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SWATH-MS in EF1A1- and EF1A2-deficient Schwann and MPNST cells

ABSTRACT: The proteins expressed in normal human Schwann and sNF96.2 MPNST cells treated with EF1A1- and EF1A2-siRNA were profiled by SWATH-MS.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Norie Araki

PROVIDER: PXD007603 | JPOST Repository | Mon Nov 05 00:00:00 GMT 2018

REPOSITORIES: jPOST

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Dataset's files

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			Action	DRS
	Data20170223_SWATH_sNF962_siControl_1.wiff	Wiff
	Data20170223_SWATH_sNF962_siControl_1.wiff.scan	Wiff
	Data20170223_SWATH_sNF962_siControl_2.wiff	Wiff
	Data20170223_SWATH_sNF962_siControl_2.wiff.scan	Wiff
	Data20170223_SWATH_sNF962_siControl_3.wiff	Wiff

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1 - 5 of 20

Publications

Identification of a Specific Translational Machinery via TCTP-EF1A2 Interaction Regulating NF1-associated Tumor Growth by Affinity Purification and Data-independent Mass Spectrometry Acquisition (AP-DIA).

Kobayashi Daiki D Tokuda Takaho T Sato Kyosuke K Okanishi Hiroki H Nagayama Megumi M Hirayama-Kurogi Mio M Ohtsuki Sumio S Araki Norie N

Molecular & cellular proteomics : MCP 20181031 2

Neurofibromatosis type 1 (NF1) is an autosomal dominant disease that predisposes individuals to developing benign neurofibromas and malignant peripheral nerve sheath tumors (MPNST). The mechanism of NF1-tumorigenesis or the curatives have not been established. Using unique trascriptome and proteome integration method, iPEACH (1), we previously identified translationally controlled tumor protein (TCTP) as a novel biological target for NF1-associated tumors (2). Here, we identified specific TCTP-i ...[more]

PMID: 30381327

Similar Datasets

SWATH-MS in TCTP-deficient MPNST cells

Project description:EF1A2-binding proteins in TCTP-deficient MPNST cells were identified by immuno-precipitation using anti-FLAG antibody and SWATH. To verify whether the change of the amount of EF1A2-binding proteins caused the cellular expression change, the proteins expressed in sNF96.2 MPNST cells treated with TCTP-siRNA were profiled by SWATH-MS.

2018-11-05 | PXD007606 | JPOST Repository

Yeast Nat Nt-acetylation SWATH MS

Project description:Yeast strains (wild type, Naa10 KO and Naa20 KO, resp: wt, natA-delta and natB-delta) were profiled for full proteome analysis by SWATH MS

2020-12-15 | PXD015217 | Pride

SWATH-MS analysis of 3-hydroxy-3-methylglutaryl-CoA synthase specific inhibitor (F-244)-treated Arabidopsis

Project description:3-Hydroxy-3-methylglutaryl-CoA synthase (HMGS) is the second enzyme in the mevalonate pathway. F-244 is the specific inhibitor of HMGS. F-244 treatment caused reduced primary root growth. SWATH-MS quantitative proteomics analysis was carried out to identify differential expressed proteins in F-244-treated primary roots.

2019-10-01 | PXD009776 | Pride

EF1A2-binding proteins in TCTP-deficient MPNST cells

Project description:EF1A2-binding proteins in TCTP-deficient MPNST cells were identified by immuno-precipitation using anti-FLAG antibody and SWATH.

2018-11-05 | PXD007605 | JPOST Repository

SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries.

Project description:The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed with peptide MS/MS assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through information dependent acquisition, or obtained from community data repositories for commonly studied organisms. However, there have been no studies performed to systematically evaluate how locally generated or repository-based assay libraries affect SWATH performance for proteomic studies. To undertake this analysis, we developed a software workflow, SwathXtend, which generates extended peptide assay libraries by integration with a local seed library and delivers statistical analysis of SWATH-quantitative comparisons. We designed test samples using peptides from a yeast extract spiked into peptides from human K562 cell lysates at three different ratios to simulate protein abundance change comparisons. SWATH-MS performance was assessed using local and external assay libraries of varying complexities and proteome compositions. These experiments demonstrated that local seed libraries integrated with external assay libraries achieve better performance than local assay libraries alone, in terms of the number of identified peptides and proteins and the specificity to detect differentially abundant proteins. Our findings show that the performance of extended assay libraries is influenced by the MS/MS feature similarity of the seed and external libraries, while statistical analysis using multiple testing corrections increases the statistical rigor needed when searching against large extended assay libraries.

| S-EPMC4937520 | biostudies-literature

Repurposing FDA-approved drugs for the treatment of malignant peripheral nerve sheath tumors

Project description:Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft tissue sarcomas developed from Schwann cell lineage. They account for up to 10% of all soft tissue sarcomas. Although there is an unmet need for new therapeutic agents for MPNSTs, to date there have been few transcriptomic analyses of this tumor type. We studied FDA approved drugs for MPNST treatment and compared their transcriptomic changes in cell lines before and after treatment. We demonstrated that Fludarabine treated NF1 MPNST cells exhibited altered signaling pathways such as the upregulation of the Wnt/Ca+ pathway and downregulation of the hedgehog and hypoxia signaling pathways in the Ingenuity Pathway Analysis (IPA) and Gene Set Enrichment Analysis (GSEA) analysis. The combined Colchicine and Fludarabine treatment enhanced the cytotoxicity of sporadic MPNST cells through altered signaling pathways, including increased Wnt/β-catenin pathway and others. The transcriptomic analysis comparing NF1/sporadic MPNST cells and normal Schwann cells indicated that NF1 MPNST cells had more splicing events, fewer single nucleotide variants, and induced RNA expression than sporadic MPNST cells. In summary, we identified a transcriptomic differences between MPNSTs and Schwann cells, between sporadic MPNST cells and NF1 MPNST cells, and between drug treated MPNST cells and vehicle treated cells.

2023-10-21 | GSE159896 | GEO

Complex-centric proteome profiling by SEC-SWATH-MS.

Project description:Proteins are major effectors and regulators of biological processes that can elicit multiple functions depending on their interaction with other proteins. The organization of proteins into macromolecular complexes and their quantitative distribution across these complexes is, therefore, of great biological and clinical significance. In this paper, we describe an integrated experimental and computational technique to quantify hundreds of protein complexes in a single operation. The method consists of size exclusion chromatography (SEC) to fractionate native protein complexes, SWATH/DIA mass spectrometry to precisely quantify the proteins in each SEC fraction, and the computational framework CCprofiler to detect and quantify protein complexes by error-controlled, complex-centric analysis using prior information from generic protein interaction maps. Our analysis of the HEK293 cell line proteome delineates 462 complexes composed of 2,127 protein subunits. The technique identifies novel sub-complexes and assembly intermediates of central regulatory complexes while assessing the quantitative subunit distribution across them. We make the toolset CCprofiler freely accessible and provide a web platform, SECexplorer, for custom exploration of the HEK293 proteome modularity.

| S-EPMC6346213 | biostudies-literature

NLRP3 immunoprecipitation SWATH-MS data

Project description:NLRP3 complexes were IP in RAW-asc cells, and IPs were analyzed by using SWATH-MS.

2023-03-25 | PXD041115 |

Tear Proteomics in Keratoconus: A Quantitative SWATH-MS Analysis.

Project description:PurposeTo elucidate dysregulated proteins in keratoconus (KC) to provide a better understanding of the molecular mechanisms that lead to the development of the disease using sequential window acquisition of all theoretical mass spectra (SWATH-MS) as a protein quantification tool of the tear proteomic profile.MethodsProspective cross-sectional study that includes 25 keratoconic eyes and 25 healthy eyes. All participants underwent a clinical, tomographic, and aberrometric exam. Tear sample was collected using Schirmer strips and analyzed by liquid chromatography with tandem mass spectrometry. SWATH-MS was used as a quantification tool of the tear proteomic profile. The expression of the quantified proteins was compared between groups, and the biological and molecular functions of the dysregulated proteins as well as their functional relationships were studied by in silico analysis.ResultsA total of 203 proteins were quantified in tear samples of patients with KC and control participants, of which 18 showed differential expression between groups (P < 0.05). An increase in the expression of 7 proteins and a decrease in the expression of 11 proteins were observed. Protein-protein interactions and gene ontology analysis showed the involvement of these dysregulated proteins in structural, inflammatory-immune, iron homeostasis, oxidative stress, and extracellular matrix proteolysis processes.ConclusionsTear protein quantification has revealed the dysregulation of proteins involved in biological processes previously associated with KC. Among them, iron homeostasis should be highlighted as a relevant pathway in the KC pathophysiology, and it should be taken into account in the development of therapeutic targets to cope with tissue damage derived from iron accumulation and toxicity.

| S-EPMC8399462 | biostudies-literature

Integrative genomic analyses of neurofibromatosis tumors identify SOX9 as biomarker and survival gene

Project description:Understanding biological pathways critical for common neurofibromatosis type 1 (NF1) peripheral nerve tumors is essential, as tumor biomarkers, prognostic factors and therapeutics are all lacking. We used gene expression profiling to define transcriptional changes between primary normal Schwann cells (n = 10), NF1-derived primary benign neurofibroma Schwann cells (n = 22), malignant peripheral nerve sheath tumor (MPNST) cell lines (n = 13), benign neurofibromas (n = 26) and MPNST (n = 6). Dermal and plexiform neurofibromas were indistinguishable. A prominent theme in the analysis was aberrant differentiation. Neurofibromas repressed gene programs normally active in Schwann cell precursors and immature Schwann cells. MPNST signatures strongly differed; genes upregulated in the sarcomas were significantly enriched for genes activated in neural crest cells. We validated differential expression of 82 genes including the neural crest transcription factor SOX9 and SOX9 predicted targets. SOX9 immunoreactivity was robust in neurofibroma and MPSNT tissue sections and targeting SOX9 - strongly expressed in NF1-related tumors - caused MPNST cell death. SOX9 is a biomarker of neurofibroma and MPNST, and possibly a therapeutic target in NF1. Keywords: tumor stage 86 microarrays, consisting of 77 samples and 9 batch reference samples: NHSC (10), dNFSC (11), pNFSC (11), MPNST cell lines (13), dNF (13), pNF (13), MPNST (6)

2009-07-15 | E-GEOD-14038 | biostudies-arrayexpress

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