Methods for comprehensive identification of membrane proteins recognized by a large number of monoclonal antibodies

Kurosawa, Gene; Sumitomo, Mariko; Akahori, Yasushi; Matsuda, Kazuki; Muramatsu, Chiho; Takasaki, Akihiko; Iba, Yoshitaka; Eguchi, Kaoru; Tanaka, Miho; Suzuki, Kazuhiro; Sato, Noriko; Sugiura, M.; Sugioka, Atsushi; Hayashi, Nobuhiro; Kurosawa, Yoshikazu

doi:10.1016/j.jim.2009.09.003

Cited by 16 publications

(17 citation statements)

References 11 publications

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“…In-gel trypsin digestion and mass spectrometry (MS) analysis were carried out essentially according to the method described previously (Kurosawa et al , 2009). SyproRuby (Invitrogen)-stained 2D gels were used.…”

Section: Methodsmentioning

confidence: 99%

Deficiency of Schnurri-2, an MHC Enhancer Binding Protein, Induces Mild Chronic Inflammation in the Brain and Confers Molecular, Neuronal, and Behavioral Phenotypes Related to Schizophrenia

Takao

Kobayashi

Hagihara

et al. 2013

Neuropsychopharmacol

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151

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Schnurri-2 (Shn-2), an nuclear factor-κB site-binding protein, tightly binds to the enhancers of major histocompatibility complex class I genes and inflammatory cytokines, which have been shown to harbor common variant single-nucleotide polymorphisms associated with schizophrenia. Although genes related to immunity are implicated in schizophrenia, there has been no study showing that their mutation or knockout (KO) results in schizophrenia. Here, we show that Shn-2 KO mice have behavioral abnormalities that resemble those of schizophrenics. The mutant brain demonstrated multiple schizophrenia-related phenotypes, including transcriptome/proteome changes similar to those of postmortem schizophrenia patients, decreased parvalbumin and GAD67 levels, increased theta power on electroencephalograms, and a thinner cortex. Dentate gyrus granule cells failed to mature in mutants, a previously proposed endophenotype of schizophrenia. Shn-2 KO mice also exhibited mild chronic inflammation of the brain, as evidenced by increased inflammation markers (including GFAP and NADH/NADPH oxidase p22 phox), and genome-wide gene expression patterns similar to various inflammatory conditions. Chronic administration of anti-inflammatory drugs reduced hippocampal GFAP expression, and reversed deficits in working memory and nest-building behaviors in Shn-2 KO mice. These results suggest that genetically induced changes in immune system can be a predisposing factor in schizophrenia.

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Section: Methodsmentioning

confidence: 99%

Deficiency of Schnurri-2, an MHC Enhancer Binding Protein, Induces Mild Chronic Inflammation in the Brain and Confers Molecular, Neuronal, and Behavioral Phenotypes Related to Schizophrenia

Takao

Kobayashi

Hagihara

et al. 2013

Neuropsychopharmacol

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151

229

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“…The excised protein bands were ingel digested with trypsin according to a modified procedure of Ref. 20, and the proteins were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) or liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). In MALDI-TOF-MS analysis, masses of the peptides were determined by Ultraflex TOF/TOF (Bruker Daltonics), and the MS data obtained were searched against a protein sequence database (Swiss-Prot) using the Mascot search program (Matrix Science).…”

Section: Methodsmentioning

confidence: 99%

“…LC-MS/MS analyses were performed using a nanoflow multidimensional HPLC system (Paradigm MS4, Michrom Bioresources) coupled to an electrospray ionization ion trap mass spectrometer (LCQ Deca XP, Thermo Fisher Scientific) according to a procedure of Ref. 20 or using a system that consisted of an inlet system (Acquity UPLC, Waters) and a Q-TOF mass spectrometer (SYNAPT G2 HDMS, Waters) by a newly constructed procedure as described below. The in-gel digested samples were injected to an inlet system with C 18 column (75-m diameter; 150-mm length; particle size, 1.7 m) at a flow rate of 0.5 l/min.…”

Section: Methodsmentioning

confidence: 99%

Atg9 Vesicles Recruit Vesicle-tethering Proteins Trs85 and Ypt1 to the Autophagosome Formation Site

Kakuta

Yamamoto

Negishi

et al. 2012

Journal of Biological Chemistry

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107

110

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Background: Atg9 vesicles are directly involved in autophagosome formation. Results: Mass spectrometric analysis revealed that Atg9 vesicles contain vesicle-tethering proteins Trs85 and Ypt1. These proteins localize to the autophagosome formation site in an Atg9-dependent manner. Conclusion: Atg9 vesicles play a role in the recruitment of the vesicle-tethering machinery. Significance: This study is the first proteomics study of Atg9 vesicles.

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“…Flow cytometric analysis demonstrated that TfR was highly expressed in both HFL-1 and HT1080 cells (Figure 1A), whereas CD46 was expressed only in HT1080 cells, and very rarely in HFL-1 cells [19]. Subsequently, recombinant retargeted H proteins were constructed by using 8 clones of anti-TfR scFvs (Additional file 1 Table S1), which recognized different epitopes of TfR, from the phage-display antibody library [32]. Anti-TfR scFvs were fused to the C terminus of a quadruple mutated H protein (Haals: Y481A, R533A, S548L and F549S), which lacked the ability to bind both CD46 and SLAM [27,33], to validate the effect of anti-TfR scFvs on cell fusion more precisely (Figure 1B).…”

Section: Resultsmentioning

confidence: 99%

Retargeting of microcell fusion towards recipient cell-oriented transfer of human artificial chromosome

et al. 2015

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BackgroundHuman artificial chromosome (HAC) vectors have some unique characteristics as compared with conventional vectors, carrying large transgenes without size limitation, showing persistent expression of transgenes, and existing independently from host genome in cells. With these features, HACs are expected to be promising vectors for modifications of a variety of cell types. However, the method of introduction of HACs into target cells is confined to microcell-mediated chromosome transfer (MMCT), which is less efficient than other methods of vector introduction. Application of Measles Virus (MV) fusogenic proteins to MMCT instead of polyethylene glycol (PEG) has partly solved this drawback, whereas the tropism of MV fusogenic proteins is restricted to human CD46- or SLAM-positive cells.ResultsHere, we show that retargeting of microcell fusion by adding anti-Transferrin receptor (TfR) single chain antibodies (scFvs) to the extracellular C-terminus of the MV-H protein improves the efficiency of MV-MMCT to human fibroblasts which originally barely express both native MV receptors, and are therefore resistant to MV-MMCT. Efficacy of chimeric fusogenic proteins was evaluated by the evidence that the HAC, tagged with a drug-resistant gene and an EGFP gene, was transferred from CHO donor cells into human fibroblasts. Furthermore, it was demonstrated that no perturbation of either the HAC status or the functions of transgenes was observed on account of retargeted MV-MMCT when another HAC carrying four reprogramming factors (iHAC) was transferred into human fibroblasts.ConclusionsRetargeted MV-MMCT using chimeric H protein with scFvs succeeded in extending the cell spectrum for gene transfer via HAC vectors. Therefore, this technology could facilitate the systematic cell engineering by HACs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12896-015-0142-z) contains supplementary material, which is available to authorized users.

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Methods for comprehensive identification of membrane proteins recognized by a large number of monoclonal antibodies

Cited by 16 publications

References 11 publications

Deficiency of Schnurri-2, an MHC Enhancer Binding Protein, Induces Mild Chronic Inflammation in the Brain and Confers Molecular, Neuronal, and Behavioral Phenotypes Related to Schizophrenia

Deficiency of Schnurri-2, an MHC Enhancer Binding Protein, Induces Mild Chronic Inflammation in the Brain and Confers Molecular, Neuronal, and Behavioral Phenotypes Related to Schizophrenia

Atg9 Vesicles Recruit Vesicle-tethering Proteins Trs85 and Ypt1 to the Autophagosome Formation Site

Retargeting of microcell fusion towards recipient cell-oriented transfer of human artificial chromosome

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