Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Perspective
  • Published:

Navigating cancer network attractors for tumor-specific therapy

Abstract

Cells employ highly dynamic signaling networks to drive biological decision processes. Perturbations to these signaling networks may attract cells to new malignant signaling and phenotypic states, termed cancer network attractors, that result in cancer development. As different cancer cells reach these malignant states by accumulating different molecular alterations, uncovering these mechanisms represents a grand challenge in cancer biology. Addressing this challenge will require new systems-based strategies that capture the intrinsic properties of cancer signaling networks and provide deeper understanding of the processes by which genetic lesions perturb these networks and lead to disease phenotypes. Network biology will help circumvent fundamental obstacles in cancer treatment, such as drug resistance and metastasis, empowering personalized and tumor-specific cancer therapies.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Properties of cancer signaling networks.
Figure 2: Challenges in cancer network biology.
Figure 3: Network-attacking cancer mutations.
Figure 4: Traditional versus network biology approaches.
Figure 5: Personalized cancer network biology.

Similar content being viewed by others

References

  1. Nash, J.F. Equilibrium points in N-person games. Proc. Natl. Acad. Sci. USA 36, 48–49 (1950).

    Article  CAS  Google Scholar 

  2. Nash, J.F. Non-cooperative games. Ann. Math. 54, 286–295 (1951).

    Article  Google Scholar 

  3. Hanahan, D. & Weinberg, R.A. Hallmarks of cancer: the next generation. Cell 144, 646–674 (2011).

    Article  CAS  Google Scholar 

  4. Hanahan, D. & Weinberg, R.A. The hallmarks of cancer. Cell 100, 57–70 (2000).

    Article  CAS  Google Scholar 

  5. Davies, H. et al. Mutations of the BRAF gene in human cancer. Nature 417, 949–954 (2002).

    Article  CAS  Google Scholar 

  6. Stratton, M.R., Campbell, P.J. & Futreal, P.A. The cancer genome. Nature 458, 719–724 (2009).

    Article  CAS  Google Scholar 

  7. Ding, L. et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 481, 506–510 (2012).

    Article  CAS  Google Scholar 

  8. Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366, 883–892 (2012).

    Article  CAS  Google Scholar 

  9. Hou, Y. et al. Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell 148, 873–885 (2012).

    Article  CAS  Google Scholar 

  10. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609–615 (2011).

  11. Wu, M., Pastor-Pareja, J.C. & Xu, T. Interaction between RasV12 and scribbled clones induces tumour growth and invasion. Nature 463, 545–548 (2010).

    Article  CAS  Google Scholar 

  12. Ng, P.C. & Henikoff, S. Predicting the effects of amino acid substitutions on protein function. Annu. Rev. Genomics Hum. Genet. 7, 61–80 (2006).

    Article  CAS  Google Scholar 

  13. Dixit, A. et al. Sequence and structure signatures of cancer mutation hotspots in protein kinases. PLoS ONE 4, e7485 (2009).

    Article  Google Scholar 

  14. Pazos, F. & Bang, J.-W. Computational prediction of functionally important regions in proteins. Curr. Bioinform. 1, 15–23 (2006).

    Article  CAS  Google Scholar 

  15. Fowler, D.M. et al. High-resolution mapping of protein sequence-function relationships. Nat. Methods 7, 741–746 (2010).

    Article  CAS  Google Scholar 

  16. Jensen, L.J. et al. Ab initio prediction of human orphan protein function from post-translational modifications and localization features. J. Mol. Biol. 319, 1257–1265 (2002).

    Article  CAS  Google Scholar 

  17. Socolich, M. et al. Evolutionary information for specifying a protein fold. Nature 437, 512–518 (2005).

    Article  CAS  Google Scholar 

  18. Russ, W., Lowery, D., Mishra, P., Yaffe, M. & Ranganathan, R. Natural-like function in artificial WW domains. Nature 437, 579–583 (2005).

    Article  CAS  Google Scholar 

  19. Puntervoll, P. et al. ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res. 31, 3625–3630 (2003).

    Article  CAS  Google Scholar 

  20. Lim, W.A. & Pawson, T. Phosphotyrosine signaling: evolving a new cellular communication system. Cell 142, 661–667 (2010).

    Article  CAS  Google Scholar 

  21. Seet, B.T., Dikic, I., Zhou, M.M. & Pawson, T. Reading protein modifications with interaction domains. Nat. Rev. Mol. Cell Biol. 7, 473–483 (2006).

    Article  CAS  Google Scholar 

  22. Halabi, N., Rivoire, O., Leibler, S. & Ranganathan, R. Protein sectors: Evolutionary units of three-dimensional structure. Cell 138, 774–786 (2009).

    Article  CAS  Google Scholar 

  23. Reynolds, K.A., McLaughlin, R. & Ranganathan, R. Hot spots for allosteric regulation on protein surfaces. Cell 147, 1564–1575 (2011).

    Article  CAS  Google Scholar 

  24. Wan, P.T. et al. Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. Cell 116, 855–867 (2004).

    Article  CAS  Google Scholar 

  25. Janes, K.A. et al. A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310, 1646–1653 (2005).

    Article  CAS  Google Scholar 

  26. Lei, K. & Davis, R.J. JNK phosphorylation of Bim-related members of the Bcl2 family induces Bax-dependent apoptosis. Proc. Natl. Acad. Sci. USA 100, 2432–2437 (2003).

    Article  CAS  Google Scholar 

  27. Lamb, J.A. et al. JunD mediates survival signaling by the JNK signal transduction pathway. Mol. Cell 11, 1479–1489 (2003).

    Article  CAS  Google Scholar 

  28. Abreu-Martin, M.T. et al. Fas activates the JNK pathway in human colonic epithelial cells: lack of a direct role in apoptosis. Am. J. Physiol. 276, G599 (1999).

    CAS  PubMed  Google Scholar 

  29. Jeong, H., Mason, S.P., Barabasi, A.L. & Oltvai, Z.N. Lethality and centrality in protein networks. Nature 411, 41–42 (2001).

    Article  CAS  Google Scholar 

  30. Shah, S.P. et al. The clonal and mutational evolution spectrum of primary triplenegative breast cancers. Nature advance online publication, doi:10.1038/nature10933 (4 April 2012).

    Google Scholar 

  31. Kauffman, S. & Levin, S. Towards a general theory of adaptive walks on rugged landscapes. J. Theor. Biol. 128, 11–45 (1987).

    Article  CAS  Google Scholar 

  32. Kauffman, S.A. & Weinberger, E.D. The NK model of rugged fitness landscapes and its application to maturation of the immune response. J. Theor. Biol. 141, 211–245 (1989).

    Article  CAS  Google Scholar 

  33. Uribesalgo, I., Benitah, S.A. & Di Croce, L. From oncogene to tumor suppressor: The dual role of Myc in leukemia. Cell Cycle 11, 1757–1764 (2012).

    Article  CAS  Google Scholar 

  34. Yang, L., Han, Y., Saurez Saiz, F. & Minden, M.D. A tumor suppressor and oncogene: the WT1 story. Leukemia 21, 868–876 (2007).

    Article  CAS  Google Scholar 

  35. Ellis, M.J. et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature 486, 353–360 (2012).

    Article  CAS  Google Scholar 

  36. Curtis, C. et al. The genomic and transcriptomic architecture of 2000 breast tumours reveals novel subgroups. Nature 486, 346–352 (2012).

    Article  CAS  Google Scholar 

  37. Kan, Z. et al. Diverse somatic mutation patterns and pathway alterations in human cancers. Nature 466, 869–873 (2010).

    Article  CAS  Google Scholar 

  38. Greenman, C. et al. Pattern of somatic mutation in human cancer genomes. Nature 446, 153–158 (2007).

    Article  CAS  Google Scholar 

  39. Waddington, C.H. The Strategy of the Genes: a Discussion of Some Aspects of Theoretical Biology (Allen & Unwin, 1957).

    Google Scholar 

  40. Huang, S. & Ingber, D.E. Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks. Exp. Cell Res. 261, 91–103 (2000).

    Article  CAS  Google Scholar 

  41. Luo, J., Solimini, N.L. & Elledge, S.J. Principles of cancer therapy: oncogene and non-oncogene addiction. Cell 136, 823–837 (2009).

    Article  CAS  Google Scholar 

  42. Songyang, Z. et al. Catalytic specificity of protein-tyrosine kinases is critical for selective signaling. Nature 373, 536–539 (1995).

    Article  CAS  Google Scholar 

  43. Zhong, Q. et al. Edgetic perturbation models of human inherited disorders. Mol. Syst. Biol. 5, 321 (2009).

    Article  Google Scholar 

  44. Dreze, M. et al. 'Edgetic' perturbation of a C. elegans BCL2 ortholog. Nat. Methods 6, 843–849 (2009).

    Article  CAS  Google Scholar 

  45. Pe'er, D. & Hacohen, N. Principles and strategies for developing network models in cancer. Cell 144, 864–873 (2011).

    Article  CAS  Google Scholar 

  46. Vidal, M., Cusick, M.E. & Barabási, A.-L.L. Interactome networks and human disease. Cell 144, 986–998 (2011).

    Article  CAS  Google Scholar 

  47. Schoeberl, B. et al. Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis. Sci. Signal. 2, ra31 (2009).

    Article  Google Scholar 

  48. Huang, P.H. et al. Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma. Proc. Natl. Acad. Sci. USA 104, 12867–12872 (2007).

    Article  CAS  Google Scholar 

  49. Miller, M.L.L. et al. Linear motif atlas for phosphorylation-dependent signaling. Sci. Signal. 1, ra2+ (2008).

    Google Scholar 

  50. Linding, R. et al. Systematic discovery of in vivo phosphorylation networks. Cell 129, 1415–1426 (2007).

    Article  CAS  Google Scholar 

  51. Mok, J. et al. Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci. Signal. 3, ra12 (2010).

    Article  Google Scholar 

  52. Brinkworth, R.I., Breinl, R.A. & Kobe, B. Structural basis and prediction of substrate specificity in protein serine/threonine kinases. Proc. Natl. Acad. Sci. USA 100, 74–79 (2003).

    Article  CAS  Google Scholar 

  53. Turk, B.E. Understanding and exploiting substrate recognition by protein kinases. Curr. Opin. Chem. Biol. 12, 4–10 (2008).

    Article  CAS  Google Scholar 

  54. Skerker, J.M. et al. Rewiring the specificity of two-component signal transduction systems. Cell 133, 1043–1054 (2008).

    Article  CAS  Google Scholar 

  55. Capra, E.J., Perchuk, B.S., Skerker, J.M. & Laub, M.T. Adaptive mutations that prevent crosstalk enable the expansion of paralogous signaling protein families. Cell 150, 222–232 (2012).

    Article  CAS  Google Scholar 

  56. Zarrinpar, A., Park, S.H. & Lim, W.A. Optimization of specificity in a cellular protein interaction network by negative selection. Nature 426, 676–680 (2003).

    Article  CAS  Google Scholar 

  57. Wang, X. et al. Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat. Biotechnol. 30, 159–164 (2012).

    Article  CAS  Google Scholar 

  58. Brehme, M. et al. Charting the molecular network of the drug target Bcr-Abl. Proc. Natl. Acad. Sci. USA 106, 7414–7419 (2009).

    Article  CAS  Google Scholar 

  59. Wong, K.M.M., Hudson, T.J. & McPherson, J.D. Unraveling the genetics of cancer: genome sequencing and beyond. Annu. Rev. Genomics Hum. Genet. 12, 407–430 (2011).

    Article  CAS  Google Scholar 

  60. Ledford, H. Big science: the cancer genome challenge. Nature 464, 972–974 (2010).

    Article  CAS  Google Scholar 

  61. Bensimon, A., Heck, A.J.R. & Aebersold, R. Mass spectrometry-based proteomics and network biology. Annu. Rev. Biochem. 81, 379–405 (2012).

    Article  CAS  Google Scholar 

  62. Geiger, T., Cox, J., Ostasiewicz, P., Wisniewski, J.R. & Mann, M. Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat. Methods 7, 383–385 (2010).

    Article  CAS  Google Scholar 

  63. Prill, R.J. et al. Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS ONE 5, e9202 (2010).

    Article  Google Scholar 

  64. Meyer, P. et al. Verification of systems biology research in the age of collaborative competition. Nat. Biotechnol. 29, 811–815 (2011).

    Article  CAS  Google Scholar 

  65. Jørgensen, C. et al. Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science 326, 1502–1509 (2009).

    Article  Google Scholar 

  66. Pawson, T. & Linding, R. Network medicine. FEBS Lett. 582, 1266–1270 (2008).

    Article  CAS  Google Scholar 

  67. Chandarlapaty, S. et al. AKT inhibition relieves feedback suppression of receptor tyrosine kinase expression and activity. Cancer Cell 19, 58–71 (2011).

    Article  CAS  Google Scholar 

  68. Lee, M.J. et al. Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell 149, 780–794 (2012).

    Article  CAS  Google Scholar 

  69. Erler, J.T. & Linding, R. Network medicine strikes a blow against breast cancer. Cell 149, 731–733 (2012).

    Article  CAS  Google Scholar 

  70. Navin, N. et al. Tumor evolution inferred by single-cell sequencing. Nature 472, 90–94 (2011).

    Article  CAS  Google Scholar 

  71. Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994–1007 (2012).

    Article  CAS  Google Scholar 

  72. Pedersen, M.W. et al. Sym004: a novel synergistic anti-epidermal growth factor receptor antibody mixture with superior anticancer efficacy. Cancer Res. 70, 588–597 (2010).

    Article  CAS  Google Scholar 

  73. Bendall, S.C. & Nolan, G.P. From single cells to deep phenotypes in cancer. Nat. Biotechnol. 30, 639–647 (2012).

    Article  CAS  Google Scholar 

  74. Roque, F.S. et al. Using electronic patient records to discover disease correlations and stratify patient cohorts. PLOS Comput. Biol. 7, e1002141 (2011).

    Article  CAS  Google Scholar 

  75. Jensen, P.B., Jensen, L.J. & Brunak, S. Mining electronic health records: towards better research applications and clinical care. Nat. Rev. Genet. 13, 395–405 (2012).

    Google Scholar 

  76. Blumenthal, R.D. & Goldenberg, D.M. Methods and goals for the use of in vitro and in vivo chemosensitivity testing. Mol. Biotechnol. 35, 185–197 (2007).

    Article  CAS  Google Scholar 

  77. Hoffman, R.M. Orthotopic mouse models expressing fluorescent proteins for cancer drug discovery. Expert Opin. Drug Discov. 5, 851–866 (2010).

    Article  CAS  Google Scholar 

  78. Gonzalez-Angulo, A.M., Hennessy, B.T. & Mills, G.B. Future of personalized medicine in oncology: a systems biology approach. J. Clin. Oncol. 28, 2777–2783 (2010).

    Article  CAS  Google Scholar 

  79. Hunter, K.W. Mouse models of cancer: does the strain matter? Nat. Rev. Cancer 12, 144–149 (2012).

    Article  CAS  Google Scholar 

  80. Cox, T.R. & Erler, J.T. Remodeling and homeostasis of the extracellular matrix: implications for fibrotic diseases and cancer. Dis. Model. Mech. 4, 165–178 (2011).

    Google Scholar 

  81. WHO. World health organization fact sheet 297 (2012). http://www.who.int/mediacentre/factsheets/fs297/en/

Download references

Acknowledgements

We apologize to our colleagues whose work could not be cited due to space limitations. We thank all members of the C-SIG (DTU), the ErlerLab (BRIC), M. Yaffe (MIT) and N. Brunner (KU) for critical input on this manuscript. R.L. is a Lundbeck Foundation Fellow and is supported by a Sapere Aude Starting Grant from The Danish Council for Independent Research and a Career Development Award from Human Frontier Science Program. J.T.E. is supported by a Hallas Møller Stipend from the Novo Nordisk Foundation. Visit http://www.networkbio.org/, http://www.lindinglab.org/ and http://www.erlerlab.org/ for more information on cancer-related network biology.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Janine T Erler or Rune Linding.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Creixell, P., Schoof, E., Erler, J. et al. Navigating cancer network attractors for tumor-specific therapy. Nat Biotechnol 30, 842–848 (2012). https://doi.org/10.1038/nbt.2345

Download citation

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/nbt.2345

This article is cited by

Search

Quick links

Nature Briefing: Cancer

Sign up for the Nature Briefing: Cancer newsletter — what matters in cancer research, free to your inbox weekly.

Get what matters in cancer research, free to your inbox weekly. Sign up for Nature Briefing: Cancer