Prediction of Synergism from Chemical-Genetic Interactions by Machine Learning

Cell Systems

Volumn 1, Issue 6, 2015, Pages 383-395

  Wildenhain, Jan ^a   Spitzer, Michaela ^a,b   Dolma, Sonam ^c,e,f   Jarvik, Nick ^c,f   White, Rachel ^a,g   Roy, Marcia ^a,h   Griffiths, Emma ^b,i   Bellows, David S ^c,j   Wright, Gerard D ^b   Tyers, Mike ^a,d  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b MCMASTER UNIVERSITY   (Canada)

^c MOUNT SINAI HOSPITAL   (Canada)

^d INSTITUTE FOR RESEARCH IN IMMUNOLOGY AND CANCER   (Canada)

^e HOSPITAL FOR SICK CHILDREN   (Canada)

^f UNIVERSITY OF TORONTO   (Canada)

^g UNIVERSITY OF EDINBURGH   (United Kingdom)

^h UNIVERSITY OF EDINBURGH   (United Kingdom)

ⁱ SIMON FRASER UNIVERSITY   (Canada)

^j VICTORIA UNIVERSITY OF WELLINGTON   (New Zealand)

more..

Author keywords

antifungal; Bayesian analysis; bipartite graph; chemical genetic interaction; combination; genetic network; machine learning; random forest; synergism

Indexed keywords

CAMPTOTHECIN; CHRYSAROBIN; CYCLOSPORIN; ERYTHROMYCIN; FENBENDAZOLE; FLUPHENAZINE; FUNGAL PROTEIN; MEBENDAZOLE; METITEPINE; MULTIPROTEIN COMPLEX; TOLNAFTATE;

ARTICLE; ASPERGILLUS FUMIGATUS; BAYESIAN LEARNING; CANDIDA ALBICANS; CANDIDA PARAPSILOSIS; CELL GROWTH; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; CHEMOGENOMICS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; CRYPTOCOCCUS GATTII; CRYPTOCOCCUS NEOFORMANS; DNA REPAIR; DRUG POTENCY; DRUG POTENTIATION; DRUG SENSITIVITY; EMBRYO; FEMALE; FUNGAL GENE; FUNGAL STRAIN; GENE DELETION; GENE INTERACTION; GENE STRUCTURE; GENETIC TRANSCRIPTION; GENOMICS; GENOTYPE; GROWTH INHIBITION; HEK293 CELL LINE; HELA CELL LINE; HUMAN; HUMAN CELL; LEARNING ALGORITHM; MACHINE LEARNING; MEMBRANE TRANSPORT; MOLECULAR INTERACTION; MOLECULAR WEIGHT; NONHUMAN; PHENOTYPE; PHYSICAL CHEMISTRY; PLEIOTROPY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN TARGETING; RANDOM FOREST; RNA PROCESSING; SOLUBILITY;

EID: 84955242863     PISSN: 24054712     EISSN: 24054720     Source Type: Journal    
DOI: 10.1016/j.cels.2015.12.003     Document Type: Article

References (49)

1. M. Bansal, J. Yang, C. Karan, M.P. Menden, J.C. Costello, H. Tang, G. Xiao, Y. Li, J. Allen, R. Zhong, et al. NCI-DREAM Community NCI-DREAM Community A community computational challenge to predict the activity of pairs of compounds Nat. Biotechnol. 32 2014 1213 1222
2. J. Besnard, G.F. Ruda, V. Setola, K. Abecassis, R.M. Rodriguiz, X.P. Huang, S. Norval, M.F. Sassano, A.I. Shin, L.A. Webster, and et al. Automated design of ligands to polypharmacological profiles Nature 492 2012 215 220
3. J.C. Brown, J. Nelson, B. VanderSluis, R. Deshpande, A. Butts, S. Kagan, I. Polacheck, D.J. Krysan, C.L. Myers, and H.D. Madhani Unraveling the biology of a fungal meningitis pathogen using chemical genetics Cell 159 2014 1168 1187
4. A. Chatr-Aryamontri, B.J. Breitkreutz, R. Oughtred, L. Boucher, S. Heinicke, D. Chen, C. Stark, A. Breitkreutz, N. Kolas, L. O'Donnell, and et al. The BioGRID interaction database: 2015 update Nucleic Acids Res. 43 2015 D470 D478
5. G. Chen, W.A. Mulla, A. Kucharavy, H.J. Tsai, B. Rubinstein, J. Conkright, S. McCroskey, W.D. Bradford, L. Weems, J.S. Haug, and et al. Targeting the adaptability of heterogeneous aneuploids Cell 160 2015 771 784
6. M. Cokol, H.N. Chua, M. Tasan, B. Mutlu, Z.B. Weinstein, Y. Suzuki, M.E. Nergiz, M. Costanzo, A. Baryshnikova, G. Giaever, and et al. Systematic exploration of synergistic drug pairs Mol. Syst. Biol. 7 2011 544
7. M. Costanzo, A. Baryshnikova, J. Bellay, Y. Kim, E.D. Spear, C.S. Sevier, H. Ding, J.L. Koh, K. Toufighi, S. Mostafavi, and et al. The genetic landscape of a cell Science 327 2010 425 431
8. A.S. Crystal, A.T. Shaw, L.V. Sequist, L. Friboulet, M.J. Niederst, E.L. Lockerman, R.L. Frias, J.F. Gainor, A. Amzallag, P. Greninger, and et al. Patient-derived models of acquired resistance can identify effective drug combinations for cancer Science 346 2014 1480 1486
9. P. Csermely, V. Agoston, and S. Pongor The efficiency of multi-target drugs: the network approach might help drug design Trends Pharmacol. Sci. 26 2005 178 182
10. D.W. Denning, and M.J. Bromley Infectious Disease. How to bolster the antifungal pipeline Science 347 2015 1414 1416
11. T. Dobzhansky Genetics of natural populations. XIII. Recombination and variability in populations of Drosophila pseudoobscura Genetics 31 1946 269 290
12. R.D. Dowell, O. Ryan, A. Jansen, D. Cheung, S. Agarwala, T. Danford, D.A. Bernstein, P.A. Rolfe, L.E. Heisler, B. Chin, and et al. Genotype to phenotype: a complex problem Science 328 2010 469
13. M. Duran-Frigola, and P. Aloy Analysis of chemical and biological features yields mechanistic insights into drug side effects Chem. Biol. 20 2013 594 603
14. L. Ejim, M.A. Farha, S.B. Falconer, J. Wildenhain, B.K. Coombes, M. Tyers, E.D. Brown, and G.D. Wright Combinations of antibiotics and nonantibiotic drugs enhance antimicrobial efficacy Nat. Chem. Biol. 7 2011 348 350
15. E. Ericson, M. Gebbia, L.E. Heisler, J. Wildenhain, M. Tyers, G. Giaever, and C. Nislow Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast PLoS Genet. 4 2008 e1000151
16. J.D. Feala, J. Cortes, P.M. Duxbury, C. Piermarocchi, A.D. McCulloch, and G. Paternostro Systems approaches and algorithms for discovery of combinatorial therapies Wiley Interdiscip. Rev. Syst. Biol. Med. 2 2010 181 193
17. J.B. Fitzgerald, B. Schoeberl, U.B. Nielsen, and P.K. Sorger Systems biology and combination therapy in the quest for clinical efficacy Nat. Chem. Biol. 2 2006 458 466
18. W.R. Greco, G. Bravo, and J.C. Parsons The search for synergy: a critical review from a response surface perspective Pharmacol. Rev. 47 1995 331 385
19. J.L. Hartman 4th, B. Garvik, and L. Hartwell Principles for the buffering of genetic variation Science 291 2001 1001 1004
20. L.H. Hartwell, P. Szankasi, C.J. Roberts, A.W. Murray, and S.H. Friend Integrating genetic approaches into the discovery of anticancer drugs Science 278 1997 1064 1068
21. M.E. Hillenmeyer, E. Fung, J. Wildenhain, S.E. Pierce, S. Hoon, W. Lee, M. Proctor, R.P. St Onge, M. Tyers, D. Koller, and et al. The chemical genomic portrait of yeast: uncovering a phenotype for all genes Science 320 2008 362 365
22. A.L. Hopkins Network pharmacology: the next paradigm in drug discovery Nat. Chem. Biol. 4 2008 682 690
23. T. Ideker, and N.J. Krogan Differential network biology Mol. Syst. Biol. 8 2012 565
24. G. Jansen, A.Y. Lee, E. Epp, A. Fredette, J. Surprenant, D. Harcus, M. Scott, E. Tan, T. Nishimura, M. Whiteway, and et al. Chemogenomic profiling predicts antifungal synergies Mol. Syst. Biol. 5 2009 338
25. M.J. Keiser, V. Setola, J.J. Irwin, C. Laggner, A.I. Abbas, S.J. Hufeisen, N.H. Jensen, M.B. Kuijer, R.C. Matos, T.B. Tran, and et al. Predicting new molecular targets for known drugs Nature 462 2009 175 181
26. H. Kitano A robustness-based approach to systems-oriented drug design Nat. Rev. Drug Discov. 6 2007 202 210
27. A.Y. Lee, R.P. St Onge, M.J. Proctor, I.M. Wallace, A.H. Nile, P.A. Spagnuolo, Y. Jitkova, M. Gronda, Y. Wu, M.K. Kim, and et al. Mapping the cellular response to small molecules using chemogenomic fitness signatures Science 344 2014 208 211
28. J. Lehar, A.S. Krueger, G.R. Zimmermann, and A.A. Borisy Therapeutic selectivity and the multi-node drug target Discov. Med. 8 2009 185 190
29. B. Lehner Genotype to phenotype: lessons from model organisms for human genetics Nat. Rev. Genet. 14 2013 168 178
30. J.A. Lucas, N.J. Hawkins, and B.A. Fraaije The evolution of fungicide resistance Adv. Appl. Microbiol. 90 2015 29 92
31. R. Mani, R.P. St Onge, J.L. Hartman 4th, G. Giaever, and F.P. Roth Defining genetic interaction Proc. Natl. Acad. Sci. USA 105 2008 3461 3466
32. S. Nelander, W. Wang, B. Nilsson, Q.B. She, C. Pratilas, N. Rosen, P. Gennemark, and C. Sander Models from experiments: combinatorial drug perturbations of cancer cells Mol. Syst. Biol. 4 2008 216
33. S.M. Nijman Functional genomics to uncover drug mechanism of action Nat. Chem. Biol. 11 2015 942 948
34. J.P. Overington, B. Al-Lazikani, and A.L. Hopkins How many drug targets are there? Nat. Rev. Drug Discov. 5 2006 993 996
35. A.B. Parsons, R.L. Brost, H. Ding, Z. Li, C. Zhang, B. Sheikh, G.W. Brown, P.M. Kane, T.R. Hughes, and C. Boone Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways Nat. Biotechnol. 22 2004 62 69
36. A.O. Pisco, A. Brock, J. Zhou, A. Moor, M. Mojtahedi, D. Jackson, and S. Huang Non-Darwinian dynamics in therapy-induced cancer drug resistance Nat. Commun. 4 2013 2467
37. S. Pu, J. Wong, B. Turner, E. Cho, and S.J. Wodak Up-to-date catalogues of yeast protein complexes Nucleic Acids Res. 37 2009 825 831
38. M. Rask-Andersen, S. Masuram, and H.B. Schiöth The druggable genome: Evaluation of drug targets in clinical trials suggests major shifts in molecular class and indication Annu. Rev. Pharmacol. Toxicol. 54 2014 9 26
39. N. Robbins, M. Spitzer, T. Yu, R.P. Cerone, A.K. Averette, Y.S. Bahn, J. Heitman, D.C. Sheppard, M. Tyers, and G.D. Wright An Antifungal Combination Matrix Identifies a Rich Pool of Adjuvant Molecules that Enhance Drug Activity against Diverse Fungal Pathogens Cell Rep. 13 2015 1481 1492
40. T. Roemer, and C. Boone Systems-level antimicrobial drug and drug synergy discovery Nat. Chem. Biol. 9 2013 222 231
41. O. Shalem, N.E. Sanjana, and F. Zhang High-throughput functional genomics using CRISPR-Cas9 Nat. Rev. Genet. 16 2015 299 311
42. J.R. Sharom, D.S. Bellows, and M. Tyers From large networks to small molecules Curr. Opin. Chem. Biol. 8 2004 81 90
43. M. Spitzer, E. Griffiths, K.M. Blakely, J. Wildenhain, L. Ejim, L. Rossi, G. De Pascale, J. Curak, E. Brown, M. Tyers, and G.D. Wright Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole Mol. Syst. Biol. 7 2011 499
44. K. Strebhardt, and A. Ullrich Paul Ehrlich's magic bullet concept: 100 years of progress Nat. Rev. Cancer 8 2008 473 480
45. X. Tan, L. Hu, L.J. Luquette 3rd, G. Gao, Y. Liu, H. Qu, R. Xi, Z.J. Lu, P.J. Park, and S.J. Elledge Systematic identification of synergistic drug pairs targeting HIV Nat. Biotechnol. 30 2012 1125 1130
46. M.B. Taylor, and I.M. Ehrenreich Higher-order genetic interactions and their contribution to complex traits Trends Genet. 31 2015 34 40
47. C.H. Waddington The Strategy of the Genes 1957 Allen & Unwin London
48. A.M. Wassermann, E. Lounkine, D. Hoepfner, G. Le Goff, F.J. King, C. Studer, J.M. Peltier, M.L. Grippo, V. Prindle, J. Tao, and et al. Dark chemical matter as a promising starting point for drug lead discovery Nat. Chem. Biol. 11 2015 958 966
49. J. Wildenhain, N. Fitzgerald, and M. Tyers MolClass: a web portal to interrogate diverse small molecule screen datasets with different computational models Bioinformatics 28 2012 2200 2201