Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2015, Article ID 901303, 11 pages
http://dx.doi.org/10.1155/2015/901303
Research Article

Deciphering the Correlation between Breast Tumor Samples and Cell Lines by Integrating Copy Number Changes and Gene Expression Profiles

Department of Central Laboratory, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China

Received 28 November 2014; Revised 16 January 2015; Accepted 26 January 2015

Academic Editor: Xiao Chang

Copyright © 2015 Yi Sun and Qi Liu. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. D. L. Holliday and V. Speirs, “Choosing the right cell line for breast cancer research,” Breast Cancer Research, vol. 13, no. 4, article 215, 2011. View at Publisher · View at Google Scholar · View at Scopus
  2. J.-P. Gillet, A. M. Calcagno, S. Varma et al., “Redefining the relevance of established cancer cell lines to the study of mechanisms of clinical anti-cancer drug resistance,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 46, pp. 18708–18713, 2011. View at Publisher · View at Google Scholar · View at Scopus
  3. R. Sandberg and I. Ernberg, “Assessment of tumor characteristic gene expression in cell lines using a tissue similarity index (TSI),” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 6, pp. 2052–2057, 2005. View at Publisher · View at Google Scholar · View at Scopus
  4. S. Domcke, R. Sinha, D. A. Levine, C. Sander, and N. Schultz, “Evaluating cell lines as tumour models by comparison of genomic profiles,” Nature Communications, vol. 4, article 2126, 2013. View at Publisher · View at Google Scholar · View at Scopus
  5. S. E. Burdall, A. M. Hanby, M. R. J. Lansdown, and V. Speirs, “Breast cancer cell lines: friend or foe?” Breast Cancer Research, vol. 5, no. 2, pp. 89–95, 2003. View at Publisher · View at Google Scholar · View at Scopus
  6. The Cancer Genome Atlas Network, “Comprehensive molecular portraits of human breast tumours,” Nature, vol. 490, no. 7418, pp. 61–70, 2012. View at Publisher · View at Google Scholar
  7. J. Barretina, G. Caponigro, N. Stransky et al., “The cancer cell Line encyclopedia enables predictive modelling of anticancer drug sensitivity,” Nature, vol. 483, no. 7391, pp. 603–607, 2012. View at Publisher · View at Google Scholar · View at Scopus
  8. E. Chaignat, E. A. Yahya-Graison, C. N. Henrichsen et al., “Copy number variation modifies expression time courses,” Genome Research, vol. 21, no. 1, pp. 106–113, 2011. View at Publisher · View at Google Scholar · View at Scopus
  9. L. D. Orozco, S. J. Cokus, A. Ghazalpour et al., “Copy number variation influences gene expression and metabolic traits in mice,” Human Molecular Genetics, vol. 18, no. 21, pp. 4118–4129, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. B. E. Stranger, M. S. Forrest, M. Dunning et al., “Relative impact of nucleotide and copy number variation on gene phenotypes,” Science, vol. 315, no. 5813, pp. 848–853, 2007. View at Publisher · View at Google Scholar · View at Scopus
  11. T.-P. Lu, L.-C. Lai, M.-H. Tsai et al., “Integrated analyses of copy number variations and gene expression in lung adenocarcinoma,” PLoS ONE, vol. 6, no. 9, Article ID e24829, 2011. View at Publisher · View at Google Scholar · View at Scopus
  12. P. Maisonneuve, D. Disalvatore, N. Rotmensz et al., “Proposed new clinicopathological surrogate definitions of luminal A and luminal B (HER2-negative) intrinsic breast cancer subtypes,” Breast Cancer Research, vol. 16, no. 3, article R65, 2014. View at Google Scholar
  13. M. Yanagawa, K. Ikemot, S. Kawauchi et al., “Luminal A and luminal B (HER2 negative) subtypes of breast cancer consist of a mixture of tumors with different genotype,” BMC Research Notes, vol. 5, article 376, 2012. View at Publisher · View at Google Scholar · View at Scopus
  14. R. C. Gentleman, V. J. Carey, D. M. Bates et al., “Bioconductor: open software development for computational biology and bioinformatics,” Genome Biology, vol. 5, no. 10, article R80, 2004. View at Publisher · View at Google Scholar · View at Scopus
  15. C. H. Mermel, S. E. Schumacher, B. Hill, M. L. Meyerson, R. Beroukhim, and G. Getz, “GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers,” Genome Biology, vol. 12, no. 4, article R41, 2011. View at Publisher · View at Google Scholar · View at Scopus
  16. G. Lenz, G. W. Wright, N. C. T. Emre et al., “Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 36, pp. 13520–13525, 2008. View at Publisher · View at Google Scholar · View at Scopus
  17. R. Agren, S. Bordel, A. Mardinoglu, N. Pornputtapong, I. Nookaew, and J. Nielsen, “Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT,” PLoS Computational Biology, vol. 8, no. 5, Article ID e1002518, 2012. View at Publisher · View at Google Scholar · View at Scopus
  18. W. da Huang, B. T. Sherman, and R. A. Lempicki, “Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources,” Nature Protocols, vol. 4, no. 1, pp. 44–57, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. C. Choi and D. M. Helfman, “The Ras-ERK pathway modulates cytoskeleton organization, cell motility and lung metastasis signature genes in MDA-MB-231 LM2,” Oncogene, vol. 33, no. 28, pp. 3668–3676, 2013. View at Publisher · View at Google Scholar · View at Scopus
  20. H. Al-Hussaini, D. Subramanyam, M. Reedijk, and S. S. Sridhar, “Notch signaling pathway as a therapeutic target in breast cancer,” Molecular Cancer Therapeutics, vol. 10, no. 1, pp. 9–15, 2011. View at Publisher · View at Google Scholar · View at Scopus
  21. R. Lamb, M. P. Ablett, K. Spence, G. Landberg, A. H. Sims, and R. B. Clarke, “Wnt pathway activity in breast cancer sub-types and stem-like cells,” PLoS ONE, vol. 8, no. 7, Article ID e67811, 2013. View at Publisher · View at Google Scholar · View at Scopus
  22. Y. Zhou, S. Eppenberger-Castori, U. Eppenberger, and C. C. Benz, “The NFkappaB pathway and endocrine-resistant breast cancer,” Endocrine-Related Cancer, vol. 12, supplement 1, pp. S37–S46, 2005. View at Publisher · View at Google Scholar · View at Scopus
  23. M. Kanehisa and S. Goto, “KEGG: kyoto encyclopedia of genes and genomes,” Nucleic Acids Research, vol. 28, no. 1, pp. 27–30, 2000. View at Publisher · View at Google Scholar · View at Scopus
  24. V. Pihur and S. Datta, “RankAggreg, an R package for weighted rank aggregation,” BMC Bioinformatics, vol. 10, article 62, 2009. View at Publisher · View at Google Scholar · View at Scopus
  25. S. P. Shah, A. Roth, R. Goya et al., “The clonal and mutational evolution spectrum of primary triple-negative breast cancers,” Nature, vol. 486, no. 7403, pp. 395–399, 2012. View at Publisher · View at Google Scholar · View at Scopus
  26. Y. Kimura, T. Noguchi, K. Kawahara, K. Kashima, T. Daa, and S. Yokoyama, “Genetic alterations in 102 primary gastric cancers by comparative genomic hybridization: gain of 20q and loss of 18q are associated with tumor progression,” Modern Pathology, vol. 17, no. 11, pp. 1328–1337, 2004. View at Publisher · View at Google Scholar · View at Scopus
  27. L. A. Emens and N. E. Davidson, “Trastuzumab in breast cancer,” Oncology, vol. 18, no. 9, pp. 1117–1128, 2004. View at Google Scholar · View at Scopus
  28. J. Baselga, “Herceptin alone or in combination with chemotherapy in the treatment of HER2-positive metastatic breast cancer: pivotal trials,” Oncology, vol. 61, supplement 2, pp. 14–21, 2001. View at Google Scholar · View at Scopus
  29. C. L. Vogel, M. A. Cobleigh, D. Tripathy et al., “First-line herceptin monotherapy in metastatic breast cancer,” Oncology, vol. 61, supplement 2, pp. 37–42, 2001. View at Publisher · View at Google Scholar · View at Scopus
  30. D. Ferreira, F. Adega, and R. Chaves, “The importance of cancer cell Lines as in vitro models in cancer methylome analysis and anticancer drugs testing,” in Oncogenomics and Cancer Proteomics—Novel Approaches in Biomarkers Discovery and Therapeutic Targets in Cancer, InTech, Rijeka, Croatia, 2013. View at Publisher · View at Google Scholar
  31. H. Kennecke, R. Yerushalmi, R. Woods et al., “Metastatic behavior of breast cancer subtypes,” Journal of Clinical Oncology, vol. 28, no. 20, pp. 3271–3277, 2010. View at Publisher · View at Google Scholar · View at Scopus
  32. R. Yerushalmi, S. Tyldesley, H. Kennecke et al., “Tumor markers in metastatic breast cancer subtypes: frequency of elevation and correlation with outcome,” Annals of Oncology, vol. 23, no. 2, pp. 338–345, 2012. View at Publisher · View at Google Scholar · View at Scopus
  33. L. Cheng, P. Wang, S. Yang et al., “Identification of genes with a correlation between copy number and expression in gastric cancer,” BMC Medical Genomics, vol. 5, article 14, 2012. View at Publisher · View at Google Scholar · View at Scopus
  34. R. X. Menezes, M. Boetzer, M. Sieswerda, G.-J. B. van Ommen, and J. M. Boer, “Integrated analysis of DNA copy number and gene expression microarray data using gene sets,” BMC Bioinformatics, vol. 10, article 203, 2009. View at Publisher · View at Google Scholar · View at Scopus
  35. P. Peterlongo, J. Chang-Claude, K. B. Moysich et al., “Candidate genetic modifiers for breast and ovarian cancer risk in BRCA1 and BRCA2 mutation carriers,” Cancer Epidemiology, Biomarkers & Prevention, vol. 24, no. 1, pp. 308–316, 2014. View at Publisher · View at Google Scholar
  36. I. M. Collins, R. L. Milne, P. C. Weideman et al., “Preventing breast and ovarian cancers in high-risk BRCA1 and BRCA2 mutation carriers,” The Medical Journal of Australia, vol. 199, no. 10, pp. 680–683, 2013. View at Publisher · View at Google Scholar · View at Scopus
  37. G. Ciriello, M. L. Miller, B. A. Aksoy, Y. Senbabaoglu, N. Schultz, and C. Sander, “Emerging landscape of oncogenic signatures across human cancers,” Nature Genetics, vol. 45, no. 10, pp. 1127–1133, 2013. View at Publisher · View at Google Scholar · View at Scopus