Mathematical modeling of signaling and gene regulatory networks has provided unique insights about systems behaviors for many cell biological problems of medical importance. Quantitative single cell monitoring has a crucial role in advancing systems modeling of molecular networks. However, due to the multidisciplinary techniques that are necessary for adaptation of such systems biology approaches, dissemination to a wide research community has been relatively slow. In this essay, I focus on some technical aspects that are often under-appreciated, yet critical in harnessing live cell imaging methods to achieve single-cell-level understanding and quantitative modeling of molecular networks. The importance of these technical considerations will be elaborated with examples of successes and shortcomings. Future efforts will benefit by avoiding some pitfalls and by utilizing the lessons collectively learned from recent applications of imaging in systems biology.
References
[1]
Sung, M.H.; McNally, J.G. Live cell imaging and systems biology. Wiley Interdiscip. Rev. Syst. Biol. Med. 2011, 3, 167–182, doi:10.1002/wsbm.108.
Lahav, G.; Rosenfeld, N.; Sigal, A.; Geva-Zatorsky, N.; Levine, A.J.; Elowitz, M.B.; Alon, U. Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat. Genet. 2004, 36, 147–150.
[4]
Yissachar, N.; Sharar Fischler, T.; Cohen, A.A.; Reich-Zeliger, S.; Russ, D.; Shifrut, E.; Porat, Z.; Friedman, N. Dynamic response diversity of NFAT isoforms in individual living cells. Mol. Cell 2013, 49, 1–9.
[5]
Sung, M.H.; Salvatore, L.; de Lorenzi, R.; Indrawan, A.; Pasparakis, M.; Hager, G.L.; Bianchi, M.E.; Agresti, A. Sustained oscillations of NF-kappaB produce distinct genome scanning and gene expression profiles. PLoS One 2009, 4, e7163.
[6]
Sung, M.H.; Lao, Q.; Ning, L.; Fraser, I.D.C.; Hager, G.L. National Institutes of Health, Bethesda, MD, USA. Unpublished work, 2013.
[7]
Lee, T.K.; Denny, E.M.; Sanghvi, J.C.; Gaston, J.E.; Maynard, N.D.; Hughey, J.J.; Covert, M.W. A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide. Sci. Signal. 2009, 2, ra65.
[8]
Nelson, D.E.; Ihekwaba, A.E.; Elliott, M.; Johnson, J.R.; Gibney, C.A.; Foreman, B.E.; Nelson, G.; See, V.; Horton, C.A.; Spiller, D.G.; et al. Oscillations in NF-kappaB signaling control the dynamics of gene expression. Science 2004, 306, 704–708, doi:10.1126/science.1099962.
microManager. Available online: https://valelab.ucsf.edu/~MM/MMwiki/ (accessed on 3 April 2013).
[15]
ImageJ. Available online: https://rsb.info.nih.gov/ij/ (accessed on 3 April 2013).
[16]
CellProfiler. Available online: https://www.cellprofiler.org/ (accessed on 3 April 2013).
[17]
PhenoRipper. Available online: https://www4.utsouthwestern.edu/altschulerwulab/phenoripper/ (accessed on 3 April 2013).
[18]
Cohen, A.A.; Geva-Zatorsky, N.; Eden, E.; Frenkel-Morgenstern, M.; Issaeva, I.; Sigal, A.; Milo, R.; Cohen-Saidon, C.; Liron, Y.; Kam, Z.; et al. Dynamic proteomics of individual cancer cells in response to a drug. Science 2008, 322, 1511–1516, doi:10.1126/science.1160165.
[19]
Cohen-Saidon, C.; Cohen, A.A.; Sigal, A.; Liron, Y.; Alon, U. Dynamics and variability of ERK2 response to EGF in individual living cells. Mol. Cell 2009, 36, 885–893, doi:10.1016/j.molcel.2009.11.025.
[20]
Tay, S.; Hughey, J.J.; Lee, T.K.; Lipniacki, T.; Quake, S.R.; Covert, M.W. Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature 2010, 466, 267–271.
[21]
Awwad, Y.; Geng, T.; Baldwin, A.S.; Lu, C. Observing single cell NF-kappaB dynamics under stimulant concentration gradient. Anal. Chem. 2012, 84, 1224–1228, doi:10.1021/ac203209t.
[22]
James, C.D.; Moorman, M.W.; Carson, B.D.; Branda, C.S.; Lantz, J.W.; Manginell, R.P.; Martino, A.; Singh, A.K. Nuclear translocation kinetics of NF-kappaB in macrophages challenged with pathogens in a microfluidic platform. Biomed. Microdevices 2009, 11, 693–700, doi:10.1007/s10544-008-9281-5.
