Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets

Nature Communications

Volumn 4, Issue , 2013, Pages

  Lu, Xiaowen ^a   Kensche, Philip R ^b   Huynen, Martijn A ^a,b   Notebaart, Richard A ^a,b  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BETA CATENIN; FBXW7 PROTEIN; HISTONE DEACETYLASE 1; LYMPHOID ENHANCER FACTOR 1; MULTIPROTEIN COMPLEX; NOTCH RECEPTOR; NSUN2 PROTEIN; TLE1 PROTEIN; UNCLASSIFIED DRUG; WNT PROTEIN;

CANCER; DISEASE TREATMENT; DRUG; EVOLUTIONARY BIOLOGY; GENOMICS; METABOLISM; PROTEIN; YEAST;

ANIMAL TISSUE; ARTICLE; CANCER CELL; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; DRUG TARGETING; GENE INTERACTION; GENE MUTATION; KNOCKOUT GENE; NONHUMAN; ONCOGENE; ONCOGENE C MYC; PHYLOGENETIC TREE; PREDICTIVE VALUE; PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SIGNAL TRANSDUCTION; TRANSCRIPTION INITIATION; TUMOR SUPPRESSOR GENE;

ANTINEOPLASTIC AGENTS; EPISTASIS, GENETIC; EVOLUTION, MOLECULAR; GENOME, FUNGAL; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MODELS, GENETIC; MOLECULAR TARGETED THERAPY; NEOPLASM PROTEINS; NEOPLASMS; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SYSTEMS BIOLOGY;

EID: 84880302198     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms3124     Document Type: Article

References (59)

1. Badano, J. L. & Katsanis, N. Beyond Mendel: an evolving view of human genetic disease transmission. Nat. Rev. Genet. 3, 779-789 (2002).
2. Moore, J. H. The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum. Hered. 56, 73-82 (2003). (Pubitemid 37465073)
3. Gavin, A. C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636 (2006).
4. Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391 (2002). (Pubitemid 34826834)
5. Krogan, N. J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643 (2006).
6. Ideker, T. & Krogan, N. J. Differential network biology. Mol. Syst. Biol. 8, 565 (2012).
7. Dirick, L. & Nasmyth, K. Positive feedback in the activation of Gl cyclins in yeast. Nature 351, 754-757 (1991). (Pubitemid 21896683)
8. Richardson, H. E., Wittenberg, C., Cross, F. & Reed, S. I. An essential G1 function for cyclin-like proteins in yeast. Cell 59, 1127-1133 (1989). (Pubitemid 20024623)
9. Mani, St R., Onge, R. P., Hartman, J. L., Giaever, G. & Roth, F. P. Defining genetic interaction. Proc. Natl Acad. Sci. USA 105, 3461-3466 (2008). (Pubitemid 351723575)
10. Weidle, U. H., Maisel, D. & Eick, D. Synthetic lethality-based targets for discovery of new cancer therapeutics. Cancer Genomics Proteomics 8, 159-171 (2011).
11. Muller, F. L. et al. Passenger deletions generate therapeutic vulnerabilities in cancer. Nature 488, 337-342 (2012).
12. Paladugu, S., Zhao, S., Ray, A. & Raval, A. Mining protein networks for synthetic genetic interactions. BMC Bioinform. 9, 426 (2008).
13. Wong, S. L. et al. Combining biological networks to predict genetic interactions. Proc. Natl Acad. Sci. USA 101, 15682-15687 (2004). (Pubitemid 39473548)
14. Burgard, A. P., Nikolaev, E. V., Schilling, C. H. & Maranas, C. D. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 14, 301-312 (2004). (Pubitemid 38219844)
15. Notebaart, R., Kensche, P., Huynen, M. & Dutilh, B. Asymmetric relationships between proteins shape genome evolution. Genome Biol. 10, R19 (2009).
16. Bowers, P. M., Cokus, S. J., Eisenberg, D. & Yeates, T. O. Use of logic relationships to decipher protein network organization. Science 306, 2246-2249 (2004). (Pubitemid 40024459)
17. Benschop, J. J. et al. A consensus of core protein complex compositions for Saccharomyces cerevisiae. Mol. Cell. 38, 916-928 (2010).
18. Pandey, G. et al. An integrative multi-network and multi-classifier approach to predict genetic interactions. PLoS Comput. Biol. 6, e1000928 (2010).
19. Kuepfer, L., Sauer, U. & Blank, L. M. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res. 15, 1421-1430 (2005). (Pubitemid 41400909)
20. Costanzo, M. et al. The genetic landscape of a cell. Science 327, 425-431 (2010).
21. Szappanos, B. et al. An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat. Genet. 43, 656-662 (2011).
22. Aguilar, P. S. et al. A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking. Nat. Struct. Mol. Biol. 17, 901-908 (2010).
23. Bandyopadhyay, S. et al. Rewiring of genetic networks in response to DNA damage. Science 330, 1385-1389 (2010).
24. Collins, S. R. et al. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446, 806-810 (2007). (Pubitemid 46582025)
25. Fiedler, D. et al. Functional organization of the S. cerevisiae phosphorylation network. Cell 136, 952-963 (2009).
26. Schuldiner, M. et al. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123, 507-519 (2005). (Pubitemid 41546679)
27. Wilmes, G. M. et al. A genetic interaction map of rna-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol. Cell. 32, 735-746 (2008).
28. Zheng, J. et al. Epistatic relationships reveal the functional organization of yeast transcription factors. Mol. Syst. Biol. 6, 420 (2010).
29. von Mering, C. et al. STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35, D358-D362 (2007).
30. Reinhardt, H. C., Jiang, H., Hemann, M. T. & Yaffe, M. B. Exploiting synthetic lethal interactions for targeted cancer therapy. Cell Cycle 8, 3112-3119 (2009).
31. Stark, C. et al. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 39, D698-D704 (2011).
32. Horn, T. et al. Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nat. Meth. 8, 341-346 (2011).
33. McQuilton, P., St Pierre, S. E., Thurmond, J. & Consortiumt. F. FlyBase 101-the basics of navigating FlyBase. Nucleic Acids Res. 40, D706-D714 (2012).
34. Havugimana, Pierre C. et al. A census of human soluble protein complexes. Cell 150, 1068-1081 (2012).
35. Ruepp, A. et al. CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Res. 38, D497-D501 (2010).
36. Futreal, P. A. et al. A census of human cancer genes. Nat. Rev. Cancer 4, 177-183 (2004). (Pubitemid 38337497)
37. Duarte, N. C. et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl Acad. Sci. USA 104, 1777-1782 (2007). (Pubitemid 46239855)
38. Marcotte, R. et al. Essential gene profiles in breast, pancreas and ovarian cancer cells. Cancer Discov. 2, 172-189 (2012).
39. Lagger, G. et al. The tumor suppressor p53 and histone deacetylase 1 are antagonistic regulators of the cyclin-dependent kinase inhibitor p21/WAF1/CIP1 gene. Mol. Cell. Biol. 23, 2669-2679 (2003). (Pubitemid 36403069)
40. Lagger, G. et al. Essential function of histone deacetylase 1 in proliferation control and CDK inhibitor repression. EMBO J. 21, 2672-2681 (2002). (Pubitemid 34619383)
41. Chen, G., Fernandez, J., Mische, S. & Courey, A. J. A functional interaction between the histone deacetylase Rpd3 and the corepressor Groucho in Drosophila development. Genes Dev. 13, 2218-2230 (1999). (Pubitemid 29426727)
42. Hussain, S. et al. The nucleolar RNA methyltransferase Misu (NSun2) is required for mitotic spindle stability. J. Cell. Biol. 186, 27-40 (2009).
43. Welcker, M. & Clurman, B. E. FBW7 ubiquitin ligase: a tumour suppressor at the crossroads of cell division, growth and differentiation. Nat. Rev. Cancer 8, 83-93 (2008). (Pubitemid 351161321)
44. Welcker, M. et al. The Fbw7 tumor suppressor regulates glycogen synthase kinase 3 phosphorylation-dependent c-Myc protein degradation. Proc. Natl Acad. Sci. USA 101, 9085-9090 (2004). (Pubitemid 38781615)
45. Matsumoto, A. et al. Fbxw7-dependent degradation of notch is required for control of "stemness" and neuronal-glial differentiation in neural stem cells. J. Biol. Chem. 286, 13754-13764 (2011).
46. Hirabayashi, Y. et al. The Wnt/b-catenin pathway directs neuronal differentiation of cortical neural precursor cells. Development 131, 2791-2801 (2004). (Pubitemid 38997270)
47. Blanco, S. et al. The RNA-methyltransferase Misu (NSun2) poises epidermal stem cells to differentiate. PLoS Genet. 7, e1002403 (2011).
48. Frye, M. & Watt, F. M. The RNA methyltransferase Misu (NSun2) mediates Myc-induced proliferation and is upregulated in tumors. Curr. Biol. 16, 971-981 (2006). (Pubitemid 43728217)
49. Mewes, H. W. et al. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 32, D41-D44 (2004). (Pubitemid 38081600)
50. Frost, A. et al. Functional repurposing revealed by comparing S. pombe and S. cerevisiae genetic interactions. Cell 149, 1339-1352 (2012).
51. Harrison, R., Papp, B., Pa?l, C., Oliver, S. G. & Delneri, D. Plasticity of genetic interactions in metabolic networks of yeast. Proc. Natl Acad. Sci. USA 104, 2307-2312 (2007). (Pubitemid 46391393)
52. Fedeles, S. V. et al. A genetic interaction network of five genes for human polycystic kidney and liver diseases defines polycystin-1 as the central determinant of cyst formation. Nat. Genet. 43, 639-647 (2011).
53. Lanson, N. A. et al. A Drosophila model of FUS-related neurodegeneration reveals genetic interaction between FUS and TDP-43. Hum. Mol. Genet. 20, 2510-2523 (2011).
54. Willis, M. S. et al. Functional redundancy of SWI/SNF catalytic subunits in maintaining vascular endothelial cells in the adult heart. Circ. Res. 111, e111-e122 (2012).
55. Swofford, D. L. PAUP Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4. (Sinauer Associates, Sunderland, massachusetts, 2003).
56. Hall, M. et al. The WEKA Data Mining Software: An Update Volume 11, Issue 1SIGKDD Explorations, 2009).
57. Kostelansky, M. S. et al. Molecular architecture and functional model of the complete yeast ESCRT-I heterotetramer. Cell 129, 485-498 (2007). (Pubitemid 46671555)
58. Curtiss, M., Jones, C. & Babst, M. Efficient cargo sorting by ESCRT-I and the subsequent release of ESCRT-I from multivesicular bodies requires the subunit Mvb12. Mol. Biol. Cell 18, 636-645 (2007). (Pubitemid 46213231)
59. Oestreich, A. J., Davies, B. A., Payne, J. A. & Katzmann, D. J. Mvb12 is a novel member of ESCRT-I involved in cargo selection by the multivesicular body pathway. Mol. Biol. Cell 18, 646-657 (2007). (Pubitemid 46213232)