2025/01/05 更新

写真a

タカミ トモヨ
高見 知代
TAKAMI Tomoyo
所属
教育研究院 医歯学系 特任助教
医歯学総合研究科 特任助教
職名
特任助教
外部リンク

学位

  • 学士(工学部) ( 1992年3月   上智大学 )

研究キーワード

  • プロテオミクス

  • バイオインフォマティクス

経歴

  • 新潟大学   医歯学総合研究科   特任助教

    2022年4月 - 現在

  • 新潟大学   教育研究院 医歯学系   特任助教

    2022年4月 - 現在

  • 新潟大学   医歯学総合研究科   特任助手

    2019年11月 - 2022年3月

  • 新潟大学   教育研究院 医歯学系   特任助手

    2019年11月 - 2022年3月

 

論文

  • jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data

    Shujiro Okuda, Akiyasu C Yoshizawa, Daiki Kobayashi, Yushi Takahashi, Yu Watanabe, Yuki Moriya, Atsushi Hatano, Tomoyo Takami, Masaki Matsumoto, Norie Araki, Tsuyoshi Tabata, Mio Iwasaki, Naoyuki Sugiyama, Yoshio Kodera, Satoshi Tanaka, Susumu Goto, Shin Kawano, Yasushi Ishihama

    Nucleic Acids Research   2024年11月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Oxford University Press (OUP)  

    Abstract

    jPOST (https://jpostdb.org/) comprises jPOSTrepo (https://repository.jpostdb.org/) (over 2000 projects), a repository for proteome mass spectrometry data, the reanalysis of raw proteome data based on a standardised protocol using UniScore, and jPOSTdb (https://globe.jpostdb.org/) (over 600 datasets), a database that integrates the reanalysed data. The jPOST reanalysis protocol rescores MS/MS spectra using a new scale, UniScore, to evaluate the extent to which the spectral peaks correspond to the amino acid sequences identified by search engines. However, the metadata registered in the repository database is insufficient for conducting the reanalysis. To address this issue, the Japanese Proteomics Society launched a data journal, the Journal of Proteome Data and Methods (JPDM), which accepts data descriptor articles detailing metadata that can be reanalysed. Within jPOST, raw proteome data is reanalysed based on the metadata described in the JPDM data descriptor articles, utilising UniScore. The reanalysed data is deposited in jPOSTdb, and a link to the JPDM articles is added to jPOSTrepo. These reanalysis accelerations within the jPOST environment will promote FAIR data principles and open science.

    DOI: 10.1093/nar/gkae1032

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  • In situ digestion of alcohol-fixed cells for quantitative proteomics. 国際誌

    Atsushi Hatano, Tomoyo Takami, Masaki Matsumoto

    Journal of biochemistry   173 ( 4 )   243 - 254   2023年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Currently, the bottom-up approach, in which proteins are digested by enzymes such as trypsin prior to mass spectrometry, is the mainstream approach in mass spectrometer-based proteomics. In this approach, the enzymatic digestion process strongly affects the reproducibility of protein identification and quantification. Here, we quantitatively evaluated the enzymatic digestion of proteins under various conditions by quantitative proteomics using data-independent acquisition and found that proteins precipitated with acetone after solubilization with SDS were fully digestible without re-solubilization. This result implies that organic solvent treatment makes cells amenable to trypsin digestion. Direct trypsin digestion of methanol-fixed cells achieved the same digestion efficiency and quantitative reproducibility as the conventional method. Furthermore, this method was found to be equally applicable to mouse liver samples. The establishment of this method indicates that the sample preparation process in bottom-up proteomics can be simplified while maintaining high digestion efficiency and is expected to become a general method for sample preparation in bottom-up proteomics in the future.

    DOI: 10.1093/jb/mvac101

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  • Senolysis by glutaminolysis inhibition ameliorates various age-associated disorders 国際誌

    Yoshikazu Johmura, Takehiro Yamanaka, Satotaka Omori, Teh-Wei Wang, Yuki Sugiura, Masaki Matsumoto, Narumi Suzuki, Soichiro Kumamoto, Kiyoshi Yamaguchi, Seira Hatakeyama, Tomoyo Takami, Rui Yamaguchi, Eigo Shimizu, Kazutaka Ikeda, Nobuyuki Okahashi, Ryuta Mikawa, Makoto Suematsu, Makoto Arita, Masataka Sugimoto, Keiichi I. Nakayama, Yoichi Furukawa, Seiya Imoto, Makoto Nakanishi

    Science   371 ( 6526 )   265 - 270   2021年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Association for the Advancement of Science (AAAS)  

    Removal of senescent cells (senolysis) has been proposed to be beneficial for improving age-associated pathologies, but the molecular pathways for such senolytic activity have not yet emerged. Here, we identified glutaminase 1 (<italic>GLS1</italic>) as an essential gene for the survival of human senescent cells. The intracellular pH in senescent cells was lowered by lysosomal membrane damage, and this lowered pH induced kidney-type glutaminase (KGA) expression. The resulting enhanced glutaminolysis induced ammonia production, which neutralized the lower pH and improved survival of the senescent cells. Inhibition of KGA-dependent glutaminolysis in aged mice eliminated senescent cells specifically and ameliorated age-associated organ dysfunction. Our results suggest that senescent cells rely on glutaminolysis, and its inhibition offers a promising strategy for inducing senolysis in vivo.

    DOI: 10.1126/science.abb5916

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  • Cell cycle–dependent localization of the proteasome to chromatin 国際誌

    Yuki Kito, Masaki Matsumoto, Atsushi Hatano, Tomoyo Takami, Kiyotaka Oshikawa, Akinobu Matsumoto, Keiichi I. Nakayama

    Scientific Reports   10 ( 1 )   5801 - 5801   2020年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    <title>Abstract</title>An integrative understanding of nuclear events including transcription in normal and cancer cells requires comprehensive and quantitative measurement of protein dynamics that underlie such events. However, the low abundance of most nuclear proteins hampers their detailed functional characterization. We have now comprehensively quantified the abundance of nuclear proteins with the use of proteomics approaches in both normal and transformed human diploid fibroblasts. We found that subunits of the 26S proteasome complex were markedly down-regulated in the nuclear fraction of the transformed cells compared with that of the wild-type cells. The intranuclear proteasome abundance appeared to be inversely related to the rate of cell cycle progression, with restraint of the cell cycle being associated with an increase in the amount of proteasome subunits in the nucleus, suggesting that the nuclear proteasome content is dependent on the cell cycle. Furthermore, chromatin enrichment for proteomics (ChEP) analysis revealed enrichment of the proteasome in the chromatin fraction of quiescent cells and its apparent dissociation from chromatin in transformed cells. Our results thus suggest that translocation of the nuclear proteasome to chromatin may play an important role in control of the cell cycle and oncogenesis through regulation of chromatin-associated transcription factors.

    DOI: 10.1038/s41598-020-62697-2

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    その他リンク: http://www.nature.com/articles/s41598-020-62697-2

  • The jPOST environment: an integrated proteomics data repository and database 国際誌

    Yuki Moriya, Shin Kawano, Shujiro Okuda, Yu Watanabe, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Yoshinori Yamanouchi, Norie Araki, Akiyasu C Yoshizawa, Tsuyoshi Tabata, Mio Iwasaki, Naoyuki Sugiyama, Satoshi Tanaka, Susumu Goto, Yasushi Ishihama

    Nucleic Acids Research   47 ( D1 )   D1218 - D1224   2019年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Oxford University Press (OUP)  

    Rapid progress is being made in mass spectrometry (MS)-based proteomics, yielding an increasing number of larger datasets with higher quality and higher throughput. To integrate proteomics datasets generated from various projects and institutions, we launched a project named jPOST (Japan ProteOme STandard Repository/Database, https://jpostdb.org/) in 2015. Its proteomics data repository, jPOSTrepo, began operations in 2016 and has accepted more than 10 TB of MS-based proteomics datasets in the past two years. In addition, we have developed a new proteomics database named jPOSTdb in which the published raw datasets in jPOSTrepo are reanalyzed using standardized protocol. jPOSTdb provides viewers showing the frequency of detected post-translational modifications, the co-occurrence of phosphorylation sites on a peptide and peptide sharing among proteoforms. jPOSTdb also provides basic statistical analysis tools to compare proteomics datasets.

    DOI: 10.1093/nar/gky899

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MISC

  • JPDMデータ論文のメタデータを用いたjPOSTデータ再解析の加速

    高橋悠志, 吉沢明康, 小林大樹, 守屋勇樹, 幡野敦, 高見知代, 松本雅記, 荒木令江, 田畑剛, 田畑剛, 岩崎未央, 杉山直幸, 小寺義男, 福島敦史, 田中聡, 五斗進, 河野信, 奥田修二郎, 石濱泰

    日本プロテオーム学会大会プログラム・抄録集   2024 (Web)   2024年

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  • プロテオーム統合データベースの機能深化

    守屋勇樹, 河野信, 奥田修二郎, 渡邉由, 松本雅記, 高見知代, 小林大樹, 山ノ内祥訓, 荒木令江, 吉沢明康, 田畑剛, 田畑剛, 岩崎未央, 杉山直幸, 田中聡, 五斗進, 石濱泰

    日本分子生物学会年会プログラム・要旨集(Web)   41st   2018年

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  • jPOSTプロジェクトが提供するプロテオミクスデータとその解析ツール

    五斗進, 守屋勇樹, 河野信, 奥田修二郎, 渡邉由, 松本雅記, 高見知代, 小林大樹, 山ノ内祥訓, 荒木令江, 吉沢明康, 田畑剛, 岩崎未央, 杉山直幸, 田中聡, 石濱泰

    日本分子生物学会年会プログラム・要旨集(Web)   41st   2018年

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  • データベース検索エンジンを用いたタンパク質同定における特異性向上

    吉沢明康, 田畑剛, 守屋勇樹, 河野信, 奥田修二郎, 渡辺由, 山本格, 松本雅記, 高見知代, 小林大樹, 荒木令江, 杉山直幸, 田中聡, 五斗進, 石濱泰

    質量分析総合討論会講演要旨集   65th   2017年

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  • jPOST:同定結果のFDR改善を目指す再解析プロトコルの開発

    吉沢明康, 田畑剛, 守屋勇樹, 河野信, 奥田修二郎, 渡辺由, 山本格, 松本雅記, 高見知代, 小林大樹, 荒木令江, 杉山直幸, 田中聡, 五斗進, 石濱泰

    日本生化学会大会(Web)   90th   2017年

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