Dataset Information

IEF fractionation OVCAR-5 cell line

ABSTRACT: Analysis of the ovarian cancer cell line OVCAR-5. A standard trypsin digest was carried out on the OVCAR-5 cell lysates which were then analysed in the un-fractionated and fractionated forms. Fractionation was completed using a peptide IEF separation method. All samples were analysed by nano-LC-ESI-MS/MS using a QTOF.

INSTRUMENT(S): maXis

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Malignant Neoplasm Of Ovary

SUBMITTER: Georgia Arentz

LAB HEAD: Peter Hoffmann

PROVIDER: PXD003547 | Pride | 2016-09-27

REPOSITORIES: Pride

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Publications

Novel IEF Peptide Fractionation Method Reveals a Detailed Profile of N-Terminal Acetylation in Chemotherapy-Responsive and -Resistant Ovarian Cancer Cells.

Weiland Florian F Arentz Georgia G Klingler-Hoffmann Manuela M McCarthy Peter P Lokman Noor A NA Kaur Gurjeet G Oehler Martin K MK Hoffmann Peter P

Journal of proteome research 20160919 11

Although acetylation is regarded as a common protein modification, a detailed proteome-wide profile of this post-translational modification may reveal important biological insight regarding differential acetylation of individual proteins. Here we optimized a novel peptide IEF fractionation method for use prior to LC-MS/MS analysis to obtain a more in depth coverage of N-terminally acetylated proteins from complex samples. Application of the method to the analysis of the serous ovarian cancer cel ...[more]

PMID: 27569743

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Project description:We previously demonstrated that the osteopontin-c (OPNc) splice variant activates several aspects of the progression of ovarian cancers. The goal of the present study was to develop cell line model to determine the impact of OPNc overexpression on main cancer signaling pathways and thus obtain insights into the mechanisms of OPNc pro-tumorigenic roles. Methods: OvCar-3 cells were stably transfected to overexpress OPNc. Transcriptomic profiling was performed on these cells and compared to controls, to identify OPNc overexpression-dependent changes in gene expression levels and pathways by qRT-PCR analyses; Results: Of 84 genes tested by using a multiplex real-time PCR Cancer Pathway Array approach, 34, were differentially expressed between OvCar-3 OPNc-overexpressing cells in relation to control clones. Differentially expressed genes are included in all main hallmarks of cancer, and several interacting proteins have been identified using an interactome network analysis. Conclusions: Overall, the present study elucidated transcriptional changes of ovarian cancer cells in response to OPNc overexpression, which provides an assessment for predicting the molecular mechanisms by which this splice variant promotes tumor progression features. Cell Culture, OPN Plasmids and Transfection; As a model to examine the signaling pathways modulated by OPNc overexpression in ovarian carcinoma, we used OvCar-3 cell line, which were provided by ATCC. The open reading frame of OPNc was cloned into the pCR3.1 mammalian expression vector as previously described [Tilli et al., 2012]. Transfections were performed using LipofectamineTM 2000 (Invitrogen, CA). Our previous data demonstrated that OvCar-3 stably transfected cells contain higher levels of protein and the mRNA OPNc splicing isoform in relation to their endogenous levels in empty vector-transfected cells. OvCar-3 transfected with empty vector (EV) were used as a negative control in these assays. Human Cancer Pathway Finder PCR Array The Human Cancer Pathway Finder SuperArray (PAHS-033A; Qiagen) was used to determine changes in the specific genes encoding proteins related to the main hallmarks of cancer in response to OPNc overexpression. The assay design criteria ensure that each qPCR reaction will generate single, gene-specific amplicons and prevent the co-amplification of non-specific products. The qPCR Assays used in PCR Arrays are optimized to work under standard conditions enabling a large number of genes to be assayed simultaneously. Their specificity is guaranteed by SABiosciences when RT2 SYBR Green qPCR Master Mixes are used as part of the complete PCR Array System protocol. Simultaneous gene expression analyses require similar qPCR efficiencies for accurate comparison among genes. RT2 qPCR Primer Assays are designed with an amplicon size ranging from 100 to 250 bp and with PCR efficiencies uniformly greater than 90%. Overall, more than 10 thermodynamic criteria are included in the design of each RT2 qPCR Primer Assay to ensure the most reliable and accurate results for pathway-based gene expression analysis in the PCR Array System. We analyzed mRNA levels of 84 genes related to cell cycle control, apoptosis and cell senescence, signal transduction molecules and transcription factors, adhesion, angiogenesis, invasion and metastasis; and also 5 housekeeping genes and genomic DNA contamination controls. The PCR plates were run using the CFX96 Real-Time System cycler (BioRad, Hercules, CA), following a superarray two-step cycling PCR protocol, in which each plate ran one cycle for 10 minutes at 95M-BM-0C, as well as 40 cycles of 95M-BM-0C for 15 seconds and 60M-BM-0C for 1 minute. After the superarray protocol was run for each plate, RT-PCR data analysis was performed using the website:http://www.SABiosciences.com/pcrarraydataanalysis.php, in order to compare gene expression of OPNc-overexpressing cells and empty vector transfected cells. Total RNA quality control, cDNA synthesis and the quantitative real-time RT-PCR (qRT-PCR) array were performed as recommended by the manufacturer (Qiagen). Data analysis of gene expression was performed using Excel-based PCR Array Data Analysis Software provided by manufacturer (Qiagen). Fold-changes in gene expression were calculated using the M-NM-^TM-NM-^TCT method, and five stably expressed housekeeping genes (M-NM-22 microglobulin, hypoxanthine phosphoribosyltransferase 1, ribosomal protein L13a, GAPDH and M-NM-2-actin) were used to normalize the level of expression. The statistical analysis was performed to compare the gene expression values for the OPNc-overexpressing cells and those transfected with empty vector. P<0.05 was considered statistically significant. Only genes showing a 1.5-fold or greater change were considered for further analysis.

Dataset Information

IEF fractionation OVCAR-5 cell line

Publications

Novel IEF Peptide Fractionation Method Reveals a Detailed Profile of N-Terminal Acetylation in Chemotherapy-Responsive and -Resistant Ovarian Cancer Cells.

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