A mass spectrometry-based proteome map of drug action in lung cancer cell lines

• Published in: Nature chemical biology Vol. 16; no. 10; pp. 1111 - 1119
• Main Authors: Ruprecht, Benjamin, Di Bernardo, Julie, Wang, Zhao, Mo, Xuan, Ursu, Oleg, Christopher, Matthew, Fernandez, Rafael B., Zheng, Li, Dill, Brian D., Wang, Huijun, Xu, Yuting, Liaw, Andy, Mortison, Jonathan D., Siriwardana, Nirodhini, Andresen, Brian, Glick, Meir, Tata, James R., Kutilek, Victoria, Cornella-Taracido, Ivan, Chi, An
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.10.2020; Nature Publishing Group
• Subjects: 631/154; 631/154/1435; 631/553; Antineoplastic Agents - pharmacology; Autophagy; Biochemical Engineering; Biochemistry; Biodegradation; Bioorganic Chemistry; Biotechnology; Cell Biology; Cell Line, Tumor; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Deconvolution; Drugs; Gene Expression Regulation, Neoplastic - drug effects; Gene Expression Regulation, Neoplastic - physiology; Humans; Lung cancer; Lung Neoplasms - metabolism; Mass Spectrometry; Mass spectroscopy; Mitochondria; Perturbation; Phagocytosis; Proteins; Proteome; Proteomes; Proteomics; Proteomics - methods; Robustness; Scientific imaging; Spectroscopy; Target recognition; Tumor cell lines; Workflow
• ISSN: 1552-4450; 1552-4469
• DOI: 10.1038/s41589-020-0572-3

Mass spectrometry-based discovery proteomics is an essential tool for the proximal readout of cellular drug action. Here, we apply a robust proteomic workflow to rapidly profile the proteomes of five lung cancer cell lines in response to more than 50 drugs. Integration of millions of quantitative protein–drug associations substantially improved the mechanism of action (MoA) deconvolution of single compounds. For example, MoA specificity increased after removal of proteins that frequently responded to drugs and the aggregation of proteome changes across cell lines resolved compound effects on proteostasis. We leveraged these findings to demonstrate efficient target identification of chemical protein degraders. Aggregating drug response across cell lines also revealed that one-quarter of compounds modulated the abundance of one of their known protein targets. Finally, the proteomic data led us to discover that inhibition of mitochondrial function is an off-target mechanism of the MAP2K1/2 inhibitor PD184352 and that the ALK inhibitor ceritinib modulates autophagy. A robust mass spectrometry workflow was developed for rapid drug perturbation profiling in multiple cell lines, enabling improved mechanistic deconvolution of single compounds and revealing novel mechanisms of action.