Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Gene Expression Signatures for Compound Response in Cancers

  • He, Ningning (Department of Biological Sciences, Sookmyung Women's University) ;
  • Yoon, Suk-Joon (Department of Biological Sciences, Sookmyung Women's University)
  • Received : 2011.11.19
  • Accepted : 2011.12.08
  • Published : 2011.12.31
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Abstract

Recent trends in generating multiple, large-scale datasets provide new challenges to manipulating the relationship of different types of components, such as gene expression and drug response data. Integrative analysis of compound response and gene expression datasets generates an opportunity to capture the possible mechanism of compounds by using signature genes on diverse types of cancer cell lines. Here, we integrated datasets of compound response and gene expression profiles on NCI60 cell lines and constructed a network, revealing the relationship for 801 compounds and 341 gene probes. As examples, obtusol, which shows an exclusive sensitivity on a small number of colon cell lines, is related to a set of gene probes that have unique overexpression in colon cell lines. We also found that the SLC7A11 gene, a direct target of miR-26b, might be a key element in understanding the action of many diverse classes of anticancer compounds. We demonstrated that this network might be useful for studying the mechanisms of varied compound response on diverse cancer cell lines.

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References

  1. Ballif, B.C., Rosenfeld, J.A., Traylor, R., Theisen, A., Bader, P.I., Ladda, R.L., Sell, S.L., Steinraths, M., Surti, U., McGuire, M., Williams, S., Farrell, S.A., Filiano, J., Schnur, R.E., Coffey, L.B., Tervo, R.C., Stroud, T., Marble, M., Netzloff, M., Hanson, K., Aylsworth, A.S., Bamforth, J.S., Babu, D., Niyazov, D.M., Ravnan, J.B., Schultz, R.A., Lamb, A.N., Torchia, B.S., Bejjani, B.A., and Shaffer, L.G. (2011). High-resolution array CGH defines critical regions and candidate genes for microcephaly, abnormalities of the corpus callosum, and seizure phenotypes in patients with microdeletions of 1q43q44. Hum. Genet. [Epub ahead of print].
  2. Blower, P.E., Verducci, J.S., Lin, S., Zhou, J., Chung, J.H., Dai, Z., Liu, C.G., Reinhold, W., Lorenzi, P.L., Kaldjian, E.P., Croce, C.M., Weinstein, J.N., and Sadee, W. (2007). MicroRNA expression profiles for the NCI-60 cancer cell panel. Mol. Cancer Ther. 6, 1483-1491. https://doi.org/10.1158/1535-7163.MCT-07-0009
  3. Chu, C.W., Holliday, J.D., and Willett, P. (2009). Effect of data standardization on chemical clustering and similarity searching. J. Chem. Inf. Model 49, 155-161. https://doi.org/10.1021/ci800224h
  4. Cote, P.N. and Goodman, L. (1973). Glucopyranosides derived from 2-hydroxy-1,4-naphthoquinones. Carbohydr. Res. 26, 247-251. https://doi.org/10.1016/S0008-6215(00)85047-8
  5. Dai, Z., Huang, Y., Sadee, W., and Blower, P. (2007). Chemoinformatics analysis identifies cytotoxic compounds susceptible to chemoresistance mediated by glutathione and cystine/glutamate transport system xc. J. Med. Chem. 50, 1896-1906. https://doi.org/10.1021/jm060960h
  6. Davoren, P.A., McNeill, R.E., Lowery, A.J., Kerin, M.J., and Miller, N. (2008). Identification of suitable endogenous control genes for microRNA gene expression analysis in human breast cancer. BMC Mol. Biol. 9, 76. https://doi.org/10.1186/1471-2199-9-76
  7. Deeken, J.F., Robey, R.W., Shukla, S., Steadman, K., Chakraborty, A.R., Poonkuzhali, B., Schuetz, E.G., Holbeck, S., Ambudkar, S.V., and Bates, S.E. (2009). Identification of compounds that correlate with ABCG2 transporter function in the National Cancer Institute Anticancer Drug Screen. Mol. Pharmacol. 76, 946-956. https://doi.org/10.1124/mol.109.056192
  8. Ehrich, M., Turner, J., Gibbs, P., Lipton, L., Giovanneti, M., Cantor, C., and van den Boom, D. (2008). Cytosine methylation profiling of cancer cell lines. Proc. Natl. Acad. Sci. U.S.A. 105, 4844-4849. https://doi.org/10.1073/pnas.0712251105
  9. Garcia, O., Saveanu, C., Cline, M., Fromont-Racine, M., Jacquier, A., Schwikowski, B., and Aittokallio, T. (2007). GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics 23, 394-396. https://doi.org/10.1093/bioinformatics/btl605
  10. Gravuer, K., von Wettberg, E.J., and Schmitt, J. (2003). Dispersal biology of Liatris scariosa var. novae-angliae (Asteraceae), a rare New England grassland perennial. Am. J. Bot. 90, 1159-1167. https://doi.org/10.3732/ajb.90.8.1159
  11. Huang, Y. and Hall, I.H. (1996). Antineoplastic activities of alpha-methyl-beta-alkylaminopropiophenone derivatives in tissue culture cells. Anticancer Res. 16, 3589-3595.
  12. Ikediobi, O.N., Davies, H., Bignell, G., Edkins, S., Stevens, C., O'Meara, S., Santarius, T., Avis, T., Barthorpe, S., Brackenbury, L., Buck, G., Butler, A., Clements, J., Cole, J., Dicks, E., Forbes, S., Gray, K., Halliday, K., Harrison, R., Hills, K., Hinton, J., Hunter, C., Jenkinson, A., Jones, D., Kosmidou, V., Lugg, R., Menzies, A., Mironenko, T., Parker, A., Perry, J., Raine, K., Richardson, D., Shepherd, R., Small, A., Smith, R., Solomon, H., Stephens, P., Teague, J., Tofts, C., Varian, J., Webb, T., West, S., Widaa, S., Yates, A., Reinhold, W., Weinstein, J.N., Stratton, M.R., Futreal, P.A., and Wooster, R. (2006). Mutation analysis of 24 known cancer genes in the NCI-60 cell line set. Mol. Cancer Ther. 5, 2606-2612. https://doi.org/10.1158/1535-7163.MCT-06-0433
  13. Jiang, G., Cao, F., Ren, G., Gao, D., Bhakta, V., Zhang, Y., Cao, H., Dong, Z., Zang, W., Zhang, S., Wong, H.H., Hiley, C., Crnogorac-Jurcevic, T., Lemoine, N.R., and Wang, Y. (2010). PRSS3 promotes tumour growth and metastasis of human pancreatic cancer. Gut 59, 1535-1544. https://doi.org/10.1136/gut.2009.200105
  14. Jobson, A.G., Cardellina, J.H.2nd, Scudiero, D., Kondapaka, S., Zhang, H., Kim, H., Shoemaker, R., and Pommier, Y. (2007). Identification of a Bis-guanylhydrazone [4,4'-Diacetyldiphenylurea- bis(guanylhydrazone); NSC 109555] as a novel chemotype for inhibition of Chk2 kinase. Mol. Pharmacol. 72, 876-884. https://doi.org/10.1124/mol.107.035832
  15. Lee, J.S., Paull, K., Alvarez, M., Hose, C., Monks, A., Grever, M., Fojo, A.T., and Bates, S.E. (1994). Rhodamine efflux patterns predict P-glycoprotein substrates in the National Cancer Institute drug screen. Mol. Pharmacol. 46, 627-638.
  16. Liu, W., Wu, X., Zhang, W., Montenegro, R.C., Fackenthal, D.L., Spitz, J.A., Huff, L.M., Innocenti, F., Das, S., Cook, E.H.Jr., Cox NJ, Bates, S.E., and Ratain, M.J. (2007). Relationship of EGFR mutations, expression, amplification, and polymorphisms to epidermal growth factor receptor inhibitors in the NCI60 cell lines. Clin. Cancer Res. 13, 6788-6795. https://doi.org/10.1158/1078-0432.CCR-07-0547
  17. Liu, X.X., Li, X.J., Zhang, B., Liang, Y.J., Zhou, C.X., Cao, D.X., He, M., Chen, G.Q., He, J.R., and Zhao, Q. (2011). MicroRNA-26b is underexpressed in human breast cancer and induces cell apoptosis by targeting SLC7A11. FEBS Lett. 585, 1363-1367. https://doi.org/10.1016/j.febslet.2011.04.018
  18. Merico, D., Gfeller, D., and Bader, G.D. (2009). How to visually interpret biological data using networks. Nat. Biotechnol. 27, 921-924. https://doi.org/10.1038/nbt.1567
  19. Nishizuka, S., Charboneau, L., Young, L., Major, S., Reinhold, W.C., Waltham, M., Kouros-Mehr, H., Bussey, K.J., Lee, J.K., Espina, V., Munson, P.J., Petricoin, E.3rd., Liotta, L.A., and Weinstein, J.N. (2003). Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc. Natl. Acad. Sci. U.S.A. 100, 14229-14234. https://doi.org/10.1073/pnas.2331323100
  20. Pe'er, D. and Hacohen, N. (2011). Principles and strategies for developing network models in cancer. Cell. 144, 864-873. https://doi.org/10.1016/j.cell.2011.03.001
  21. Peng, H., Kim, D.I., Sarkaria, J.N., Cho, Y.S., Abraham, R.T., and Zalkow, L.H. (2002). Novel pyrrolo-quinoline derivatives as potent inhibitors for PI3-kinase related kinases. Bioorg. Med. Chem. 10, 167-174. https://doi.org/10.1016/S0968-0896(01)00260-7
  22. Scudiero, D.A., Shoemaker, R.H., Paull, K.D., Monks, A., Tierney, S., Nofziger, T.H., Currens, M.J., Seniff, D., and Boyd, M.R. (1988). Evaluation of a soluble tetrazolium/ formazan assay for cell growth and drug sensitivity in culture using human and other tumor cell lines. Cancer Res. 48, 4827-4833.
  23. Shankavaram, U.T., Reinhold, W.C., Nishizuka, S., Major, S., Morita, D., Chary, K.K., Reimers, M.A., Scherf, U., Kahn, A., Dolginow, D., Cossman, J., Kaldjian, E.P., Scudiero, D.A., Petricoin, E., Liotta, L., Lee, J.K., and Weinstein, J.N. (2007). Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol. Cancer Ther. 6, 820-832. https://doi.org/10.1158/1535-7163.MCT-06-0650
  24. Shoemaker, R.H. (2006). The NCI60 human tumour cell line anticancer drug screen. Nat. Rev. Cancer 6, 813-823. https://doi.org/10.1038/nrc1951
  25. Somers-Edgar, T.J., Taurin, S., Larsen, L., Chandramouli, A., Nelson, M.A., and Rosengren, R.J. (2011). Mechanisms for the activity of heterocyclic cyclohexanone curcumin derivatives in estrogen receptor negative human breast cancer cell lines. Invest. New. Drugs. 29, 87-97. https://doi.org/10.1007/s10637-009-9339-0
  26. Svechnikova, I., Svechnikov, K., and Soder, O. (2007). The influence of di-(2-ethylhexyl) phthalate on steroidogenesis by the ovarian granulosa cells of immature female rats. J. Endocrinol. 194, 603-609. https://doi.org/10.1677/JOE-07-0238
  27. Takigawa, I., Tsuda, K., and Mamitsuka, H. (2011). Mining significant substructure pairs for interpreting polypharmacology in drug-target network. PLoS One 6, e16999. https://doi.org/10.1371/journal.pone.0016999
  28. Vairappan, C.S. (2003). Potent antibacterial activity of halogenated metabolites from Malaysian red algae, Laurencia majuscula (Rhodomelaceae, Ceramiales). Biomol. Eng. 20, 255-259. https://doi.org/10.1016/S1389-0344(03)00067-4
  29. Vairappan, C.S., Daitoh, M., Suzuki, M., Abe, T., and Masuda, M. (2001). Antibacterial halogenated metabolites from the Malaysian Laurencia species. Phytochemistry 58, 291-297. https://doi.org/10.1016/S0031-9422(01)00243-6
  30. Weinstein, J.N. (2006). Spotlight on molecular profiling: Integromic analysis of the NCI-60 cancer cell lines. Mol. Cancer Ther. 5, 2601-2605. https://doi.org/10.1158/1535-7163.MCT-06-0640
  31. Williams, G.W., Barton, G.M., White, A.A., and Won, H. (1976). Cluster analysis applied to symptom ratings of psychiatric patients: an evaluation of its predictive ability. Br. J. Psychiatry 129, 178-185. https://doi.org/10.1192/bjp.129.2.178
  32. Xu, K. and Cote, T.R. (2011). Database identifies FDA-approved drugs with potential to be repurposed for treatment of orphan diseases. Brief. Bioinform 12, 341-345. https://doi.org/10.1093/bib/bbr006
  33. Zhou, L. and Rocke, D.M. (2005). An expression index for Affymetrix GeneChips based on the generalized logarithm. Bioinformatics 21, 3983-3989. https://doi.org/10.1093/bioinformatics/bti665