Combining CRISPRi and metabolomics for functional annotation of compound libraries

Autor: Miquel Anglada-Girotto, Gabriel Handschin, Karin Ortmayr, Adrian I. Campos, Ludovic Gillet, Pablo Manfredi, Claire V. Mulholland, Michael Berney, Urs Jenal, Paola Picotti, Mattia Zampieri
Jazyk: angličtina
Rok vydání: 2022
Předmět:
Zdroj: Nat Chem Biol
Nature Chemical Biology, 18 (5)
ISSN: 1552-4450
Popis: Molecular profiling of small molecules offers invaluable insights into the function of compounds and allows for hypothesis generation about small-molecule direct targets and secondary effects. However, current profiling methods are limited in either the number of measurable parameters or throughput. Here we developed a multiplexed, unbiased framework that, by linking genetic to drug-induced changes in nearly a thousand metabolites, allows for high-throughput functional annotation of compound libraries in Escherichia coli. First, we generated a reference map of metabolic changes from CRISPR interference (CRISPRi) with 352 genes in all major essential biological processes. Next, on the basis of the comparison of genetic changes with 1,342 drug-induced metabolic changes, we made de novo predictions of compound functionality and revealed antibacterials with unconventional modes of action (MoAs). We show that our framework, combining dynamic gene silencing with metabolomics, can be adapted as a general strategy for comprehensive high-throughput analysis of compound functionality from bacteria to human cell lines. ISSN:1552-4450 ISSN:1552-4469
Databáze: OpenAIRE
Externí odkaz: