Microarrays pp 211-226 | Cite as

Expression Profiling Using Microfluidic Living Cell Arrays

  • Kevin R. King
  • Martin L. Yarmush
  • Arul Jayaraman
Part of the Integrated Analytical Systems book series (ANASYS)

10.1 Introduction to the Living Cell Array Concept

The cellular microenvironment is remarkably complex. In the small space near each cell, growth factors are liberated from extracellular matrix, cytokines are secreted by neighboring cells, and hormones arrive from distant endocrine organs through the circulation. These soluble cues are detected by surface or cytoplasmic receptors and integrated using complex signal transduction cascades to modulate the activity of transcription factors (TFs), the primary regulators of gene expression. Transcription factors serve as points of convergence between the vast number of extracellular signaling molecules and the equally vast number of target genes. For perspective, the human genome contains approximately 1500 identified transcription factors regulating more than 20,000 target genes [1].

Adding further complexity to the picture, transcription factors often cooperate, compete, and regulate each other, forming transcriptional regulatory networks...


Green Fluorescent Protein Microfluidic Device Transcriptional Regulatory Network Cell Array Master Mold 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was supported in part by a Texas Engineering Experiment Station Award to AJ and grants from the NIH (BRP AI063795 and P41 EB002503) to MLY.


  1. 1.
    Pennisi, E. (2002). Genomics. Sequence tells mouse, human genome secrets. Science 298(5600), 1863–1865.CrossRefGoogle Scholar
  2. 2.
    Duncan, S., M. Navas, D. Dufort, J. Rossant, and M. Stoffel. (1998). Regulation of a transcription factor network required for differentiation and metabolism. Science 281(5377), 692–695.CrossRefGoogle Scholar
  3. 3.
    Odom, D.T., N. Zizlsperger, D.B. Gordon, G.W. Bell, N.J. Rinaldi, H.L. Murray, et al. (2004). Control of pancreas and liver gene expression by HNF transcription factors. Science 303(5662), 1378–1381.CrossRefGoogle Scholar
  4. 4.
    Odom, D.T., R.D. Dowell, E.S. Jacobsen, L. Nekludova, P.A. Rolfe, T.W. Danford, et al. (2006). Core transcriptional regulatory circuitry in human hepatocytes. Molecular Systems Biology 2, 2006 0017.Google Scholar
  5. 5.
    Yamagata, K. (2003). Regulation of pancreatic beta-cell function by the HNF transcription network: Lessons from maturity-onset diabetes of the young (MODY). Endocrinology Journal 50(5), 491–499.Google Scholar
  6. 6.
    Levchenko, A. (2003). Dynamical and integrative cell signaling: Challenges for the new biology. Biotechnology & Bioengineering 84, 773–782.CrossRefGoogle Scholar
  7. 7.
    Hoffmann, A., A. Levchenko, M. Scott, and D. Baltimore. (2002). The IkappaB-NF-kappaB signaling module: Temporal control and selective gene activation. Science 298, 1241–1245.CrossRefGoogle Scholar
  8. 8.
    Thompson, D.M., K.R. King, K.J. Wieder, M. Toner, M.L. Yarmush, and A. Jayaraman. (2004). Dynamic gene expression profiling using a microfabricated living cell array. Analytical Chemistry 76, 4098–4103.CrossRefGoogle Scholar
  9. 9.
    Wieder, K.J., K.R. King, D.M. Thompson, C. Zia, M.L. Yarmush, and A. Jayaraman. (2005). Optimization of reporter cells for expression profiling in a microfluidic device. Biomedical Microdevices 7, 213–222.CrossRefGoogle Scholar
  10. 10.
    King, K.L., S. Wang, D. Irimia, A. Jayaraman, M. Toner, and M.R. Yarmush. (2007). A high- throughput microfluidic real-time gene expression living cell array. Lab-on-Chip 7, 77–85.CrossRefGoogle Scholar
  11. 11.
    Gu, W., X. Zhu, N. Futai, B. Cho, and S. Takayama. (2004). Computerized microfluidic cell culture using elastomeric channels and Braille displays. Proceedings of the National Academy of Sciences USA 101, 15861–15866.CrossRefGoogle Scholar
  12. 12.
    Kim, L., M. Vahey, H. Lee, and J. Voldman. (2006). Microfluidic arrays for logarithmically perfused embryonic stem cell culture. Lab-on-Chip 6, 394–406.CrossRefGoogle Scholar
  13. 13.
    Lee, P., P. Hung, V. Rao, and L. Lee. (2006). Nanoliter scale microbioreactor array for quantitative cell biology. Biotechnology & Bioengineering 94, 5–14.CrossRefGoogle Scholar
  14. 14.
    Cubitt, A., R. Heim, S. Adams, A. Boyd, L. Gross, and R. Tsien. (1995). Understanding, improving and using green fluorescence proteins. Trends in Biochemical Sciences 20, 448–455.CrossRefGoogle Scholar
  15. 15.
    Li, X., X. Zhao, Y. Fang, X. Jiang, T. Duong, C. Fan, et al. (1998). Generation of destabilized green fluorescent protein as a transcription reporter. Journal of Biological Chemistry 273, 34970–34975.CrossRefGoogle Scholar
  16. 16.
    Zhao, X., T. Duong, C. Huang, S. Kain, and X. Li. (1999). Comparison of enhanced green fluorescent protein and its destabilized form as transcription reporters. Methods in Enzymology 302, 32–38.CrossRefGoogle Scholar
  17. 17.
    Ozbudak, E., M. Thattai, I. Kurtser, A. Grossman, and A. van Oudenaarden. (2002). Regulation of noise in the expression of a single gene. Nature Genetics 31, 69–73.CrossRefGoogle Scholar
  18. 18.
    Pedraza, J., and A. van Oudenaarden. (2005). Noise propagation in gene networks. Science 307, 1965–1969.CrossRefGoogle Scholar
  19. 19.
    Swain, P., M. Elowitz, and E. Siggia. (2002). Intrinsic and extrinsic contributions to sto-chasticity in gene expression. Proceedings of the National Academy of Sciences USA 99, 12795–12800.CrossRefGoogle Scholar
  20. 20.
    Nelson, D., A. Ihekwaba, M. Elliott, J. Johnson, C. Gibney, B. Foreman, et al. (2004). Oscillations in NF-kappaB signaling control the dynamics of gene expression. Science 306, 704–708.CrossRefGoogle Scholar
  21. 21.
    Lahav, G., N. Rosenfeld, A. Sigal, N. Geva-Zatorsky, A. Levine, M. Elowitz, et al. (2004). Dynamics of the p53-Mdm2 feedback loop in individual cells. Nature Genetics 36, 147–150.CrossRefGoogle Scholar
  22. 22.
    Zhang, J., R. Campbell, A. Ting, and R. Tsien. (2002). Creating new fluorescent probes for cell biology. Nature Reviews Molecular and Cell Biology 3, 906–918.CrossRefGoogle Scholar
  23. 23.
    Giepmans, B., S. Adams, M. Ellisman, and R. Tsien. (2006). The fluorescent toolbox for assessing protein location and function. Science 312, 217–224.CrossRefGoogle Scholar
  24. 24.
    Niswender, K., S. Blackman, L. Rohde, M. Magnuson, and D. Piston. (1998). Quantitative imaging of green fluorescent protein in cultured cells: comparison of microscopic techniques, use in fusion proteins and detection limits. Journal of Microscopy 180, 109–116.Google Scholar
  25. 25.
    Furtado, A., and R. Henry. (2002). Measurement of green fluorescent protein concentration in single cells by image analysis. Analytical Biochemistry 310, 84–92.CrossRefGoogle Scholar
  26. 26.
    Tilles, A., H. Baskaran, P. Roy, M. Yarmush, and M. Toner. (2001). Effects of oxygenation and flow on the viability and function of rat hepatocytes cocultured in a microchannel flat-plate bioreactor. Biotechnology & Bioengineering 73, 379–389.CrossRefGoogle Scholar
  27. 27.
    McDonald, J., D. Duffy, J. Anderson, D. Chiu, H. Wu, O. Schueller, et al. (2000). Fabrication of microfluidic systems in poly(dimethylsiloxane). Electrophoresis 21, 27–40.CrossRefGoogle Scholar
  28. 28.
    Unger, M., H. Chou, T. Thorsen, A. Scherer, and S. Quake. (2000). Monolithic microfabri-cated valves and pumps by multilayer soft lithography. Science 288, 113–116.CrossRefGoogle Scholar
  29. 29.
    Thorsen, T., R. Roberts, F. Arnold, and S. Quake. (2001). Dynamic pattern formation in a vesicle-generating microfluidic device. Physical Review Letters 86, 4163–4166.CrossRefGoogle Scholar
  30. 30.
    Li, N., C. Hsu, and A. Folch. (2005). Parallel mixing of photolithographically defined nano-liter volumes using elastomeric microvalve arrays. Electrophoresis 26, 3758–3764.CrossRefGoogle Scholar
  31. 31.
    Irimia, D., and M. Toner. (2006). Cell handling using microstructured membranes. Lab-on-Chip 6, 345–352.CrossRefGoogle Scholar
  32. 32.
    Jiang, X., Q. Xu, S. Dertinger, A. Stroock, T. Fu, and G. Whitesides. (2005). A general method for patterning gradients of biomolecules on surfaces using microfluidic networks. Analytical Chemistry 77, 2338–2347.CrossRefGoogle Scholar
  33. 33.
    King, K.R., S. Wang, A. Jayaraman, M.L. Yarmush, and M. Toner. (2008). Microfluidic flow-encoded switching for parallel control of dynamic cellular environments, Lab-on-chip 8, 107–116.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Kevin R. King
    • 1
  • Martin L. Yarmush
    • 1
    • 2
  • Arul Jayaraman
    • 3
  1. 1.Center for Engineering in MedicineMass. General Hospital & Harvard Medical SchoolBoston
  2. 2.Center for Bioelectronics and BiosensorsArizona State UniversityTempe
  3. 3.Department of Chemical EngineeringTexas A & M UniversityCollege Station

Personalised recommendations