Reverse Chemical Genetics: Comprehensive Fitness Profiling Reveals the Spectrum of Drug Target Interactions

• Published in: PLoS genetics Vol. 12; no. 9; p. e1006275
• Main Authors: Wong, Lai H, Sinha, Sunita, Bergeron, Julien R, Mellor, Joseph C, Giaever, Guri, Flaherty, Patrick, Nislow, Corey
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 02.09.2016; Public Library of Science (PLoS)
• Subjects: Alleles; Bayes Theorem; Biology and Life Sciences; Cancer; Cancer therapies; Colleges & universities; Dihydrofolate reductase; Drug interactions; Drug resistance; Drug Resistance, Neoplasm - genetics; Drug therapy; Folic Acid Antagonists - therapeutic use; Funding; Genetics; Humans; Library collections; Medicine and Health Sciences; Methotrexate - therapeutic use; Mutation; Neoplasms - drug therapy; Neoplasms - genetics; Observations; Pharmaceutical sciences; Pharmaceuticals; Research and Analysis Methods; Tetrahydrofolate Dehydrogenase - genetics; Tetrahydrofolate Dehydrogenase - metabolism; Massachusetts
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1006275

The emergence and prevalence of drug resistance demands streamlined strategies to identify drug resistant variants in a fast, systematic and cost-effective way. Methods commonly used to understand and predict drug resistance rely on limited clinical studies from patients who are refractory to drugs or on laborious evolution experiments with poor coverage of the gene variants. Here, we report an integrative functional variomics methodology combining deep sequencing and a Bayesian statistical model to provide a comprehensive list of drug resistance alleles from complex variant populations. Dihydrofolate reductase, the target of methotrexate chemotherapy drug, was used as a model to identify functional mutant alleles correlated with methotrexate resistance. This systematic approach identified previously reported resistance mutations, as well as novel point mutations that were validated in vivo. Use of this systematic strategy as a routine diagnostics tool widens the scope of successful drug research and development.