Project description:Proteomic analysis of membrane fractions from U-2 OS control and Lunapark knockout cells to determine protein abundance per mRNA. Membrane proteins were extracted, digested, and analyzed by DIA LC–MS/MS on a Thermo Orbitrap Ascend Tribrid mass spectrometer with Vanquish Neo LC system
Project description:Shotgun proteomics of normal versus germ-free mouse terminal ileum. 39 mice. Male and female. BALBc and C57BL10. The samples were labeled using iTRAQ 8plex and analyzed using a nano-LC-LTQ-Orbitrap-Velos-MSMS. This is the proteomics data from an n-omics project.
Project description:RET rearrangement is a newly identified oncogenic mutation in lung adenocarcinoma (LADC). Activity of dovitinib (TKI258), a potent inhibitor of FGFR, VEGFR, and PDGFR, in RET-rearranged LADC has not been reported. The aims of the study are to explore anti-tumor effects and mechanisms of acquired resistance of dovitinib in RET-rearranged LADC. Using structural modeling and in vitro analysis, we demonstrated that dovitinib induced cell cycle arrest at G0/G1 phase and apoptosis by selective inhibition of RET kinase activity and ERK1/2 signaling in RET-rearranged LC-2/ad cells. Strong anti-tumor effect of dovitinib was observed in LC-2/ad tumor xenograft model. To identify the acquired resistance mechanisms to dovitinib, LC-2/ad cells were exposed to increasing concentrations of dovitinib to generate LC-2/ad DR cells. Gene set enrichment analysis of gene expression and receptor tyrosine kinase assay revealed that Src, a central gene in focal adhesion , was activated in LC-2/ad DR cells. Saracatinib, a src kinase inhibitor, suppressed ERK1/2 phosphorylation and growth of LC-2/ad DR cells. Taken together, these findings suggest that dovitinib can be a potential therapeutic option for RET-rearranged LADC, in which acquired resistance to dovitinib can be overcome by targeting Src. To identify potential mechanisms of acquired resistance to dovitinib, we established LC-2/ad DR cells with acquired resistance to dovitinib by exposing LC-2/ad cells to increasing doses of dovitinib. LC-2/ad DR cells showed strong resistance to dovitinib (IC50> 3 μmol/L). Next, LC-2/ad and LC-2/ad DR cells were subjected to genome-wide gene expression profiling using cDNA microarray.
Project description:Lipid Data Analyzer (LDA; http://genome.tugraz.at/lda2) provides automated and reliable annotation of lipid species and their molecular structures in high-throughput data from chromatography-coupled tandem mass spectrometry using embedded rule sets. Using various low- and high-resolution mass spectrometry instruments with several collision energies, the method's platform independence is proved. The software's reliability, flexibility, and ability to identify novel lipid molecular species may now render current state-of-the-art lipid libraries obsolete. </br></br> In a benchmark test of LDA versus LipidBlast, data from both the first control experiment and the biological experiment, both acquired on the Orbitrap Velos Pro in CID +50 and -50, was used. In addition, the biological experiment was benchmarked for the lower resolution QTRAP 4000 for +45 eV and -45 eV. For LipidBlast evaluation, the parameters recommended by NIST MSPepSearchGUI (http://peptide.nist.gov/software/ms_pep_search_gui/MSPepSearch.html) were used. The same m/z tolerances were applied in both LipidBlast and LDA. The specificity and sensitivity of LipidBlast depend on a so called matching factor, a value ranging from 0-999. Using the default setting of 450 for the matching factor, many lipid standards in Control experiment 1 were not detected. Consequently, the matching factor was lowered to 10, in which case LipidBlast detected almost all of the lipid standards in negative ion mode. Further reduction did not improve the sensitivity of LipidBlast. In positive ion mode, irrespective of the matching factor setting, LipidBlast was not able to identify as many lipid molecular species as was LDA. In this benchmark test, only lipid subclasses/adducts that both LDA and LipidBlast are able to detect were used. Correct assignment of lipid species and lipid molecular species identified in liver lipidomes was verified by manual inspection of the spectra, and by aligning them with the respective retention time data.</br></br>Control experiment 1 assays for this study can be found in the MetaboLights study MTBLS394.</br> Control experiment 2 assays for this study can be found in the MetaboLights study MTBLS391.</br> Control experiment 3 assays for this study can be found in the MetaboLights study MTBLS398.</br> Murine liver lipidome experiment assays for this study can be found in the MetaboLights study MTBLS396.</br> HCD characterization and regioisomer detection assays for this study can be found in the MetaboLights study MTBLS462.</br> <br/>Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS391' target='_blank'><span class='label label-success'>MTBLS391</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS394' target='_blank'><span class='label label-success'>MTBLS394</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS396' target='_blank'><span class='label label-success'>MTBLS396</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS398' target='_blank'><span class='label label-success'>MTBLS398</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS462' target='_blank'><span class='label label-success'>MTBLS462</span></a>
Project description:RET rearrangement is a newly identified oncogenic mutation in lung adenocarcinoma (LADC). Activity of dovitinib (TKI258), a potent inhibitor of FGFR, VEGFR, and PDGFR, in RET-rearranged LADC has not been reported. The aims of the study are to explore anti-tumor effects and mechanisms of acquired resistance of dovitinib in RET-rearranged LADC. Using structural modeling and in vitro analysis, we demonstrated that dovitinib induced cell cycle arrest at G0/G1 phase and apoptosis by selective inhibition of RET kinase activity and ERK1/2 signaling in RET-rearranged LC-2/ad cells. Strong anti-tumor effect of dovitinib was observed in LC-2/ad tumor xenograft model. To identify the acquired resistance mechanisms to dovitinib, LC-2/ad cells were exposed to increasing concentrations of dovitinib to generate LC-2/ad DR cells. Gene set enrichment analysis of gene expression and receptor tyrosine kinase assay revealed that Src, a central gene in focal adhesion , was activated in LC-2/ad DR cells. Saracatinib, a src kinase inhibitor, suppressed ERK1/2 phosphorylation and growth of LC-2/ad DR cells. Taken together, these findings suggest that dovitinib can be a potential therapeutic option for RET-rearranged LADC, in which acquired resistance to dovitinib can be overcome by targeting Src.