Enrichment analysis for discovering biological associations in phenotypic screens

Journal of Chemical Information and Modeling

Volumn 54, Issue 2, 2014, Pages 377-386

  Polyakov, Valery R ^a   Moorcroft, Neil D ^a   Drawid, Amar ^a  

^a SANOFI   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOLOGY;

ANALYSIS ALGORITHMS; ANALYSIS METHOD; BIOLOGICAL PATHWAYS; COMPLEX BIOLOGICAL SYSTEMS; DNA FRAGMENTATION; INDISPENSABLE TOOLS; MECHANISM OF ACTION; RELEVANT TARGET;

CHEMICAL ANALYSIS;

TUMOR NECROSIS FACTOR RELATED APOPTOSIS INDUCING LIGAND;

ALGORITHM; ARTICLE; DNA FRAGMENTATION; DRUG EFFECT; DRUG SCREENING; HIGH THROUGHPUT SCREENING; METABOLISM; METHODOLOGY; PHENOTYPE;

ALGORITHMS; DNA FRAGMENTATION; DRUG EVALUATION, PRECLINICAL; HIGH-THROUGHPUT SCREENING ASSAYS; PHENOTYPE; TNF-RELATED APOPTOSIS-INDUCING LIGAND;

EID: 84894641359     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400245c     Document Type: Article

References (83)

1. Hart, C. P. Finding the target after screening the phenotype Drug Discovery Today 2005, 10, 513-519
2. Wale, N.; Karypis, G. Target fishing for chemical compounds using target-ligand activity data and ranking based methods J. Chem. Inf. Model. 2009, 49 (10) 2190-2201
3. Haggarty, S. J. The principle of complementarity: Chemical versus biological space Curr. Opin. Chem. Biol. 2005, 9 (3) 296-303
4. Swinney, D. C.; Anthony, J. How were new medicines discovered? Nat. Rev. Drug Discovery 2011, 10 (7) 507-19
5. Hosack, D. A.; Dennis, G., Jr.; Sherman, B. T.; Lane, H. C.; Lempicki, R. A. Identifying biological themes within lists of genes with EASE Genome Biol. 2003, 4 (10) R70
6. Huang, D. W.; Sherman, B. T.; Tan, Q.; Kir, J.; Liu, D.; Bryant, D.; Guo, Y.; Stephens, R.; Stephens, R.; Baseler, M. W.; Lane, H. C.; Lempicki, R. A. DAVID Bioinformatics Resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists Nucleic Acids Res. 2007, 35 (Suppl 2) W169-175
7. Dennis, G., Jr.; Sherman, B. T.; Hosack, D. A.; Yang, J.; Gao, W.; Lane, H. C.; Lempicki, R. A. DAVID: Database for Annotation, Visualization, and Integrated Discovery Genome Biol. 2003, 4 (5) P3
8. Ashkenazi, A.; Dixit, V. Death receptors: Signaling and modulation Science 1998, 281 (28) 1305-1308
9. Abdulghani, J.; El-Deiry, W. S. TRAIL receptor signaling and therapeutics Expert Opin. Ther. Targets 2010, 1091-1108
10. Koschny, R.; Walczak, H.; Ganten, T. The promise of TRAIL-potential and risks of a novel anticancer therapy J. Mol. Med. (Heidelberg, Ger.) 2007, 85, 923-935
11. Li, Y.; Wang, H.; Wang, Z.; Makhija, S.; Buchsbaum, D.; LoBuglio, A.; Kimberly, R.; Zhou, T. Inducible resistance of tumor cells to tumor necrosis factor-related apoptosis-inducing ligand receptor 2-mediated apoptosis by generation of a blockade at the death domain function Cancer Res. 2006, 66 (17) 8520-8528
12. Booth, N. L.; Sayers, T. J.; Brooks, A. D.; Thomas, C. L.; Jacobsen, K.; Goncharova, E. I.; McMahon, J. B.; Henrich, C. J. A cell-based high-throughput screen to identify synergistic TRAIL sensitizers Cancer Immunol. Immunother. 2009, 58 (8) 1229-1244
13. Schimmer, A. D.; Thomas, M. P.; Hurren, R.; Gronda, M.; Pellecchia, M.; Pond, G. R.; Konopleva, M.; Gurfinkel, D.; Mawji, I. A.; Brown, E.; Reed, J. C. Identification of small molecules that sensitize resistant tumor cells to tumor necrosis factor-family death receptors Cancer Res. 2006, 66 (4) 2367-2375
14. Elmore, S. Apoptosis: A review of programmed cell death Toxicol. Pathol. 2007, 35 (4) 495-516
15. Guchelaar, H. J.; Vermes, A.; Vermes, I.; Haanen, C. Apoptosis: Molecular mechanisms and implications for cancer chemotherapy Pharm. World Sci. 1997, 19 (3) 119-125
16. Fleiss, J. L. Statistical Methods for Rates and Proportions, 2 nd ed.; John Wiley & Sons: New York, 1981; p 236.
17. Lenovo. http://shop.lenovo.com/ISS-Static/WW/EMAT/products/workstation/ thinkstation/en/pdf/C20-C20x-DS-EN.pdf (accessed on September 14, 2011).
18. Microsoft. http://windows.microsoft.com/en-US/windows7/help (accessed on September 14, 2011).
19. Intel. http://ark.intel.com/products/47922/Intel-Xeon-Processor-X5650- (12M-Cache-2-66-GHz-6-40-GTs-Intel-QPI) (accessed on September 14, 2011).
20. Microsoft. http://msdn.microsoft.com/library/zw4w595w.aspx (accessed on September 14, 2011).
21. Microsoft. http://msdn.microsoft.com/en-us/library/ms228593.aspx (accessed on September 14, 2011).
22. Ekins, S.; Nikolsky, Y.; Bugrim, A.; Kirillov, E.; Nikolskaya, T. Pathway mapping tools for analysis of high content data Methods Mol. Biol. 2007, 356, 319-350
23. Rayasam, G. V.; Tulasi, V. K.; Sodhi, R.; Davis, J. A.; Ray, A. Glycogen synthase kinase 3: more than a namesake Br. J. Pharmacol. 2009, 156, 885-898
24. Lesuisse, D.; Tiraboschi, G.; Krick, A.; Abecassis, P.-Y.; Dutruc-Rosset, G.; Babin, D.; Halley, F.; Chaîtreau, F.; Lachaud, S.; Chevalier, A.; Quarteronet, D.; Burgevin, M.-C.; Amara, C.; Bertrand, P.; Rooney, T. Design of potent and selective GSK3β inhibitors with acceptable safety profile and pharmacokinetics Bioorg. Med. Chem. Lett. 2010, 20 (7) 2344-2349
25. Lesuisse, D.; Dutruc-Rosset, G.; Tiraboschi, G.; Dreyer, M. K.; Maignan, S.; Chevalier, A.; Halley, F.; Bertrand, P.; Burgevin, M.-C.; Quarteronet, D.; Rooney, T. Rational design of potent GSK3beta inhibitors with selectivity for Cdk1 and Cdk2 Bioorg. Med. Chem. Lett. 2010, 20 (6) 1985-1989
26. Liao, X.; Zhang, L.; J. Thrasher, B.; Du, J.; Li, B. Glycogen synthase kinase-3beta suppression eliminates tumor necrosis factor-related apoptosis-inducing ligand resistance in prostate cancer Mol. Cancer Ther. 2003, 2, 1215-1222
27. Beurel, E.; Blivet-Van Eggelpoël, M.-J.; Kornprobst, M.; Moritz, S.; Delelo, R.; Paye, F.; Housset, C.; Desbois-Mouthon, C. Glycogen synthase kinase-3 inhibitors augment TRAIL-induced apoptotic death in human hepatoma cells Biochem. Pharmacol. 2009, 77 (1) 54-65
28. Cantarella, G.; Di Benedetto, G.; Pezzino, S.; Risuglia, N.; Bernardini, R. TRAIL-related neurotoxicity implies interaction with the Wnt pathway in human neuronal cells in vitro J. Neurochem. 2008, 105, 1915-1923
29. Beurel, E.; Jope, R. S. The Paradoxical Pro- and Anti-apoptotic Actions of GSK3 in the Intrinsic and Extrinsic Apoptosis Signaling Pathways Prog. Neurobiol. 2006, 79 (4) 173-189
30. Scaffidi, C.; Fulda, S.; Srinivasan, A.; Friesen, C.; Li, F.; Tomaselli, K. J.; Debatin, K.-M.; Krammer, P. H.; Peter, M. E. Two CD95 (APO-1/Fas) signaling pathways EMBO J. 1998, 17 (6) 1675-1687
31. Linseman, D. A.; Butts, B. D.; Precht, T. A.; Phelps, R. A.; Le, S. S.; Laessig, T. A.; Bouchard, R. J.; Florez-McClure, M. L.; Heidenreich, K. A. Glycogen synthase kinase-3beta phosphorylates Bax and promotes its mitochondrial localization during neuronal apoptosis J. Neurosci. 2004, 24, 9993-10002
32. Maurer, U.; Charvet, C.; Wagman, A. S.; Dejardin, E.; Green, D. R. Glycogen synthase kinase-3 regulates mitochondrial outer membrane permeabilization and apoptosis by destabilization of MCL-1 Mol. Cell 2006, 21 (6) 749-760
33. Bilim, V.; Ougolkov, A.; Yuuki, K.; Naito, S.; Kawazoe, H.; Muto, A.; Oya, M.; Billadeau, D.; Motoyama, T.; Tomita, Y. Glycogen synthase kinase-3: A new therapeutic target in renal cell carcinoma Br. J. Cancer 2009, 101, 2005-2014
34. Yang, L.; Lin, C.; Liu, Z.-R. P68 RNA helicase mediates PDGF-induced epithelial mesenchymal transition by displacing Axin from beta-catenin Cell 2006, 127 (1) 139-155
35. Luo, J.; Chen, J.; Deng, Z.-L.; Luo, X.; Song, W.-X.; Sharff, K. A.; Tang, N.; Haydon, R. C.; Luu, H. H.; He, T. C. Wnt signaling and human diseases: What are the therapeutic implications? Lab. Invest. 2007, 87 (2) 97-103
36. Senthivinayagam, S.; Mishra, P.; Paramasivam, S. K.; Yallapragada, S.; Chatterjee, M.; Wong, L.; Rana, A.; Rana, B. Caspase-mediated cleavage of β-catenin precedes drug-induced apoptosis in resistant cancer cells J. Biol. Chem. 2009, 284 (20) 13577-13588
37. Yost, C.; Torres, M.; Miller, J. R.; Huang, E.; Kimelman, D.; Moon, R. T. The axis-inducing activity, stability, and subcellular distribution of beta-catenin is regulated in Xenopus embryos by glycogen synthase kinase 3 Genes Dev. 1996, 10 (12) 1443-1454
38. Wu, D.; Pan, W. GSK3: A multifaceted kinase in Wnt signaling Trends Biochem. Sci. 2010, 35 (3) 161-168
39. Polakis, P. The oncogenic activation of beta-catenin Curr. Opin. Genet. Dev. 1999, 9 (1) 15-21
40. Rodriguez, R.; Muller, S.; Yeoman, J. A.; Trentesaux, C.; Riou, J.-F.; Balasubramanian, S. A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres J. Am. Chem. Soc. 2008, 130 (47) 15758-15759
41. Ou, T.-M.; Lu, Y.-J.; Zhang, C.; Huang, Z.-S.; Wang, X.-D.; Tan, J.-H.; Chen, Y.; Ma, D.-L.; Wong, K.-Y.; Tang, J. C.-O.; Chan, A. S.-C.; Gu, L.-Q. Stabilization of G-Quadruplex DNA and Down-Regulation of Oncogene c-myc by Quindoline Derivatives J. Med. Chem. 2007, 50 (7) 1465-1474
42. Kuribayashi, K.; Krigsfeld, G.; Wang, W.; Xu, J.; Mayes, P. A.; Dicker, D. T.; Wu, G. S.; El-Deiry, W. S. TNFSF10 (TRAIL), a p53 target gene that mediates p53-dependent cell death Cancer Biol. Ther. 2008, 7 (12) 2034-2038
43. Ding, L.; Yuan, C.; Wei, F.; Wang, G.; Zhang, J.; Bellail, A. C.; Zhang, Z.; Olson, J. J.; Hao, C. Cisplatin Restores TRAIL apoptotic pathway in Glioblastoma-Derived Stem Cells through Up-regulation of DR5 and Down-regulation of c-FLIP Cancer Invest. 2011, 29 (8) 511-520
44. Vazquez, A.; Bond, E. E.; Levine, A. J.; Bond, G. L. The genetics of the p53 pathway, apoptosis and cancer therapy Nat. Rev. Drug Discovery 2008, 7, 979-987
45. Urashima, M.; Teoh, G.; Chauhan, D.; Ogata, A.; Shirahama, S.; Kaihara, C.; Matsuzaki, M.; Matsushima, H.; Akiyama, M.; Yuza, Y.; Maekawa, K.; Anderson, K. C. MDM2 Protein Overexpression Inhibits Apoptosis of TF-1 Granulocyte-Macrophage Colony-Stimulating Factor-Dependent Acute Myeloblastic Leukemia Cells Blood 1998, 92 (3) 959-967
46. Rosas, M.; Birkenkamp, K. U.; Lammers, J.-W. J.; Koenderman, L.; Coffer, P. J. Cytokine mediated suppression of TF-1 apoptosis requires PI3K activation and inhibition of Bim expression FEBS Lett. 2005, 579 (1) 191-198
47. Zhu, Y. M.; Bradbury, D. A.; Russell, N. H. Wild-type p53 is required for apoptosis induced by growth factor deprivation in factor-dependent leukaemic cells Br. J. Cancer 1994, 69 (3) 468-472
48. Chen, K.-F.; Tai, W.-T.; Liu, T.-H.; Huang, H.-P.; Lin, Y.-C.; Shiau, C.-W.; Li, P.-K.; Chen, P.-J.; Cheng, A.-L. Sorafenib overcomes TRAIL resistance of hepatocellular carcinoma cells through the inhibition of STAT3 Clin. Cancer Res. 2010, 16 (21) 5189-5199
49. Kim, Y.-S.; Jin, H.-O.; Seo, S.-K.; Woo, S. H.; Choe, T.-B.; An, S.; Hong, S.-I.; Lee, S.-J.; Lee, K.-H.; Park, I.-C. Sorafenib induces apoptotic cell death in human non-small cell lung cancer cells by down-regulating mammalian target of rapamycin (mTOR)-dependent survivin expression Biochem. Pharmacol. 2011, 82 (3) 216-226
50. Meng, X. W.; Lee, S.-H.; Dai, H.; Loegering, D.; Yu, C.; Flatten, K.; Schneider, P.; Dai, N. T.; Kumar, S. K.; Smith, B. D.; Karp, J. E.; Adjei, A. A.; Kaufmann, S. H. Mcl-1 as a buffer for proapoptotic Bcl-2 family members during TRAIL-induced apoptosis: A mechanistic basis for sorafenib (Bay 43-9006)-induced TRAIL sensitization J. Biol. Chem. 2007, 282 (41) 29831-29846
51. Rosato, R. R.; Almenara, J. A.; Coe, S.; Grant, S. The multikinase inhibitor sorafenib potentiates TRAIL lethality in human leukemia cells in association with Mcl-1 and cFLIPL down-regulation Cancer Res. 2007, 67 (19) 9490-9500
52. Ding, W.; Cai, T.; Zhu, H.; Wu, R.; Tu, C.; Yang, L.; Lu, W.; He, Q.; Yang, B. Synergistic antitumor effect of TRAIL in combination with sunitinib in vitro and in vivo Cancer Lett. 2010, 293 (2) 158-166
53. Karasic, T. B.; Hei, T. K.; Ivanov, V. N. Disruption of IGF-1R signaling increases TRAIL-induced apoptosis: a new potential therapy for the treatment of melanoma Exp. Cell Res. 2010, 316 (12) 1994-2007
54. Pennarun, B.; Kleibeuker, J. H.; Oenema, T.; Stegehuis, J. H.; de Vries, E. G. E.; de Jong, S. Inhibition of IGF-1R-dependent PI3K activation sensitizes colon cancer cells specifically to DR5-mediated apoptosis but not to rhTRAIL Cell. Oncol. 2011, 34 (3) 245-259
55. Kim, M.; Liao, J.; Dowling, M. L.; Voong, K. R.; Parker, S. E.; Wang, S.; El-Deiry, W. S.; Kao, G. D. TRAIL inactivates the mitotic checkpoint and potentiates death induced by microtubule-targeting agents in human cancer cells Cancer Res. 2008, 68 (9) 3440-3449
56. Gasparian, M. E.; Domnina, L. V.; Ivanova, O. Y.; Izyumov, D. S.; Lomakin, A. Y.; Popova, E. N.; Yagolovich, A. V.; Pletjushkina, O. Y.; Dolgikh, D. A.; Chernyak, B. V. Cytoskeleton inhibitors combined with TRAIL induce apoptosis in HeLa carcinoma cells overexpressing antiapoptotic protein bcl-2 Biochemistry (Moscow) 2008, 73 (3) 358-362
57. Dhanasekaran, D. N.; Reddy, E. P. JNK signaling in apoptosis Oncogene 2008, 27 (48) 6245-6251
58. Guan, B.; Yue, P.; Lotan, R.; Sun, S.-Y. Evidence that the human death receptor 4 is regulated by activator protein 1 Oncogene 2002, 21 (20) 3121-3129
59. Mahalingam, D.; Keane, M.; Pirianov, G.; Mehmet, H.; Samali, A.; Szegezdi, E. Differential activation of JNK1 isoforms by TRAIL receptors modulate apoptosis of colon cancer cell lines Br. J. Cancer 2009, 100 (9) 1415-1424
60. Mucha, S. R.; Rizzani, A.; Gerbes, A. L.; Camaj, P.; Thasler, W. E.; Bruns, C. J.; Eichhorst, S. T.; Gallmeier, E.; Kolligs, F. T.; Göke, B.; De Toni, E. N. JNK inhibition sensitises hepatocellular carcinoma cells but not normal hepatocytes to the TNF-related apoptosis-inducing ligand Gut 2009, 58 (5) 688-698
61. Beurel, E.; Blivet-Van Eggelpoël, M.-J.; Kornprobst, M.; Moritz, S.; Delelo, R.; Paye, F.; Housset, C.; Desbois-Mouthon, C. GSK-3β inhibition by lithium confers resistance to chemotherapy-induced apoptosis through the repression of CD95 (Fas/APO-1) expression Biochem. Pharmacol. 2009, 77 (1) 54-64
62. Sánchez-Pérez, T.; Ortiz-Ferrón, G.; López-Rivas, A. Mitotic arrest and JNK-induced proteasomal degradation of FLIP and Mcl-1 are key events in the sensitization of breast tumor cells to TRAIL by antimicrotubule agents Cell Death Differ. 2010, 17 (5) 883-894
63. Vermeulen, K.; Berneman, Z. N.; Van Bockstaele, D. R. Cell cycle and apoptosis Cell Proliferation 2003, 36 (3) 165-175
64. Kim, E. H.; Kim, S. U.; Shin, D. Y.; Choi, K. S. Roscovitine sensitizes glioma cells to TRAIL-mediated apoptosis by downregulation of survivin and XIAP Oncogene 2004, 23 (2) 446-456
65. Festa, M.; Petrella, A.; Alfano, S.; Parente, L. R-roscovitine sensitizes anaplastic thyroid carcinoma cells to TRAIL-induced apoptosis via regulation of IKK/NF-kappaB pathway Int. J. Cancer 2009, 124 (11) 2728-2736
66. Ortiz-Ferrón, G.; Yerbes, R.; Eramo, A.; López- Pérez, A. I.; De Maria, R.; López-Rivas, A. Roscovitine sensitizes breast cancer cells to TRAIL-induced apoptosis through a pleiotropic mechanism Cell Res. 2008, 18 (6) 664-676
67. Retzer-Lidl, M.; Schmid, R. M.; Schneider, G. Inhibition of CDK4 impairs proliferation of pancreatic cancer cells and sensitizes towards TRAIL-induced apoptosis via downregulation of survivin Int. J. Cancer 2007, 121 (1) 66-75
68. Ham, Y.-M.; Choi, K.-J.; Song, S.-Y.; Jin, Y.-H.; Chun, M.-W.; Lee, S.-K. Xylocydine, a Novel Inhibitor of Cyclin-Dependent Kinases, Prevents the Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand-Induced Apoptotic Cell Death of SK-HEP-1 Cells J. Pharmacol. Exp. Ther. 2004, 308 (3) 814-819
69. Dey, A.; Tergaonkar, V.; Lane, D. P. Double-edged swords as cancer therapeutics: Simultaneously targeting p53 and NF-kappaB pathways Nat. Rev. Drug Discovery 2008, 7 (12) 1031-1040
70. Gross, A.; Li, R.; Majid, T.; Moorcroft, N.; Yu, K.; Zilberstein, A. Preparation of tetrahydrocarboline derivatives as Eg5 inhibitors for treating cell proliferation disorders. PCT Int. Appl. WO 2011084439, Dec 15, 2010
71. Chem. Abstr. 2011, 155, 182041.
72. Endow, S. A. Microtubule motors in spindle and chromosome motility Eur. J. Biochem. 1999, 262 (1) 12-18
73. Chin, G. M.; Herbst, R. Induction of apoptosis by monastrol, an inhibitor of the mitotic kinesin Eg5, is independent of the spindle checkpoint Mol. Cancer Ther. 2006, 5 (10) 2580-2591
74. UniProt Knowledgebase (UniProtKB). UniProt release 2013-11. http://www.uniprot.org (accessed December 2, 2013).
75. Flaherty, D. B.; Soria, J. P.; Tomasiewicz, H. G.; Wood, J. G. Phosphorylation of human Tau protein by microtubule-associated kinases: GSK3β and cdk5 are key participants J. Neurosci. Res. 2000, 62 (3) 463-472
76. Hannak, E.; Kirkham, M.; Hyman, A. A.; Oegema, K. Aurora-A kinase is required for centrosome maturation in Caenorhabditis elegans J. Cell Biol. 2001, 155 (7) 1109-1116
77. Wang, Y.; Bolton, E.; Dracheva, S.; Karapetyan, K.; Shoemaker, B. A.; Suzek, T. O.; Wang, J.; Xiao, J.; Zhang, J.; Bryant, S. H. An overview of the PubChem BioAssay resource Nucleic Acids Res. 2010, 38 (Jan) D 255-266
78. Mehta, C. R.; Senchaudhuri, P. Conditional versus Unconditional Exact Tests for Comparing Two Binomials. http://www.cytel.com/Papers/twobinomials.pdf (accessed September 22, 2013).
79. Schaefer, C. F.; Anthony, K.; Krupa, S.; Buchoff, J.; Day, M.; Hannay, T.; Buetow, K. H. PID: The Pathway Interaction Database Nucleic Acids Res. 2009, 37, D 674-679
80. Kanehisa, M.; Goto, S.; Sato, Y.; Furumichi, M.; Tanabe, M. KEGG for integration and interpretation of large-scale molecular data sets Nucleic Acids Res. 2012, 40 (Jan) D109-114
81. Kanehisa, M.; Goto, S. KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res. 2000, 28 (1) 27-30
82. Garyantes, T.; Li, Z.; Yan, Y.; Anthony, J.; Yu, J.; Zilberstein, A. DNA fragmentation assay using DNA intercalators. PCT Int. Appl. WO 2007149896, June 20, 2007
83. Chem. Abstr. 2007, 148, 96018.