Institute of Fundamental Technological Research
Polish Academy of Sciences

Partners

Stephen Quake

Stanford University (US)


Recent publications
1.  Kellogg R.A., Tian C., Lipniacki T., Quake S.R., Tay S., Digital signaling decouples activation probability and population heterogeneity, eLife, ISSN: 2050-084X, DOI: 10.7554/eLife.08931, Vol.4, pp.e08931-1-26, 2015

Abstract:
Digital signaling enhances robustness of cellular decisions in noisy environments, but it is unclear how digital systems transmit temporal information about a stimulus. To understand how temporal input information is encoded and decoded by the NF-κB system, we studied transcription factor dynamics and gene regulation under dose- and duration-modulated inflammatory inputs. Mathematical modeling predicted and microfluidic single-cell experiments confirmed that integral of the stimulus (or area, concentration × duration) controls the fraction of cells that activate NF-κB in the population. However, stimulus temporal profile determined NF-κB dynamics, cell-to-cell variability, and gene expression phenotype. A sustained, weak stimulation lead to heterogeneous activation and delayed timing that is transmitted to gene expression. In contrast, a transient, strong stimulus with the same area caused rapid and uniform dynamics. These results show that digital NF-κB signaling enables multidimensional control of cellular phenotype via input profile, allowing parallel and independent control of single-cell activation probability and population heterogeneity.

Affiliations:
Kellogg R.A. - Eidgenössische Technische Hochschule Zürich (CH)
Tian C. - University of Copenhagen (DK)
Lipniacki T. - IPPT PAN
Quake S.R. - Stanford University (US)
Tay S. - Eidgenössische Technische Hochschule Zürich (CH)
2.  Tay S., Hughey J.J., Lee T.K., Lipniacki T., Quake S.R., Covert M.W., Single-cell NF-kB dynamics reveal digital activation and analogue information processing, NATURE, ISSN: 0028-0836, DOI: 10.1038/nature09145, Vol.466, pp.267-271, 2010

Abstract:
Cells operate in dynamic environments using extraordinary communication capabilities that emerge from the interactions of genetic circuitry. The mammalian immune response is a striking example of the coordination of different cell types1. Cell-to-cell communication is primarily mediated by signalling molecules that form spatiotemporal concentration gradients, requiring cells to respond to a wide range of signal intensities2. Here we use high-throughput microfluidic cell culture3 and fluorescence microscopy, quantitative gene expression analysis and mathematical modelling to investigate how single mammalian cells respond to different concentrations of the signalling molecule tumour-necrosis factor (TNF)-α, and relay information to the gene expression programs by means of the transcription factor nuclear factor (NF)-κB. We measured NF-κB activity in thousands of live cells under TNF-α doses covering four orders of magnitude. We find, in contrast to population-level studies with bulk assays2, that the activation is heterogeneous and is a digital process at the single-cell level with fewer cells responding at lower doses. Cells also encode a subtle set of analogue parameters to modulate the outcome; these parameters include NF-κB peak intensity, response time and number of oscillations. We developed a stochastic mathematical model that reproduces both the digital and analogue dynamics as well as most gene expression profiles at all measured conditions, constituting a broadly applicable model for TNF-α-induced NF-κB signalling in various types of cells. These results highlight the value of high-throughput quantitative measurements with single-cell resolution in understanding how biological systems operate.

Keywords:
Cell biology, Biophysics, Immunology, Genetics, Genomics

Affiliations:
Tay S. - Eidgenössische Technische Hochschule Zürich (CH)
Hughey J.J. - Stanford University (US)
Lee T.K. - Stanford University (US)
Lipniacki T. - IPPT PAN
Quake S.R. - Stanford University (US)
Covert M.W. - Stanford University (US)

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