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McMillan EA, Kwon G, Clemenceau JR, Fisher KW, Vaden RM, Shaikh AF, Neilsen BK, Kelly D, Potts MB, Sung YJ, Mendiratta S, Hight SK, Lee Y, MacMillan JB, Lewis RE, Kim HS, White MA. A Genome-wide Functional Signature Ontology Map and Applications to Natural Product Mechanism of Action Discovery. Cell Chem Biol 2019; 26:1380-1392.e6. [PMID: 31378711 PMCID: PMC9161285 DOI: 10.1016/j.chembiol.2019.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 05/30/2019] [Accepted: 07/17/2019] [Indexed: 12/29/2022]
Abstract
Gene expression signature-based inference of functional connectivity within and between genetic perturbations, chemical perturbations, and disease status can lead to the development of actionable hypotheses for gene function, chemical modes of action, and disease treatment strategies. Here, we report a FuSiOn-based genome-wide integration of hypomorphic cellular phenotypes that enables functional annotation of gene network topology, assignment of mechanistic hypotheses to genes of unknown function, and detection of cooperativity among cell regulatory systems. Dovetailing genetic perturbation data with chemical perturbation phenotypes allowed simultaneous generation of mechanism of action hypotheses for thousands of uncharacterized natural products fractions (NPFs). The predicted mechanism of actions span a broad spectrum of cellular mechanisms, many of which are not currently recognized as "druggable." To enable use of FuSiOn as a hypothesis generation resource, all associations and analyses are available within an open source web-based GUI (http://fusion.yuhs.ac).
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Affiliation(s)
- Elizabeth A McMillan
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gino Kwon
- Graduate Program for Nanomedical Science, Yonsei University, Seoul, Korea
| | - Jean R Clemenceau
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kurt W Fisher
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Rachel M Vaden
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anam F Shaikh
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Beth K Neilsen
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - David Kelly
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Malia B Potts
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yeo-Jin Sung
- Severance Biomedical Science Institute, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Saurabh Mendiratta
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Suzie K Hight
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yunji Lee
- Severance Biomedical Science Institute, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - John B MacMillan
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Robert E Lewis
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Hyun Seok Kim
- Severance Biomedical Science Institute, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea; Graduate Program for Nanomedical Science, Yonsei University, Seoul, Korea.
| | - Michael A White
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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