Target identification with systematic CRISPR-based chemical-genetic profiling in human HAP1 cells

2023 年度 実績報告書

• 研究課題/領域番号: 22H02224
• 配分区分: 補助金
• 研究機関: 国立研究開発法人理化学研究所
• 研究代表者: BOONE CHARLES 国立研究開発法人理化学研究所, 環境資源科学研究センター, チームリーダー (70601342)
• 研究分担者: Pham LienThiKim 国立研究開発法人理化学研究所, 環境資源科学研究センター, 特別研究員 (50865300) ; 八代田 陽子 国立研究開発法人理化学研究所, 環境資源科学研究センター, 副チームリーダー (60360658)
• 研究期間 (年度): 2022-04-01 – 2025-03-31
• キーワード: Target identification / Chemical genomics / CRISPR-Cas9

研究実績の概要

Natural products have long served as a valuable reservoir of compounds for drug discovery. A critical phase in drug development involves identifying the cellular targets and off-target interactions of compounds with promising bioactivities. However, our capacity to engineer or extract purified compounds from natural sources has surpassed our ability to functionally annotate them. To tackle this challenge, we are constructing a large-scale chemical-genetic network in human cells to comprehensively annotate chemical libraries. In FY2022, we established a CRISPR-Cas9-based, high-throughput chemical-genetic screening platform in human HAP1 cells. In this FY2023, this platform has been employed to assess many selected natural compounds derived the RIKEN NPDepo and the University of Tokyo DDI Core Libraries, resulting in a comprehensive compendium of chemical-genetic interaction profiles that offer valuable functional insights. This dataset represents a potent resource poised to enhance our comprehension of the druggable target space, to elucidate drug modes of action, and to identify novel drug candidates, or chemical probes to uncover novel gene functions.

現在までの達成度 (区分)

2: おおむね順調に進展している

理由

In FY2023, we screened 35 natural compounds, including:
- Compounds selected through target predictions in our yeast Chemical-genomics profiling: Upon comparing the resulting chemical-genetic interactions in HAP1 cells with those in yeast cells, we observed that many compounds predicted the same target pathway as indicated by our yeast CG data.
- Reference compounds: their chemical-genetic profiles clearly indicated the expected target pathway.
- Compounds provided by our collaborators.
Also, we established a CRISPR database to make all chemical genomics profiles accessible online (currently restricted to internal access only).
Based on these findings, we have determined and implemented the approaches for target validation for potent compounds.

今後の研究の推進方策

In FY2023, we screened ~35 selected compounds including some reference and our collaborators’ compounds for chemical-genetic interactions using the genome-wide CRISPR-Cas9 screening platform in HAP1 cells. We have compared the resultant chemical-genetic interactions in HAP1 cells with the ones in yeast cells and the reference database of human chemical-genetic interactions. Based on that, optimal methods for target validation have been considered and carried out. In FY2024, we will continue the target validation for the compounds whose targets are previously uncharacterized, such as inhibitors for sphingolipid biosynthesis, glycosylation, etc. We will collaborate with some experts for metabolome analysis and elucidate modes-of-action of new classes of inhibitors.

備考

“Deadly fungi beaten with fatty acid synthase inhibitor”
https://itaintmagic.riken.jp/hot-off-the-press/deadly-fungi-beaten-with-fatty-acid-synthase-inhibitor/

研究成果

• [国際共同研究] University of Toronto/University of British Columbia(カナダ)
  • 国名: カナダ
  • 外国機関名: University of Toronto/University of British Columbia
• [国際共同研究] University of Minnesota(米国)
  • 国名: 米国
  • 外国機関名: University of Minnesota
• [雑誌論文] N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity. (2023)
  • 著者名/発表者名: Varland S, Silva RD, Kjosas I, Faustino A, Bogaert A, Billmann M, Boukhatmi H, Kellen B, Costanzo M, Drazic A, Osberg C, Chan K, Zhang X, Tong AHY, Andreazza S, Lee JJ, Nedyalkova L, Usaj M, Whitworth AJ, Andrews BJ, Moffat J, Myers CL, Gevaert K, Boone C, Martinho RG, Arnesen T.
  • 雑誌名: Nat. Commun. 巻: 14 ページ: 6774
  • DOI: 10.1038/s41467-023-42342-y
  • 査読あり / 国際共著
• [雑誌論文] Identification of triazenyl indoles as inhibitors of fungal fatty acid biosynthesis with broad-spectrum activity (2023)
  • 著者名/発表者名: Iyer KR, Li SC, Revie NM, Lou JW, Duncan D, Fallah S, Sanchez H, Skulska I, Usaj MM, Safizadeh H, Larsen B, Wong C, Aman A, Kiyota T, Yoshimura M, Kimura H, Hirano H, Yoshida M, Osada H, Gingras AC, Andes DR, Shapiro RS, Robbins N, Mazhab-Jafari MT, Whitesell L, Yashiroda Y, Boone C, Cowen LE.
  • 雑誌名: Cell Chem. Biol. 巻: 30 ページ: 795-810
  • DOI: 10.1016/j.chembiol.2023.06.005
  • 査読あり / 国際共著
• [雑誌論文] Overexpression profiling reveals cellular requirements in the context of genetic backgrounds and environments. (2023)
  • 著者名/発表者名: Saeki N, Yamamoto C, Eguchi Y, Sekito T, Shigenobu S, Yoshimura M, Yashiroda Y, Boone C, Moriya H.
  • 雑誌名: PLoS Genetics 巻: 19 ページ: e1010732
  • DOI: 10.1371/journal.pgen.1010732
  • 査読あり / オープンアクセス / 国際共著
• [雑誌論文] The proteomic landscape of genome-wide genetic perturbations. (2023)
  • 著者名/発表者名: Messner CB, Demichev V, Muenzner J, Aulakh SK, Barthel N, Rohl A, Herrera-Dominguez L, Egger AS, Kamrad S, Hou J, Tan G, Lemke O, Calvani E, Szyrwiel L, Mulleder M, Lilley KS, Boone C, Kustatscher G, Ralser M.
  • 雑誌名: Cell Chem. Biol. 巻: 186 ページ: 2018-2034.e21
  • DOI: 10.1016/j.cell.2023.03.026
  • 査読あり / オープンアクセス / 国際共著
• [学会発表] 分裂酵母Schizosaccharomyces pombeにおいてペンタデカン酸が誘導する脂肪毒性 (2024)
  • 著者名/発表者名: 星川陽次郎、代田夏帆、松山晃久、木村聡、Sheena LI 、八代田陽子、Charles BOONE、津川裕司、有田誠、吉田稔、西村慎一
  • 学会等名: 日本農芸化学会2024年度大会
• [学会発表] エルゴステロール合成経路を標的とする抗真菌薬の開発 (2024)
  • 著者名/発表者名: 八代田陽子
  • 学会等名: 東京大学医科学研究所－千葉大学真菌医学研究センター 国際共同研究・共同研究拠点事業 2023年度 成果報告会
  • 招待講演
• [学会発表] Exogenous pentadecanoic acid perturbs the membrane lipid profile to generate the giant endoplasmic reticulum sheet (2023)
  • 著者名/発表者名: Hoshikawa Y, Matsuyama A, Li S, Yashiroda Y, Boone C, Tsugawa H, Arita M, Yoshida M, Nishimura S.
  • 学会等名: The 11th International Fission Yeast Meeting (Pombe 2023)
  • 国際学会
• [学会発表] Mapping genetic and chemical-genetic networks in yeast (2023)
  • 著者名/発表者名: Boone CM.
  • 学会等名: 31st International Conference on Yeast Genetics and Molecular Biology (ICYGMB31)
  • 国際学会 / 招待講演
• [学会発表] 抗真菌剤ポアシジエンは細胞質鉄イオンの蓄積を引き起こす (2023)
  • 著者名/発表者名: 趙天宇、小川樹、吉村麻美、八代田陽子、Charles Boone
  • 学会等名: 酵母遺伝学フォーラム第56回研究報告会
• [学会発表] 抗真菌剤NPD2560の細胞内作用機序に関する研究 (2023)
  • 著者名/発表者名: 劉薇、関口宙暉、山中大輔、八代田陽子、Sheena Li 、Charles Boone 、一刀かおり、大矢禎一
  • 学会等名: 酵母遺伝学フォーラム第56回研究報告会
• [学会発表] Mapping genetic interaction networks in yeast and human cells (2023)
  • 著者名/発表者名: Boone CM.
  • 学会等名: The 2023 Cold Spring Harbor Asia Conference, Yeast and Life Sciences
  • 国際学会 / 招待講演
• [学会発表] Identification of potential therapeutic lead compounds targeting serine-palmitoyltransferase (2023)
  • 著者名/発表者名: Pham L, Yoshimura M, Yashiroda Y, Li S, Usaj M, Burke RM, oshida M, Boone C.
  • 学会等名: The 2023 Cold Spring Harbor Asia Conference, Yeast and Life Sciences
  • 国際学会
• [学会発表] Mode-of-action analysis of inhibitors targeting ergosterol (2023)
  • 著者名/発表者名: Yashiroda Y, Yoshimura M, Usui M, Kimura H, Isuhuaylas LAV, Pham LTK, Niwa T, Takahashi I, Hosoya T, Ilies L, Yoshida M, Boone C.
  • 学会等名: The 2023 Cold Spring Harbor Asia Conference, Yeast and Life Sciences
  • 国際学会
• [備考] 脂肪酸合成を阻害する新たな抗真菌化合物の発見－世界的脅威である真菌感染症の新しい治療薬として期待－
  • URL: https://www.riken.jp/press/2023/20230711_1/index.html
• [産業財産権] Compounds as antifungal agents, derivatives thereof and novel compounds (2023)
  • 発明者名: Oya, Yashiroda, Boone, et al.
  • 権利者名: Oya, Yashiroda, Boone, et al.
  • 産業財産権種類: 特許
  • 産業財産権番号: 63/578668
  • 外国