Skip to main content

The Apoptotic Signaling Network Dynamically Interprets the Outputs of Individual Signaling Pathways in an Early Analog and Late Digital Manner

  • Conference paper
Systems Biology

Changes in cell behavior are determined by a network of proteins that actively transmits signaling information (Irish et al., 2004; Jordan et al., 2000; Pawson, 2004). Modulation of total levels of key proteins, as well as their posttranslational states and enzymatic activities, could all potentially act as “molecular signals” that are monitored and interpreted. To understand how complex signal-transduction events control cell responses, these molecular signals must be measured dynamically and then mapped to downstream changes in cell outcome (Gaudet et al., 2005; Janes et al., 2005). Such approaches can accurately predict diverse cellular responses and suggest how molecular information is organized and propagated within the cell (Miller-Jensen et al., 2007).

One crucial cell decision is whether to die or to survive (Green and Evan, 2002; Kyriakis, 2001; Tran et al., 2004). Apoptosis is a common mechanism of cell death in response to many intrinsic and extrinsic cytotoxic cues such as cytokines and DNA damage (Strasser et al., 2000; Zhou and Elledge, 2000). Neighboring cells can also directly induce apoptosis in a target cell by secreting prodeath factors. Although cell death is important for normal development and tissue homeostasis, it is irreversible, requiring apoptosis to be tightly controlled. Deregulated apoptosis is known to be involved in many human diseases such as cancer (Rudin and Thompson, 1997; Vaux, 1993).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Aggarwal, B. B. (2003). Signalling pathways of the TNF superfamily: a double-edged sword. Nat Rev Immunol 3:745–756.

    Article  PubMed  CAS  Google Scholar 

  • Alon, U., Camarena, L., Surette, M. G., Aguera y Arcas, B., Liu, Y., Leibler, S., and Stock, J. B. (1998). Response regulator output in bacterial chemotaxis. EMBO J 17:4238–4248.

    Article  PubMed  Google Scholar 

  • Altan-Bonnet, G., and Germain, R. N. (2005). Modeling T cell antigen discrimination based on feedback control of digital ERK responses. PLoS Biol 3:e356.

    Article  PubMed  Google Scholar 

  • Baud, V., and Karin, M. (2001). Signal transduction by tumor necrosis factor and its relatives. Trends Cell Biol 11:372–377.

    Article  PubMed  CAS  Google Scholar 

  • Chansawat, K., Yim, S. C. S., and Miller, T. H. (2006). Nonlinear finite element analysis of a FRP-strengthened reinforced concrete bridge. J Bridge Eng 11:21–32.

    Article  Google Scholar 

  • Deng, Y., Ren, X., Yang, L., Lin, Y., and Wu, X. (2003). A JNK-dependent pathway is required for TNF-alpha-induced apoptosis. Cell 115:61–70.

    Article  PubMed  CAS  Google Scholar 

  • Garcia-Lloret, M. I., Yui, J., Winkler-Lowen, B., and Guilbert, L. J. (1996). Epidermal growth factor inhibits cytokine-induced apoptosis of primary human trophoblasts. J Cell Physiol 167:324–332.

    Article  PubMed  CAS  Google Scholar 

  • Gaudet, S., Janes, K. A., Albeck, J. G., Pace, E. A., Lauffenburger, D. A., and Sorger, P. K. (2005). A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol Cell Proteomics 4:1569–1590.

    Article  PubMed  CAS  Google Scholar 

  • Geladi, P., and Kowalski, B. R. (1986). Partial least-squares regression: a tutorial. Anal Chim Acta 185:1–17.

    Article  CAS  Google Scholar 

  • Green, D. R., and Evan, G. I. (2002). A matter of life and death. Cancer Cell 1:19–30.

    Article  PubMed  CAS  Google Scholar 

  • Hasty, J., McMillen, D., and Collins, J. J. (2002). Engineered gene circuits. Nature (Lond) 420:224–230.

    Article  CAS  Google Scholar 

  • Hood, L., and Galas, D. (2003). The digital code of DNA. Nature (Lond) 421:444–448.

    Article  Google Scholar 

  • Hua, F., Cornejo, M. G., Cardone, M. H., Stokes, C. L., and Lauffenburger, D. A. (2005). Effects of bcl-2 levels on fas signaling-induced caspase-3 activation: molecular genetic tests of computational model predictions. J Immunol 175:985–995.

    PubMed  CAS  Google Scholar 

  • Irish, J. M., Hovland, R., Krutzik, P. O., Perez, O. D., Bruserud, O., Gjertsen, B. T., and Nolan, G. P. (2004). Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell 118:217–228.

    Article  PubMed  CAS  Google Scholar 

  • Janes, K. A., and Yaffe, M. B. (2006). Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol 7:820–828.

    Article  PubMed  CAS  Google Scholar 

  • Janes, K. A., Kelly, J. R., Gaudet, S., Albeck, J. G., Sorger, P. K., and Lauffenburger, D. A. (2004). Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data. J Comput Biol 11:544–561.

    Article  PubMed  CAS  Google Scholar 

  • Janes, K. A., Albeck, J. G., Gaudet, S., Sorger, P. K., Lauffenburger, D. A., and Yaffe, M. B. (2005). A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310:1646–1653.

    Article  PubMed  CAS  Google Scholar 

  • Janes, K. A., Gaudet, S., Albeck, J. G., Nielsen, U. B., Lauffenburger, D. A., and Sorger, P. K. (2006). The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell 124:1225–1239.

    Article  PubMed  CAS  Google Scholar 

  • Jordan, J. D., Landau, E. M., and Iyengar, R. (2000). Signaling networks: the origins of cellular multitasking. Cell 103:193–200.

    Article  PubMed  CAS  Google Scholar 

  • Karin, M., and Ben-Neriah, Y. (2000). Phosphorylation meets ubiquitination: the control of NF-[kappa]B activity. Annu Rev Immunol 18:621–663.

    Article  PubMed  CAS  Google Scholar 

  • Khatir, Z., Lefebvre, S., and Saint-Eve, F. (2007). Experimental and numerical investigations on delayed short-circuit failure mode of single chip IGBT devices. Microelectron Reliab 47:422–428.

    Article  Google Scholar 

  • Kyriakis, J. M. (2001). Life-or-death decisions. Nature (Lond) 414:265–266.

    Article  CAS  Google Scholar 

  • Lamb, J. A., Ventura, J. J., Hess, P., Flavell, R. A., and Davis, R. J. (2003). JunD mediates survival signaling by the JNK signal transduction pathway. Mol Cell 11:1479–1489.

    Article  PubMed  CAS  Google Scholar 

  • Marshall, C. J. (1995). Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation. Cell 80:179–185.

    Article  PubMed  CAS  Google Scholar 

  • McAdams, H. H., and Shapiro, L. (1995). Circuit simulation of genetic networks. Science 269:650–656.

    Article  PubMed  CAS  Google Scholar 

  • McAdams, H. H., and Shapiro, L. (2003). A bacterial cell-cycle regulatory network operating in time and space. Science 301:1874–1877.

    Article  PubMed  CAS  Google Scholar 

  • Micheau, O., and Tschopp, J. (2003). Induction of TNF receptor I-mediated apoptosis via two sequential signaling complexes. Cell 114:181–190.

    Article  PubMed  CAS  Google Scholar 

  • Miller-Jensen, K., Janes, K. A., Brugge, J. S., and Lauffenburger, D. A. (2007). Common effector processing mediates cell-specific responses to stimuli. Nature (Lond) 448:604–608.

    Article  CAS  Google Scholar 

  • Murphy, L. O., and Blenis, J. (2006). MAPK signal specificity: the right place at the right time. Trends Biochem Sci 31:268–275.

    Article  PubMed  CAS  Google Scholar 

  • Pawson, T. (2004). Specificity in signal transduction: from phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell 116:191–203.

    Article  PubMed  CAS  Google Scholar 

  • Price, N. D., Papin, J. A., Schilling, C. H., and Palsson, B. O. (2003). Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol 21:162–169.

    Article  PubMed  CAS  Google Scholar 

  • Remacle-Bonnet, M. M., Garrouste, F. L., Heller, S., Andre, F., Marvaldi, J. L., and Pommier, G. J. (2000). Insulin-like growth factor-I protects colon cancer cells from death factor-induced apoptosis by potentiating tumor necrosis factor alpha-induced mitogen-activated protein kinase and nuclear factor kappaB signaling pathways. Cancer Res 60:2007–2017.

    PubMed  CAS  Google Scholar 

  • Riedl, S. J., and Shi, Y. (2004). Molecular mechanisms of caspase regulation during apoptosis. Nat Rev Mol Cell Biol 5:897–907.

    Article  PubMed  CAS  Google Scholar 

  • Roulston, A., Reinhard, C., Amiri, P., and Williams, L. T. (1998). Early activation of c-Jun N-terminal kinase and p38 kinase regulate cell survival in response to tumor necrosis factor alpha. J Biol Chem 273:10232–10239.

    Article  PubMed  CAS  Google Scholar 

  • Rudin, C. M., and Thompson, C. B. (1997). Apoptosis and disease: regulation and clinical relevance of programmed cell death. Annu Rev Med 48:267–281.

    Article  PubMed  CAS  Google Scholar 

  • Ruf, F., Park, M. J., Hayot, F., Lin, G., Roysam, B., Ge, Y., and Sealfon, S. C. (2006). Mixed analog/digital gonadotrope biosynthetic response to gonadotropin-releasing hormone. J Biol Chem 281:30967–30978.

    Article  PubMed  CAS  Google Scholar 

  • Strasser, A., O'Connor, L., and Dixit, V. M. (2000). Apoptosis signaling. Annu Rev Biochem 69:217–245.

    Article  PubMed  CAS  Google Scholar 

  • Tran, S. E., Meinander, A., and Eriksson, J. E. (2004). Instant decisions: transcription-independent control of death-receptor-mediated apoptosis. Trends Biochem Sci 29:601–608.

    Article  PubMed  CAS  Google Scholar 

  • Truman, C. E., and Booker, J. D. (2007). Analysis of a shrink-fit failure on a gear hub/shaft assembly. Eng Fail Anal 14:557–572.

    Article  Google Scholar 

  • Vaux, D. L. (1993). Toward an understanding of the molecular mechanisms of physiological cell death. Proc Natl Acad Sci USA 90:786–789.

    Article  PubMed  CAS  Google Scholar 

  • Ventura, J. J., Cogswell, P., Flavell, R. A., Baldwin, A. S., Jr., and Davis, R. J. (2004). JNK potentiates TNF-stimulated necrosis by increasing the production of cytotoxic reactive oxygen species. Genes Dev 18:2905–2915.

    Article  PubMed  CAS  Google Scholar 

  • Wajant, H., Pfizenmaier, K., and Scheurich, P. (2003). Tumor necrosis factor signaling. Cell Death Differ 10:45–65.

    Article  PubMed  CAS  Google Scholar 

  • Zhou, B. B., and Elledge, S. J. (2000). The DNA damage response: putting checkpoints in perspective. Nature (Lond) 408:433–439.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer

About this paper

Cite this paper

Janes, K.A., Reinhardt, H.C., Yaffe, M.B. (2009). The Apoptotic Signaling Network Dynamically Interprets the Outputs of Individual Signaling Pathways in an Early Analog and Late Digital Manner. In: Nakanishi, S., Kageyama, R., Watanabe, D. (eds) Systems Biology. Springer, Tokyo. https://doi.org/10.1007/978-4-431-87704-2_11

Download citation

Publish with us

Policies and ethics