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Zhao HN, Kvitne KE, Brungs C, Mohan S, Charron-Lamoureux V, Bittremieux W, Tang R, Schmid R, Lamichhane S, El Abiead Y, Andalibi MS, Mannochio-Russo H, Ambre M, Avalon NE, Bryant M, Caraballo-Rodríguez AM, Maya MC, Chin L, Ellis RJ, Franklin D, Girod S, Gomes PWP, Hansen L, Heaton R, Iudicello JE, Jarmusch AK, Khatib L, Letendre S, Magyari S, McDonald D, Mohanty I, Cumsille A, Moore DJ, Rajkumar P, Ross DH, Sapre H, Shahneh MRZ, Thomas SP, Tribelhorn C, Tubb HM, Walker C, Wang CX, Xing S, Zemlin J, Zuffa S, Wishart DS, Kaddurah-Daouk R, Wang M, Raffatellu M, Zengler K, Pluskal T, Xu L, Knight R, Tsunoda SM, Dorrestein PC. Empirically establishing drug exposure records directly from untargeted metabolomics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.07.617109. [PMID: 39416075 PMCID: PMC11482764 DOI: 10.1101/2024.10.07.617109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Despite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based GNPS Drug Library. This resource integrates MS/MS data for drugs and their metabolites/analogs with controlled vocabularies on exposure sources, pharmacologic classes, therapeutic indications, and mechanisms of action. It enables direct analysis of drug exposure and metabolism from untargeted metabolomics data independent of clinical records. Our library facilitates stratification of individuals in clinical studies based on the empirically detected medications, exemplified by drug-dependent microbiota-derived N-acyl lipid changes in a cohort with human immunodeficiency virus. The GNPS Drug Library holds potential for broader applications in drug discovery and precision medicine.
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Affiliation(s)
- Haoqi Nina Zhao
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kine Eide Kvitne
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Corinna Brungs
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Siddharth Mohan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Vincent Charron-Lamoureux
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Runbang Tang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Robin Schmid
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Santosh Lamichhane
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistönkatu 6A, 20520 Turku, Finland
| | - Yasin El Abiead
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mohammadsobhan S Andalibi
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- HIV Neurobehavioral Research Program, University of California San Diego, La Jolla, CA, USA
| | - Helena Mannochio-Russo
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Madison Ambre
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Martin Casas Maya
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Loryn Chin
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Ronald J Ellis
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Donald Franklin
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Sagan Girod
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Paulo Wender P Gomes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Faculty of Chemistry, Federal University of Para, Belem, PA, Brazil
| | - Lauren Hansen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert Heaton
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | | | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Lora Khatib
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Scott Letendre
- HIV Neurobehavioral Research Program, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sarolt Magyari
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ipsita Mohanty
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Andrés Cumsille
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Microbiology and Cell Sciences, University of Florida, Museum Drive, Gainesville, FL, USA
| | - David J Moore
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- HIV Neurobehavioral Research Program, University of California San Diego, La Jolla, CA, USA
| | - Prajit Rajkumar
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Dylan H Ross
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
- Current address: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Harshada Sapre
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Sydney P Thomas
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Caitlin Tribelhorn
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Corinn Walker
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Crystal X Wang
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- HIV Neurobehavioral Research Program, University of California San Diego, La Jolla, CA, USA
| | - Shipei Xing
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Jasmine Zemlin
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Simone Zuffa
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - David S Wishart
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, 27708, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
| | - Manuela Raffatellu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Chiba University, UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA
| | - Karsten Zengler
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Program in Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0418, USA
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Halicioğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
| | - Shirley M Tsunoda
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
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