2023 Fiscal Year Annual Research Report
Target identification with systematic CRISPR-based chemical-genetic profiling in human HAP1 cells
| Project/Area Number |
22H02224
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| Allocation Type | Single-year Grants |
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| Research Institution | Institute of Physical and Chemical Research |
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Principal Investigator |
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)
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| Co-Investigator(Kenkyū-buntansha) |
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)
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| Project Period (FY) |
2022-04-01 – 2025-03-31
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| Keywords | Target identification / Chemical genomics / CRISPR-Cas9 |
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| Outline of Annual Research Achievements |
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.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
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.
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| Strategy for Future Research Activity |
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.
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| Remarks |
“Deadly fungi beaten with fatty acid synthase inhibitor”
https://itaintmagic.riken.jp/hot-off-the-press/deadly-fungi-beaten-with-fatty-acid-synthase-inhibitor/
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[Journal Article] N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity.2023
Author(s)
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.
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Journal Title
Nat. Commun.
Volume: 14
Pages: 6774
DOI
Peer Reviewed / Int'l Joint Research
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[Journal Article] Identification of triazenyl indoles as inhibitors of fungal fatty acid biosynthesis with broad-spectrum activity2023
Author(s)
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.
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Journal Title
Cell Chem. Biol.
Volume: 30
Pages: 795-810
DOI
Peer Reviewed / Int'l Joint Research
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[Journal Article] The proteomic landscape of genome-wide genetic perturbations.2023
Author(s)
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.
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Journal Title
Cell Chem. Biol.
Volume: 186
Pages: 2018-2034.e21
DOI
Peer Reviewed / Open Access / Int'l Joint Research
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[Presentation] Mode-of-action analysis of inhibitors targeting ergosterol2023
Author(s)
Yashiroda Y, Yoshimura M, Usui M, Kimura H, Isuhuaylas LAV, Pham LTK, Niwa T, Takahashi I, Hosoya T, Ilies L, Yoshida M, Boone C.
Organizer
The 2023 Cold Spring Harbor Asia Conference, Yeast and Life Sciences
Int'l Joint Research
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