Metabolomics-based phenotypic screens for evaluation of drug synergy via direct-infusion mass spectrometry

Xiyuan Lu; G Lavender Hackman; Achinto Saha; Atul Singh Rathore; Meghan Collins; Chelsea Friedman; S Stephen Yi; Fumio Matsuda; John DiGiovanni; Alessia Lodi; Stefano Tiziani

doi:10.1016/j.isci.2022.104221

Metabolomics-based phenotypic screens for evaluation of drug synergy via direct-infusion mass spectrometry

iScience. 2022 Apr 7;25(5):104221. doi: 10.1016/j.isci.2022.104221. eCollection 2022 May 20.

Authors

Xiyuan Lu^{1

2}, G Lavender Hackman^{1

2}, Achinto Saha³, Atul Singh Rathore^{1

2}, Meghan Collins^{1

2}, Chelsea Friedman³, S Stephen Yi^{4

5

6

7}, Fumio Matsuda⁸, John DiGiovanni^{2

3

4}, Alessia Lodi^{1

2}, Stefano Tiziani^{1

2

4

5}

Affiliations

¹ Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA.
² Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX 78723, USA.
³ Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin,TX 78712, USA.
⁴ Department of Oncology, Dell Medical School, Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX 78723, USA.
⁵ Institute for Cellular and Molecular Biology (ICMB), College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA.
⁶ Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
⁷ Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX 78712, USA.
⁸ Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.

Abstract

Drugs used in combination can synergize to increase efficacy, decrease toxicity, and prevent drug resistance. While conventional high-throughput screens that rely on univariate data are incredibly valuable to identify promising drug candidates, phenotypic screening methodologies could be beneficial to provide deep insight into the molecular response of drug combination with a likelihood of improved clinical outcomes. We developed a high-content metabolomics drug screening platform using stable isotope-tracer direct-infusion mass spectrometry that informs an algorithm to determine synergy from multivariate phenomics data. Using a cancer drug library, we validated the drug screening, integrating isotope-enriched metabolomics data and computational data mining, on a panel of prostate cell lines and verified the synergy between CB-839 and docetaxel both in vitro (three-dimensional model) and in vivo. The proposed unbiased metabolomics screening platform can be used to rapidly generate phenotype-informed datasets and quantify synergy for combinatorial drug discovery.

Keywords: bioinformatics; metabolomics; omics; pharmacoinformatics.

Abstract

Grants and funding