Dataset Information

EGAD00000000049

ABSTRACT: RNA-SEQ data from oestrogen-receptor-alpha-positive metastatic lobular breast cancer sample

PROVIDER: EGAD00000000049 | EGA |

REPOSITORIES: EGA

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Publications

Mutation of FOXL2 in granulosa-cell tumors of the ovary.

Shah Sohrab P SP Köbel Martin M Senz Janine J Morin Ryan D RD Clarke Blaise A BA Wiegand Kimberly C KC Leung Gillian G Zayed Abdalnasser A Mehl Erika E Kalloger Steve E SE Sun Mark M Giuliany Ryan R Yorida Erika E Jones Steven S Varhol Richard R Swenerton Kenneth D KD Miller Dianne D Clement Philip B PB Crane Colleen C Madore Jason J Provencher Diane D Leung Peter P DeFazio Anna A Khattra Jaswinder J Turashvili Gulisa G Zhao Yongjun Y Zeng Thomas T Glover J N Mark JN Vanderhyden Barbara B Zhao Chengquan C Parkinson Christine A CA Jimenez-Linan Mercedes M Bowtell David D L DD Mes-Masson Anne-Marie AM Brenton James D JD Aparicio Samuel A SA Boyd Niki N Hirst Martin M Gilks C Blake CB Marra Marco M Huntsman David G DG

The New England journal of medicine 20090610 26

<h4>Background</h4>Granulosa-cell tumors (GCTs) are the most common type of malignant ovarian sex cord-stromal tumor (SCST). The pathogenesis of these tumors is unknown. Moreover, their histopathological diagnosis can be challenging, and there is no curative treatment beyond surgery.<h4>Methods</h4>We analyzed four adult-type GCTs using whole-transcriptome paired-end RNA sequencing. We identified putative GCT-specific mutations that were present in at least three of these samples but were absent ...[more]

PMID: 19516027

Publication: 1/2

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Project description:About one-third of oestrogen receptor alpha- positive breast cancer patients treated with tamoxifen relapse. Here we identify the nuclear receptor retinoic acid receptor alpha as a marker of tamoxifen resistance. Using quantitative mass spectrometry-based proteomics, we show that retinoic acid receptor alpha protein networks and levels differ in a tamoxifen-sensitive (MCF7) and a tamoxifen-resistant (LCC2) cell line. High intratumoural retinoic acid receptor alpha protein levels also correlate with reduced relapse-free survival in oestrogen receptor alpha-positive breast cancer patients treated with adjuvant tamoxifen solely. A similar retinoic acid receptor alpha expression pattern is seen in a comparable independent patient cohort. An oestrogen receptor alpha and retinoic acid receptor alpha ligand screening reveals that tamoxifen-resistant LCC2 cells have increased sensitivity to retinoic acid receptor alpha ligands and are less sensitive to oestrogen receptor alpha ligands compared with MCF7 cells. Our data indicate that retinoic acid receptor alpha may be a novel therapeutic target and a predictive factor for oestrogen receptor alpha-positive breast cancer patients treated with adjuvant tamoxifen. Peptide and protein identification data set 1: Peptide identification from the MALDI-TOF/TOF data was carried out using the Paragon algorithm in the ProteinPilot 2.0 software package (Applied Biosystems) 46. Default settings for a 4800 instrument were used (i.e., no manual settings for mass tolerance was given). The following parameters were selected in the analysis method: iTRAQ 4plex peptide labelled as sample type, MMTS as alkylating agent of cysteine, trypsin as digesting enzyme, 4800 as instrument, gel based ID and Urea denaturation as special factors, biological modifications as ID focus, and thorough ID as search effort. Peptide identification from the Q-TOF data was carried out using the Spectrum Mill Protein Identification software (Agilent). Data was extracted between MH+ 600 and 4000 Da (Agilent's definition). Scans with the same precursor m/z 90 sec, 0.05 m/z matching with a minimum of 20 peaks in MS2 were merged. Peptide and protein identification data set 2: Proteome discoverer 1.3 with sequest-percolator was used for protein identification. Precursor mass tolerance was set to 10 ppm and for fragments 0.8 Da and 0.02 Da were used for detection in the linear iontrap and the orbitrap, respectively. Oxidized methionine and phosphorylation on S,T and Y was set as dynamic modifications, and carbamidomethylation, N-terminal 8plex iTRAQ, and lysyl 8plex iTRAQ as fixed modifications. Spectra were matched to ensembl 68 limited to human protein sequences, and results were filtered to 1% FDR.

Dataset Information

EGAD00000000049

Publications

Mutation of FOXL2 in granulosa-cell tumors of the ovary.

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