「リポクオリティ」領域研究の国際連携

• Project Area: Quality of lipids in biological systems
• Project/Area Number: 15K21738
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Multi-year Fund
• Review Section: Biological Sciences
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: 有田 誠 国立研究開発法人理化学研究所, 生命医科学研究センター, チームリーダー (80292952)
• Co-Investigator(Kenkyū-buntansha): 有田 正規 国立遺伝学研究所, 生命情報研究センター, 教授 (10356389)
• Project Period (FY): 2015-11-06 – 2023-03-31
• Project Status: Granted (Fiscal Year 2021)
• Budget Amount: ¥66,820,000 (Direct Cost: ¥51,400,000、Indirect Cost: ¥15,420,000); Fiscal Year 2019: ¥14,690,000 (Direct Cost: ¥11,300,000、Indirect Cost: ¥3,390,000); Fiscal Year 2018: ¥14,690,000 (Direct Cost: ¥11,300,000、Indirect Cost: ¥3,390,000); Fiscal Year 2017: ¥14,690,000 (Direct Cost: ¥11,300,000、Indirect Cost: ¥3,390,000); Fiscal Year 2016: ¥14,690,000 (Direct Cost: ¥11,300,000、Indirect Cost: ¥3,390,000); Fiscal Year 2015: ¥8,060,000 (Direct Cost: ¥6,200,000、Indirect Cost: ¥1,860,000)
• Keywords: リピドミクス / 国際連携 / 国際標準 / データベース

Outline of Annual Research Achievements

年度はじめにリポクオリティ事務局を再開し、領域に関与した計画班および公募研究者全員と連絡を取って最新の研究成果をとりまとめた。刷新した情報は領域ウェブサイトに反映させ、特に文献情報を中心に更新した。
年度初めはコロナウイルスの影響が大きく海外渡航支援業務を開始できなかったが、コロナウイルス５波後に全国で感染者数がほぼ０になった。そのタイミングで領域関係者に海外渡航支援の案内を出し、日仏間１件の短期海外研修をサポートできた。しかしコロナウイルス第６波のために事務局機能を閉鎖せざるを得ず、残予算を翌年度に繰り越す措置をとった。
研究面では海外のリピドミクス研究者と連携して、リピドミクスにおけるメタデータ記述のガイドラインを作成した。そしてリピドミクス情報を再利用するために必要なメタデータを記載するエクセルフォーマットを策定している。この形式は生データを格納するリポジトリで利用する予定である。また領域で作成したリポクオリティデータベースが格納されるサーバのOSが古くなっていたため(CentOS6)、これを新しいバージョン (CentOS7)に置き換え、それに合わせて上位のアプリケーション層も新しいものに入れ替える作業を実施した。このためMediaWikiバージョンを大幅に変更せざるを得ず、一部の機能が動かなくなった。動作不良の部分は部分ごとに現在も改修、再構築している段階である。ただし繰り越した予算は翌年度の海外渡航支援に使うこととし、事務局機能やサーバ更新には利用しない予定である。

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

コーディネータ室
領域ホームページを最新情報に更新した。国際連携オフィスの受付業務はコロナウイルス感染者が収まった期間のみ再開して１件の海外渡航を支援した。活動期間以外は人件費を０に抑え、翌年度渡航支援の準備資金とした。

データベース及び国際標準化
リピドミクスを実施する研究者の国際コンソーシアムを通じて測定情報（メタデータ）記載のガイドラインづくりに貢献した。またリピドミクス研究の生データを受付けて保存するリポジトリ受付用に利用プラットフォームやプロトコルの整理をおこなった。またリポクオリティデータベースが格納されているサーバのOSおよびアプリケーション全体を更新した。

Strategy for Future Research Activity

コーディネータ室
研究コーディネータとしての役目は終了し、海外渡航支援の事務局業務のみを実施する。

データベース及び国際標準化
領域は終了しているため、リポクオリティデータベースの情報をより利用しやすい形で公開する手法を検討する。標準プロトコールや標準データについてMetaboBank リポジトリ等と連携して再利用を促す工夫をする。

Research Products

• [Int'l Joint Research] National University of Singapore(シンガポール)
• [Int'l Joint Research] Inst of Agro-Process Sci and Technol/Sichuan Academy of Agricultural Sciences/Chinese Acad of Agricult Sci(中国)
• [Int'l Joint Research] Karolinska Institutet(スウェーデン)
• [Int'l Joint Research] Universiti Kebangsaan Malaysia(マレーシア)
• [Int'l Joint Research] University of Eastern Finland(フィンランド)
• [Int'l Joint Research] National University of Singapore(シンガポール)
• [Int'l Joint Research] Sichuan Academy of Agricultural Sciences(中国)
• [Int'l Joint Research] Karolinska Institutet(スウェーデン)
• [Int'l Joint Research] Universiti Kebangsaan Malaysia(マレーシア)
• [Int'l Joint Research] University of Eastern Finland(フィンランド)
• [Int'l Joint Research] National University of Singapore(シンガポール)
• [Int'l Joint Research] Sichuan Academy of Agricultural Sciences(中国)
• [Int'l Joint Research] University of California Davis(米国)
• [Int'l Joint Research] IMBA(オーストリア)
• [Int'l Joint Research] University of Copenhagen(デンマーク)
• [Int'l Joint Research] University of Eastern Finland(フィンランド)
• [Int'l Joint Research] University of Glasgow(英国)
• [Int'l Joint Research] University of California Davis(米国)
• [Int'l Joint Research]
• [Int'l Joint Research] University of Milan Dept. of Biosciences/National Research Council of Italy(イタリア)
• [Int'l Joint Research] Shanghai Ninth Peoples's Hospital/Shanghai Jiao Tong University(中国)
• [Int'l Joint Research] IMBA(オーストリア)
• [Journal Article] A lipidome atlas in MS-DIAL 4 (2020)
  • Author(s): Tsugawa Hiroshi、Ikeda Kazutaka、Takahashi Mikiko、Satoh Aya、Mori Yoshifumi、Uchino Haruki、Okahashi Nobuyuki、Yamada Yutaka、Tada Ipputa、Bonini Paolo、Higashi Yasuhiro、Okazaki Yozo、Zhou Zhiwei、Zhu Zheng-Jiang、Koelmel Jeremy、Cajka Tomas、Fiehn Oliver、Saito Kazuki、Arita Masanori、Arita Makoto
  • Journal Title: Nature Biotechnology Volume: 38 Issue: 10 Pages: 1159-1163
  • DOI: 10.1038/s41587-020-0531-2
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses (2020)
  • Author(s): Yasuda Shu、Okahashi Nobuyuki、Tsugawa Hiroshi、Ogata Yusuke、Ikeda Kazutaka、Suda Wataru、Arai Hiroyuki、Hattori Masahira、Arita Makoto
  • Journal Title: iScience Volume: 23 Issue: 12 Pages: 101841-101841
  • DOI: 10.1016/j.isci.2020.101841
  • Peer Reviewed / Open Access
• [Journal Article] A lipidome atlas in MS-DIAL 4 (2020)
  • Author(s): Tsugawa H, Ikeda K, Takahashi M, Satoh A, Mori Y, Uchino H, Okahashi N, Yamada Y, Tada I, Bonini P, Higashi Y, Okazaki Y, Zhou Z, Zhu Z, Koelmel J, Cajka T, Fiehn O, Saito K, Arita M, Arita M.
  • Journal Title: Nature Biotechnology Volume: in press
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms (2019)
  • Author(s): Tsugawa Hiroshi、Nakabayashi Ryo、Mori Tetsuya、Yamada Yutaka、Takahashi Mikiko、Rai Amit、Sugiyama Ryosuke、Yamamoto Hiroyuki、Nakaya Taiki、Yamazaki Mami、Kooke Rik、Bac-Molenaar Johanna A.、Oztolan-Erol Nihal、Keurentjes Joost J. B.、Arita Masanori、Saito Kazuki
  • Journal Title: Nature Methods Volume: 16 Issue: 4 Pages: 295-298
  • DOI: 10.1038/s41592-019-0358-2
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Lipidomics needs more standardization (2019)
  • Author(s): Lipidomics Standards Initiative Consortium
  • Journal Title: Nature Metabolism Volume: 1 Issue: 8 Pages: 745-747
  • DOI: 10.1038/s42255-019-0094-z
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Creating a Reliable Mass Spectral-Retention Time Library for All Ion Fragmentation-Based Metabolomics (2019)
  • Author(s): Tada Ipputa、Tsugawa Hiroshi、Meister Isabel、Zhang Pei、Shu Rie、Katsumi Riho、Wheelock Craig E.、Arita Masanori、Chaleckis Romanas
  • Journal Title: Metabolites Volume: 9 Issue: 11 Pages: 251-251
  • DOI: 10.3390/metabo9110251
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics (2019)
  • Author(s): Tsugawa Hiroshi、Satoh Aya、Uchino Haruki、Cajka Tomas、Arita Makoto、Arita Masanori
  • Journal Title: Metabolites Volume: 9 Issue: 6 Pages: 119-119
  • DOI: 10.3390/metabo9060119
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines (2018)
  • Author(s): Burla Bo、Arita Makoto、Arita Masanori et al.
  • Journal Title: Journal of Lipid Research Volume: 59 Issue: 10 Pages: 2001-2017
  • DOI: 10.1194/jlr.s087163
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics (2017)
  • Author(s): Lai Z, Tsugawa H, Wohlgemuth G, Mehta S, Mueller M, Zheng Y, Ogiwara A, Meissen J, Showalter M, Takeuchi K, Kind T, Beal P, Arita M, Fiehn O
  • Journal Title: Nature Methods Volume: 15 Issue: 1 Pages: 53-56
  • DOI: 10.1038/nmeth.4512
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Identification of small molecules using accurate mass MS/MS search (2017)
  • Author(s): Kind T, Tsugawa H, Cajka T, Ma Y, Lai Z, Mehta SS, Wohlgemuth G, Barupal DK, Showalter MR, Arita M, Fiehn O
  • Journal Title: Mass Spectrometry Reviews Volume: - Issue: 4 Pages: 513-532
  • DOI: 10.1002/mas.21535
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] SPLASH, a hashed identifier for mass spectra (2016)
  • Author(s): Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O
  • Journal Title: Nat Biotechnol Volume: 34 Issue: 11 Pages: 1099-1101
  • DOI: 10.1038/nbt.3689
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Editorial: Metabolome Informatics and Statistics: Current State and Emerging Trends (2016)
  • Author(s): Carroll AJ, Salek RM, Arita M, Kopka J, Walther D
  • Journal Title: Front Bioeng Biotechnol Volume: 4 Pages: 63-63
  • DOI: 10.3389/fbioe.2016.00063
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Data standards can boost metabolomics research, and if there is a will, there is a way (2016)
  • Author(s): Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A, Ebbels T, Goodacre R, Hastings J, Haug K, Koulman A, Nikolski M, Oresic M, Sansone SA, Schober D, Smith J, Steinbeck C, Viant MR, Neumann S
  • Journal Title: Metabolomics Volume: 12 Issue: 1 Pages: 14-14
  • DOI: 10.1007/s11306-015-0879-3
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] Advanced non-targeted lipidomics and its application to vascular biology (2022)
  • Author(s): Makoto Arita
  • Organizer: 10th International Singapore Lipid Symposium (iSLS10)
  • Int'l Joint Research / Invited
• [Presentation] Biology of LipoQuality: Advanced lipidomics technology and its application in biology (2020)
  • Author(s): Makoto Arita
  • Organizer: 9th International Singapore Lipid Symposium (iSLS9)
  • Int'l Joint Research / Invited
• [Presentation] Cheminformatics for Predicting Structures from Mass Spectra (2019)
  • Author(s): Masanori Arita
  • Organizer: 1st Annual Conference of Chinese Society of Metabolomics
  • Int'l Joint Research / Invited
• [Presentation] Data sharing and the power of omics integration (2019)
  • Author(s): Masanori Arita
  • Organizer: 6th Global Forum of Leaders for Agricultural Science and Technology
  • Int'l Joint Research / Invited
• [Presentation] Biology of LipoQuality: omega-3 fatty acid cascade that controls inflammation and tissue homeostasis (2019)
  • Author(s): Makoto Arita
  • Organizer: 2nd International Conference on LipoQuality
  • Int'l Joint Research / Invited
• [Presentation] Database for understanding the quality of lipids (2019)
  • Author(s): Masanori Arita
  • Organizer: 2nd International Conference on LipoQuality
  • Int'l Joint Research / Invited
• [Presentation] The importance of LipoQuality in biological systems (2019)
  • Author(s): Makoto Arita
  • Organizer: William Harvey Research Institute Seminar
  • Int'l Joint Research / Invited
• [Presentation] Open genome analysis in the post-genomic era (2018)
  • Author(s): Masanori Arita
  • Organizer: International Workshop on Data Science
  • Int'l Joint Research / Invited
• [Presentation] Computational Metabolomics (2018)
  • Author(s): Masanori Arita
  • Organizer: 6th Annual Korea Metabolomics Society (plenary)
  • Int'l Joint Research / Invited
• [Presentation] Distribution of Glycosphingolipids Revealed by LipidBank (2018)
  • Author(s): Masanori Arita
  • Organizer: International Life Science Integration Workshop
  • Int'l Joint Research / Invited
• [Presentation] The importance of LipoQuality in biological system (2018)
  • Author(s): Makoto Arita
  • Organizer: 7th International Singapore Lipid Symposium 2018 (iSLS7)
  • Int'l Joint Research / Invited
• [Presentation] Identifying Metabolites with Theoretical References (2017)
  • Author(s): Masanori Arita
  • Organizer: The 26th International KOGO Annual Conference
  • Int'l Joint Research / Invited
• [Presentation] Prediction of Molecular Structures from their Spectra (2017)
  • Author(s): Masanori Arita
  • Organizer: The 4th International Conference on Plant Metabolism (ICPM 2017)
  • Int'l Joint Research / Invited
• [Presentation] MS2スペクトルのフラグメンテーション解析と前駆体構造予測 (2016)
  • Author(s): 有田 正規, 津川裕司
  • Organizer: 日本分子生物学会年会 シンポジウム「生命システムを俯瞰するための質量分析情報解析技術とデータベースの活用」
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2016-11-30
• [Presentation] Comprehensive lipidomics and Mass/LipidBank databases (2015)
  • Author(s): 有田正規
  • Organizer: BMB2015
  • Place of Presentation: ポートピアホテル（兵庫・神戸）
  • Year and Date: 2015-12-04
  • Invited
• [Presentation] Comprehensive Acquisition of MS/MS Spectra Benefits Database Research (2015)
  • Author(s): 有田正規
  • Organizer: 6th International Singapore Lipid Symposium
  • Place of Presentation: Singapore (Singapore)
  • Year and Date: 2015-12-01
  • Int'l Joint Research / Invited
• [Remarks] リポクオリティ領域HP
  • URL: https://sites.google.com/site/lipoqualityjpn/
• [Remarks] リエゾンオフィス・ホームページ
  • URL: https://sites.google.com/site/lipoqualityjpn/home/liaison-office
• [Remarks] 国際連携支援・申請ページ
  • URL: https://docs.google.com/a/nig.ac.jp/forms/d/1n3f_ozI5ICUJmFJZrGb9Ln1GsoHGZwSV1xly2M1tewA
• [Remarks] 国際連携支援・報告書ページ
  • URL: https://docs.google.com/forms/u/0/d/1juKXiLVPAuCmTwGt8LWOp1paaFarqS-71d7NR5G2BM0/viewform
• [Remarks] リポクオリティ・データベース
  • URL: http://jcbl.jp/wiki/Lipoquality:Search
• [Funded Workshop] LipoQuality International Workshop on Lipidomics (2019)