factors with an EWSR1 transactivation domain fused to an ETS family DNA binding domain. microRNAs are post-transcriptional regulators of gene expression and aberrantly expressed microRNAs have been identified as tumor suppressors or oncogenes in most cancer types. To identi ...[more]

PMID: 24667836

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Project description:Most (70%) epithelial ovarian cancers (EOCs) are diagnosed late. Non-invasive biomarkers that facilitate disease detection and predict outcome are needed. The microRNAs (miRNAs) represent a new class of biomarkers. This study was to identify and validate plasma miRNAs as biomarkers in EOC. We evaluated plasma samples of 360 EOC patients and 200 healthy controls from two institutions. All samples were grouped into screening, training and validation sets. We scanned the circulating plasma miRNAs by TaqMan low-density array in the screening set and identified/validated miRNA markers by real-time polymerase chain reaction assay in the training set. Receiver operating characteristic and logistic regression analyses established the diagnostic miRNA panel, which were confirmed in the validationsets. We found higher plasma miR-205 and lower let-7f expression in cases than in controls. MiR-205 and let-7f together provided high diagnostic accuracy for EOC, especially in patients with stage I disease. The combination of these two miRNAs and carbohydrate antigen-125 (CA-125) further improved the accuracy of detection. MiR-483-5p expression was elevated in stages III and IV compared with in stages I and II, which was consistent with its expression pattern in tumor tissues. Furthermore, lower levels of let-7f were predictive of poor prognosis in EOC patients. Our findings indicate that plasma miR-205 and let-7f are biomarkers for ovarian cancer detection that complement CA-125; let-7f may be predictive of ovarian cancer prognosis. We designed a multi-stage, retrospective, nested case-control study to determine whether serum miRNA profiles can be used to predict EOC development. All samples were grouped into screening, training, and validation sets. A total of 560 plasma samples (360 cases and 200 controls) were obtained from Tianjin Medical University Cancer Institute and Hospital (TCIH) and Cancer Center of Nanjing Medical University. The cases and controls were well matched for age. The International Federation of Gynaecology and Obstetrics (FIGO) staging system was used to stage cases. All patients and controls were genetically unrelated, ethnic Han Chinese women who were permanent residents of the urban area of Tianjin and Nanjing. Controls with cardiovascular, respiratory, digestive, urinary, reproductive, and endocrine diseases were excluded. The study protocols were approved by the Tianjin and Nanjing Center review committees. In screening set, to detect generalizable miRNA signatures, we pooled serum samples of 10 early-stage cases (stage I), 10 late-stage cases (stage IIIc-IV), and 10 healthy controls, respectively, and analyzed these three pool samples using a TaqMan low-density array (TLDA set 2.0, Applied Biosystems) chip screening in the discovery stage. In training set, the miRNAs identified in the screening set were validated using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) on individual plasma samples of 76 EOC patients and 30 normal controls. In validation set, the validation set comprised a two-phase process. Promising associations from the screening and training set were evaluated in the validation phase I set, comprising 134 cases and 70 controls from Tianjin Center. The validation phase II set included samples of 77 EOC cases and 50 normal controls were from Tianjin Center and 73 EOC cases and 50 normal controls were from Nanjing Center.

Project description:MicroRNAs (miRNAs) are abundant in the circulation and play a central role in diverse biological processes; they may be useful for early diagnosis of hepatocellular carcinoma (HCC). We conducted a two-phase, case-control study (20 pairs for the discovery set and 49 pairs for the validation set) to test the hypothesis that genome-wide dysregulation of circulating miRNAs differentiate HCC cases from controls. Taqman low density arrays were used to examine genome-wide miRNA expression for the discovery set, and quantitative RT-PCR was used to validate candidate miRNAs for both discovery and validation sets. Sixty-six miRNAs were found to be significantly over-expressed in plasma of HCC cases compared to controls after adjusting for false discovery rate (p<0.05). A volcano plot indicated that 7 miRNAs had greater than 2-fold case-control differences with p<0.01. Four significant miRNAs (miR-150, miR-30c, miR-483-5p and miR-520b) detectable in all samples with varied expression levels were further validated in a validation set. MiR-483-5p was statistically significantly over-expressed in HCC cases compared with controls (3.20 vs. 0.82, p<0.0001). HCC risk factors and clinic-pathological characteristics did not influence miR-483-5p expression. The combination of plasma miR-483-5p level and HCV status can significantly differentiate HCC cases from controls with an AUC of 0.908 (p<0.0001). The sensitivity and specificity were, respectively, 75.5% and 89.8%. These preliminary results suggest the importance of dysregulated circulating miR-483-5p as a potential HCC biomarker. Confirmation of aberrant expression of miR-483-5p in a large prospective HCC study will provide support for its application to HCC detection. A hospital-based HCC case-control study including 20 HCC patients and 20 controls is conducted in Columbia University Medical Center (CUMC), which is approved by the Institutional Review Board. Cases were newly diagnosed HCC patients who were treated in the Hepatobiliary Oncology Clinics, CUMC, and examined pathologically. Controls were recruited from volunteers through the Research Recruitment and Minority Outreach (RRMO) core of Herbert Irving Comprehensive Cancer Center (HICCC). Flyers were placed at strategic locations around CUMC where hospital visitors and employees frequent or were handed out at inreach events at the hospital or at outreach events in the community. Interested participants were directed to contact the trained recruitment staff from the RRMO and given further information about participation. Interested participants were excluded from the control group if diagnosed for any kind of cancer or liver disease. Eligible controls were asked to fill out the same demographic and epidemiological questionnaire as HCC cases. In the current study, controls were matched with HCC cases on age (M-BM-15 yrs), gender (male/female) and ethnicities (Caucasian/Hispanic/African-American/Asian).

Dataset Information

MiRNA expression profiles from Ewing sarcoma samples, Ewing sarcoma cell lines and mesenchymal stem cells

Publications

Differentially expressed miRNAs in Ewing sarcoma compared to mesenchymal stem cells: low miR-31 expression with effects on proliferation and invasion.

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