Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility

Journal of Molecular Cell Biology

Volumn 7, Issue 3, 2015, Pages 187-202

  Wang, Yongbo ^a   Cheng, Han ^a   Pan, Zhicheng ^a   Ren, Jian ^b   Liu, Zexian ^a   Xue, Yu ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b SUN YAT SEN UNIVERSITY   (China)

Author keywords

genetic variation; nsSNP; phosphorylation; phosSNP; phosSNP associated kinase substrate network

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; INSULIN RECEPTOR SUBSTRATE 1; RAF PROTEIN; PROTEIN KINASE;

ARTICLE; CANCER GROWTH; CANCER SUSCEPTIBILITY; CONTROLLED STUDY; DRUG TARGETING; ENZYME SUBSTRATE; EPIDERMAL GROWTH FACTOR RECEPTOR GENE; GENE IDENTIFICATION; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HUMAN; INSULIN RECEPTOR SUBSTRATE 1 GENE; PHOSPHORYLATION; PROTEIN PHOSPHORYLATION; RAF1 GENE; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR GENE; BIOLOGY; DISEASE COURSE; GENETIC ASSOCIATION STUDY; GENETIC PREDISPOSITION; GENETICS; METABOLISM; NEOPLASM; PATHOLOGY; PROTEIN PROCESSING;

COMPUTATIONAL BIOLOGY; DISEASE PROGRESSION; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; HUMANS; METABOLIC NETWORKS AND PATHWAYS; NEOPLASMS; PHOSPHORYLATION; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN KINASES; PROTEIN PROCESSING, POST-TRANSLATIONAL; SIGNAL TRANSDUCTION;

EID: 84938845610     PISSN: 16742788     EISSN: 17594685     Source Type: Journal    
DOI: 10.1093/jmcb/mjv013     Document Type: Article

References (63)

1. Genomes Project Consortium. (2010). A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073.
2. Albertson, D.G. (2006). Gene amplification in cancer. Trends Genet. 22, 447-455.
3. Bader, G.D., and Hogue, C.W. (2003). An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4, 2.
4. Cargill, M., Altshuler, D., Ireland, J., et al. (1999). Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22, 231-238.
5. Carter, H., Chen, S., Isik, L., et al. (2009). Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res. 69, 6660-6667.
6. Celi, F.S., Negri, C., Tanner, K., et al. (2000). Molecular scanning for mutations in the insulin receptor substrate-1 (IRS-1) gene in Mexican Americans with Type 2 diabetes mellitus. Diabetes Metab. Res. Rev. 16, 370-377.
7. Chang, Q., Li, Y., White, M.F., et al. (2002). Constitutive activation of insulin receptor substrate 1 is a frequent event in human tumors: therapeutic implications. Cancer Res. 62, 6035-6038.
8. Choura, M., Frikha, F., Kharrat, N., et al. (2010). Investigating the function of three non-synonymous SNPs in EGFR gene: structural modelling and association with breast cancer. Protein J. 29, 50-54.
9. Collins, F.S., Brooks, L.D., and Chakravarti, A. (1998). A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8, 1229-1231.
10. Courtois, G., Smahi, A., Reichenbach, J., et al. (2003). A hypermorphic IκBα mutation is associated with autosomal dominant anhidrotic ectodermal dysplasia and T cell immunodeficiency. J. Clin. Invest. 112, 1108-1115.
11. Erxleben, C., Liao, Y., Gentile, S., et al. (2006). Cyclosporin and Timothy syndrome increase mode 2 gating of CaV1.2 calcium channels through aberrant phosphorylation of S6 helices. Proc. Natl Acad. Sci. USA 103, 3932-3937.
12. Flicek, P., Ahmed, I., Amode, M.R., et al. (2013). Ensembl 2013. Nucleic Acids Res. 41, D48-D55.
13. Forbes, S.A., Tang, G., Bindal, N., et al. (2010). COSMIC (the Catalogueof Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res. 38, D652-D657.
14. Futreal, P.A., Coin, L., Marshall, M., et al. (2004). A census of human cancer genes. Nat. Rev. Cancer 4, 177-183.
15. Gentile, S., Martin, N., Scappini, E., et al. (2008). The human ERG1 channel polymorphism, K897T, creates a phosphorylation site that inhibits channel activity. Proc. Natl Acad. Sci. USA 105, 14704-14708.
16. Gonzaga-Jauregui, C., Lupski, J.R., and Gibbs, R.A. (2012). Human genome sequencing in health and disease. Annu. Rev. Med. 63, 35-61.
17. Greenman, C., Stephens, P., Smith, R., et al. (2007). Patterns of somatic mutation in human cancer genomes. Nature 446, 153-158.
18. Gunther, T., Schmitt, A.O., Bortfeldt, R.H., et al. (2011). Where in the genome are significant single nucleotide polymorphisms from genome-wide association studies located? OMICS 15, 507-512.
19. Haber, D.A., and Settleman, J. (2007). Cancer: drivers and passengers. Nature 446, 145-146.
20. Hochgrafe, F., Zhang, L., O'Toole, S.A., et al. (2010). Tyrosine phosphorylation profiling reveals the signaling network characteristics of Basal breast cancer cells. Cancer Res. 70, 9391-9401.
21. Hudson, T.J., Anderson, W., Artez, A., et al. (2010). International network of cancer genome projects. Nature 464, 993-998.
22. Jensen, L.J., Kuhn, M., Stark, M., et al. (2009). STRING 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 37, D412-D416.
23. Jin, G., Zhang, S., Zhang, X.S., et al. (2007). Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast. PLoS One 2, e1207.
24. Johnson, M., Zaretskaya, I., Raytselis, Y., et al. (2008). NCBI BLAST: a better web interface. Nucleic Acids Res. 36, W5-W9.
25. Kanehisa, M., Goto, S., Kawashima, S., et al. (2004). The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277-D280.
26. Kettunen, J., Tukiainen, T., Sarin, A.P., et al. (2012). Genome-wide association study identifies multiple loci influencing human serum metabolite levels. Nat. Genet. 44, 269-276.
27. Landrum, M.J., Lee, J.M., Riley, G.R., et al. (2014). ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 42, D980-D985.
28. Li, S., Iakoucheva, L.M., Mooney, S.D., et al. (2010). Loss of post-translational modification sites in disease. Pac. Symp. Biocomput. 15, 337-347.
29. Li, L., Tibiche, C., Fu, C., et al. (2012a). The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer. Genome Res. 22, 1222-1230.
30. Li, M.J., Wang, P., Liu, X., et al. (2012b). GWASdb: a database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res. 40, D1047-D1054.
31. Lin, C.Y., Chin, C.H., Wu, H.H., et al. (2008). Hubba: hub objects analyzer - a framework of interactome hubs identification for network biology. Nucleic Acids Res. 36, W438-W443.
32. Liu, P., Gan, W., Inuzuka, H., et al. (2013a). Sin1 phosphorylation impairs mTORC2 complex integrity and inhibits downstream Akt signalling to suppress tumorigenesis. Nat. Cell Biol. 15, 1340-1350.
33. Liu, Z., Ren, J., Cao, J., et al. (2013b). Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes. Brief. Bioinform. 14, 344-360.
34. Macek, B., Mann, M., and Olsen, J.V. (2009). Global and site-specific quantitative phosphoproteomics: principles and applications. Annu. Rev. Pharmacol. Toxicol. 49, 199-221.
35. Manning, B.D., and Cantley, L.C. (2007). AKT/PKB signaling: navigating downstream. Cell 129, 1261-1274.
36. Manolio, T.A., Brooks, L.D., and Collins, F.S. (2008). A HapMap harvest of insights into the genetics of common disease. J. Clin. Invest. 118, 1590-1605.
37. Mermel, C.H., Schumacher, S.E., Hill, B., et al. (2011). GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41.
38. Nilsson, C.L. (2012). Advances in quantitative phosphoproteomics. Anal. Chem. 84, 735-746.
39. Olsen, J.V., Blagoev, B., Gnad, F., et al. (2006). Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635-648.
40. Pruitt, K.D., Tatusova, T., and Maglott, D.R. (2007). NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61-D65.
41. Radivojac, P., Baenziger, P.H., Kann, M.G., et al. (2008). Gain and loss of phosphorylation sites in human cancer. Bioinformatics 24, i241-i247.
42. Reimand, J., and Bader, G.D. (2013). Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol. Syst. Biol. 9, 637.
43. Ren, J., Jiang, C., Gao, X., et al. (2010). PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. Mol. Cell. Proteomics 9, 623-634.
44. Reumers, J., Maurer-Stroh, S., Schymkowitz, J., et al. (2006). SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics 22, 2183-2185.
45. Ryu, G.M., Song, P., Kim, K.W., et al. (2009). Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases. Nucleic Acids Res. 37, 1297-1307.
46. Savas, S., and Ozcelik, H. (2005). Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs. BMC Cancer 5, 107.
47. Schriml, L.M., Arze, C., Nadendla, S., et al. (2012). Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res. 40, D940-D946.
48. Shannon, P., Markiel, A., Ozier, O., et al. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504.
49. Sherry, S.T., Ward, M.H., Kholodov, M., et al. (2001). dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308-311.
50. Song, C., Ye, M., Liu, Z., et al. (2012). Systematic analysis of protein phosphorylation networks from phosphoproteomic data. Mol. Cell. Proteomics 11, 1070-1083.
51. Stenson, P.D., Mort, M., Ball, E.V., et al. (2009). The human gene mutation database: 2008 update. Genome Med. 1, 13.
52. UniProt Consortium. (2013). Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res. 41, D43-D47.
53. Vandin, F., Upfal, E., and Raphael, B.J. (2012). De novo discovery of mutated driver pathways in cancer. Genome Res. 22, 375-385.
54. Wang, E., Lenferink, A., and O'Connor-McCourt, M. (2007). Cancer systems biology: exploring cancer-associated genes on cellular networks. Cell. Mol. Life Sci. 64, 1752-1762.
55. Wishart, D.S., Knox, C., Guo, A.C., et al. (2008). DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 36, D901-D906.
56. Wood, L.D., Parsons, D.W., Jones, S., et al. (2007). The genomic landscapes of human breast and colorectal cancers. Science 318, 1108-1113.
57. Xue, Y., Ren, J., Gao, X., et al. (2008). GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol. Cell. Proteomics 7, 1598-1608.
58. Xue, Y., Liu, Z., Cao, J., et al. (2011). GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. Protein Eng. Des. Sel. 24, 255-260.
59. Yang, C.Y., Chang, C.H., Yu, Y.L., et al. (2008a). PhosphoPOINT: a comprehensive human kinaseinteractome and phospho-protein database. Bioinformatics24, i14-i20.
60. Yang, Y., Houle, A.M., Letendre, J., et al. (2008b). RET Gly691Ser mutation is associated with primary vesicoureteral reflux in the French-Canadian population from Quebec. Hum. Mutat. 29, 695-702.
61. Yue, P., and Moult, J. (2006). Identification and analysis of deleterious human SNPs. J. Mol. Biol. 356, 1263-1274.
62. Zaman, N., Li, L., Jaramillo, M.L., et al. (2013). Signaling network assessment of mutations and copy number variations predict breast cancer subtype-specific drug targets. Cell Rep. 5, 216-223.
63. Zeng, W., Peng, J., Wan, X., et al. (2000). The mutation of insulin receptor substrate-1 gene in Chinese patients with non-insulin-dependent diabetes mellitus. Chin. Med. J. (Engl.) 113, 80-83.