Functional annotation of chemical libraries across diverse biological processes

Jeff S. Piotrowski, Sheena C. Li, Raamesh Deshpande, Scott W. Simpkins, Justin Nelson, Yoko Yashiroda, Jacqueline M. Barber, Hamid Safizadeh, Erin Wilson, Hiroki Okada, Abraham A. Gebre, Karen Kubo, Nikko P. Torres, Marissa A. Leblanc, Kerry Andrusiak, Reika Okamoto, Mami Yoshimura, Eva Derango-Adem, Jolanda Van Leeuwen, Katsuhiko ShirahigeAnastasia Baryshnikova, Grant W. Brown, Hiroyuki Hirano, Michael Costanzo, Brenda Andrews, Yoshikazu Ohya, Hiroyuki Osada, Minoru Yoshida, Chad L. Myers, Charles Boone

Research output: Contribution to journalArticlepeer-review

29 Scopus citations

Abstract

Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells in the presence of a compound, revealing chemical-genetic interactions that can elucidate a compound's mode of action. We developed a highly parallel, unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized diagnostic mutant collection that is predictive for all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode-sequencing protocol, enabling the assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened seven different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.

Original languageEnglish (US)
Pages (from-to)982-993
Number of pages12
JournalNature Chemical Biology
Volume13
Issue number9
DOIs
StatePublished - Sep 1 2017

Bibliographical note

Funding Information:
This work was supported by RIKEN Strategic Programs for R&D. J.S.P. and S.C.L. were funded by a RIKEN Foreign Postdoctoral Fellowship. S.W.S. is supported by an NSF Graduate Research Fellowship (00039202), an NIH Biotechnology training grant (T32GM008347), and a one-year BICB fellowship from the University of Minnesota. H.O. is a research fellow of the Japan Society for the Promotion of Science (JSPS). R.D., J.N., E.W., and C.L.M. are supported by National Institutes of Health Grants 1R01HG005084-01A1, 1R01GM104975-01, and R01HG005853 and National Science Foundation Grant DBI 0953881. C.B. and Y.O. are supported by JSPS KAKENHI Grant Numbers 15H04483. C.B. and B.A. were supported by the Canadian Institutes of Health Research, grants FDN-143264 and FDN-143265, respectively. C.L.M., C.B., M.C., J.L., and B.A. are supported by the Canadian Institute for Advanced Research Genetic Networks Program. Y.O. is supported by Ministry of Education, Culture, Sports, Science and Technology, Japan Grant for Scientific Research 24370002 and JSPS KAKENHI Grant Numbers 15H04402. M. Yoshida is supported by JSPS KAKENHI Grant Number 26221204. A.B. is supported by a Lewis Sigler fellowship at Princeton University.

Funding Information:
G.W.B. and N.P.T. are supported by Canadian Cancer Society Research Institute impact grant 702310. K.S. is supported by The Core Research for Evolutional Science and Technology (CREST) from the Japan Science and Technology Agency (JST). We thank Astellas Pharma, Inc. (Tokyo, Japan) for their kind gift of micafungin. We thank T. Saito for help with NPDepo compound access. Sequencing was provided by RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Genome Network Analysis Support Facility (GeNAS) RIKEN CLST and the University of Chicago.

Funding Information:
This work was supported by RIKEN Strategic Programs for R&D. J.S.P. and S.C.L. were funded by a RIKEN Foreign Postdoctoral Fellowship. S.W.S. is supported by an NSF Graduate Research Fellowship (00039202), an NIH Biotechnology training grant (T32GM008347), and a one-year BICB fellowship from the University of Minnesota. H.O. is a research fellow of the Japan Society for the Promotion of Science (JSPS). R.D., J.N., E.W., and C.L.M. are supported by National Institutes of Health Grants 1R01HG005084-01A1, 1R01GM104975-01, and R01HG005853 and National Science Foundation Grant DBI 0953881. C.B. and Y.O. are supported by JSPS KAKENHI Grant Numbers 15H04483. C.B. and B.A. were supported by the Canadian Institutes of Health Research, grants FDN-143264 and FDN-143265, respectively. C.L.M., C.B., M.C., J.L., and B.A. are supported by the Canadian Institute for Advanced Research Genetic Networks Program. Y.O. is supported by Ministry of Education, Culture, Sports, Science and Technology, Japan Grant for Scientific Research 24370002 and JSPS KAKENHI Grant Numbers 15H04402. M. Yoshida is supported by JSPS KAKENHI Grant Number 26221204. A.B. is supported by a Lewis Sigler fellowship at Princeton University. G.W.B. and N.P.T. are supported by Canadian Cancer Society Research Institute impact grant 702310. K.S. is supported by The Core Research for Evolutional Science and Technology (CREST) from the Japan Science and Technology Agency (JST). We thank Astellas Pharma, Inc. (Tokyo, Japan) for their kind gift of micafungin. We thank T. Saito for help with NPDepo compound access. Sequencing was provided by RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Genome Network Analysis Support Facility (GeNAS) RIKEN CLST and the University of Chicago.

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