101
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Spencer SL, Sorger PK. Measuring and modeling apoptosis in single cells. Cell 2011; 144:926-39. [PMID: 21414484 PMCID: PMC3087303 DOI: 10.1016/j.cell.2011.03.002] [Citation(s) in RCA: 259] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 02/25/2011] [Accepted: 03/01/2011] [Indexed: 01/23/2023]
Abstract
Cell death plays an essential role in the development of tissues and organisms, the etiology of disease, and the responses of cells to therapeutic drugs. Here we review progress made over the last decade in using mathematical models and quantitative, often single-cell, data to study apoptosis. We discuss the delay that follows exposure of cells to prodeath stimuli, control of mitochondrial outer membrane permeabilization, switch-like activation of effector caspases, and variability in the timing and probability of death from one cell to the next. Finally, we discuss challenges facing the fields of biochemical modeling and systems pharmacology.
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Affiliation(s)
- Sabrina L. Spencer
- Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Peter K. Sorger
- Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Correspondence:
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102
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Sung MH, McNally JG. Live cell imaging and systems biology. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2011; 3:167-82. [PMID: 20730797 PMCID: PMC2992103 DOI: 10.1002/wsbm.108] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Much of the experimental data used to construct mathematical models of molecular networks are derived from in vitro measurements. However, there is increasing evidence that in vitro measurements fail to capture both the complexity and the individuality found in single, living cells. These limitations can be overcome by live cell microscopy which is evolving to enable in vivo biochemistry. Here, we survey the current capabilities of live cell microscopy and illustrate how a number of different imaging approaches could be applied to analyze a specific molecular network. We argue that incorporation of such quantitative live-cell imaging methods is critical for the progress of systems biology.
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103
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Abstract
NF-κB (nuclear factor κB) regulates cellular stress and the immune responses to infection. Its activation results in oscillations in nuclear NF-κB abundance. We treated cells with repeated short pulses of TNFα (tumour necrosis factor α) at various intervals to mimic pulsatile inflammatory signals. At all pulse intervals analysed, we observed synchronous cycles of NF-κB nuclear translocation. Lower frequency stimulations gave repeated full-amplitude translocations, whereas higher frequency pulses gave translocations with reduced amplitude, indicating that the system failed to reset completely. Deterministic and stochastic mathematical models predicted how negative feedback loops might regulate both system resetting and cellular heterogeneity. Altering the stimulation interval gave different patterns of NF-κB-dependent gene expression, supporting a functional role for oscillation frequency. The causes of cell-to-cell variation and the possible functions of these processes in cells and tissues are discussed. The NF-κB system is just one of a number of known biological oscillators that include calcium signalling, transcription cycles, p53, the segmentation clock, the circadian clock, the cell cycle and seasonal rhythms. The way such cycles are integrated could be part of the answer as to how organisms achieve complexity while retaining the robustness of cellular decision-making processes.
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104
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Paszek P, Jackson DA, White MR. Oscillatory control of signalling molecules. Curr Opin Genet Dev 2010; 20:670-6. [PMID: 20850963 DOI: 10.1016/j.gde.2010.08.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 07/23/2010] [Accepted: 08/19/2010] [Indexed: 10/19/2022]
Abstract
The emergence of biological function from the dynamic control of cellular signalling molecules is a fundamental process in biology. Key questions include: How do cells decipher noisy environmental cues, encode these signals to control fate decisions and propagate information through tissues? Recent advances in systems biology, and molecular and cellular biology, exemplified by analyses of signalling via the transcription factor Nuclear Factor kappaB (NF-κB), reveal a critical role of oscillatory control in the regulation of these biological functions. The emerging view is that the oscillatory dynamics of signalling molecules and the epigenetically regulated specificity for target genes contribute to robust regulation of biological function at different levels of cellular organisation through frequency-dependent information encoding.
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Affiliation(s)
- Pawel Paszek
- Centre for Cell Imaging, School of Biological Sciences, The Biosciences Building, University of Liverpool, Crown St., Liverpool L69 7ZB, UK.
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105
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Abstract
This review explores advances in our understanding of dynamicism in cellular signaling. Areas highlighted include the role of stochasticity in producing diversity in analogous signaling circumstances; population desynchronization's effect in masking newly appreciated repetitive bursts in protein phosphorylation and messenger RNA production; double-positive feedback interactions and their ability to synchronize multiple signal transduction pathways; scaffolding proteins control over signaling feedback; and frequency-responsive transcriptional regulation as an example of dynamicism in signaling.
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Affiliation(s)
- Jameel Iqbal
- Department of Animal Biology, University of Pennsylvania Veterinary School, Philadelphia, Pennsylvania, USA.
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106
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Modeling oscillatory control in NF-κB, p53 and Wnt signaling. Curr Opin Genet Dev 2010; 20:656-64. [PMID: 20934871 DOI: 10.1016/j.gde.2010.08.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/11/2010] [Accepted: 08/31/2010] [Indexed: 01/22/2023]
Abstract
Oscillations are commonly observed in cellular behavior and span a wide range of timescales, from seconds in calcium signaling to 24 hours in circadian rhythms. In between lie oscillations with time periods of 1-5 hours seen in NF-κB, p53 and Wnt signaling, which play key roles in the immune system, cell growth/death and embryo development, respectively. In the first part of this article, we provide a brief overview of simple deterministic models of oscillations. In particular, we explain the mechanism of saturated degradation that has been used to model oscillations in the NF-κB, p53 and Wnt systems. The second part deals with the potential physiological role of oscillations. We use the simple models described earlier to explore whether oscillatory signals can encode more information than steady-state signals. We then discuss a few simple genetic circuits that could decode information stored in the average, amplitude or frequency of oscillations. The presence of frequency-detector circuit downstream of NF-κB or p53 would be a strong clue that oscillations are important for the physiological response of these signaling systems.
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107
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Lee TK, Covert MW. High-throughput, single-cell NF-κB dynamics. Curr Opin Genet Dev 2010; 20:677-83. [PMID: 20846851 DOI: 10.1016/j.gde.2010.08.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/23/2010] [Accepted: 08/19/2010] [Indexed: 01/08/2023]
Abstract
Single cells in a population often respond differently to perturbations in the environment. Live-cell microscopy has enabled scientists to observe these differences at the single-cell level. Some advantages of live-cell imaging over population-based methods include better time resolution, higher sensitivity, automation, and richer datasets. One specific area where live-cell microscopy has made a significant impact is the field of NF-κB signaling dynamics, and recent efforts have focused on making live-cell imaging of these dynamics more high-throughput. We highlight the major aspects of increasing throughput and describe a current system that can monitor, image and analyze the NF-κB activation of thousands of single cells in parallel.
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Affiliation(s)
- Timothy K Lee
- Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, United States
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108
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Yu PJ, Ci W, Wang GF, Zhang JY, Wu SY, Xu W, Jin H, Zhu ZG, Zhang JJ, Pang JX, Wu SG. Praeruptorin A inhibits lipopolysaccharide-induced inflammatory response in murine macrophages through inhibition of NF-κB pathway activation. Phytother Res 2010; 25:550-6. [PMID: 20842678 DOI: 10.1002/ptr.3295] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 07/12/2010] [Accepted: 08/02/2010] [Indexed: 01/05/2023]
Abstract
Praeruptorin A (PA) is a pyranocoumarin compound isolated from the dried root of Peucedanum praeruptorum Dunn (Umbelliferae). However, the antiinflammatory effect of PA has not been reported. The present study investigated the antiinflammatory effect of PA in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophage cells. PA significantly inhibited the LPS-induced production of nitric oxide (NO), interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α). The mRNA and protein expressions of inducible nitric oxide synthase (iNOS), IL-1β and TNF-α were also suppressed by this compound. Further study showed that PA decreased the cytoplasmic loss of inhibitor κB-α (IκB-α) protein and inhibited the translocation of NF-κB from cytoplasm to nucleus. Taken together, the results suggest that PA may exert antiinflammatory effects in vitro in LPS-stimulated RAW 264.7 macrophages through inhibition of NF-κB signal pathway activation.
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Affiliation(s)
- Peng-Jiu Yu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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109
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Turner DA, Paszek P, Woodcock DJ, Nelson DE, Horton CA, Wang Y, Spiller DG, Rand DA, White MRH, Harper CV. Physiological levels of TNFalpha stimulation induce stochastic dynamics of NF-kappaB responses in single living cells. J Cell Sci 2010; 123:2834-43. [PMID: 20663918 DOI: 10.1242/jcs.069641] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Nuclear factor kappa B (NF-kappaB) signalling is activated by cellular stress and inflammation and regulates cytokine expression. We applied single-cell imaging to investigate dynamic responses to different doses of tumour necrosis factor alpha (TNFalpha). Lower doses activated fewer cells and those responding showed an increasingly variable delay in the initial NF-kappaB nuclear translocation and associated IkappaBalpha degradation. Robust 100 minute nuclear:cytoplasmic NF-kappaB oscillations were observed over a wide range of TNFalpha concentrations. The result is supported by computational analyses, which identified a limit cycle in the system with a stable 100 minute period over a range of stimuli, and indicated no co-operativity in the pathway activation. These results suggest that a stochastic threshold controls functional all-or-nothing responses in individual cells. Deterministic and stochastic models simulated the experimentally observed activation threshold and gave rise to new predictions about the structure of the system and open the way for better mechanistic understanding of physiological TNFalpha activation of inflammatory responses in cells and tissues.
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Affiliation(s)
- David A Turner
- Centre for Cell Imaging, School of Biological Sciences, Bioscience Research Building, Liverpool, UK
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110
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Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature 2010; 466:267-71. [PMID: 20581820 DOI: 10.1038/nature09145] [Citation(s) in RCA: 608] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 04/28/2010] [Indexed: 01/19/2023]
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 types. 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 intensities. Here we use high-throughput microfluidic cell culture 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)-alpha, and relay information to the gene expression programs by means of the transcription factor nuclear factor (NF)-kappaB. We measured NF-kappaB activity in thousands of live cells under TNF-alpha doses covering four orders of magnitude. We find, in contrast to population-level studies with bulk assays, 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-kappaB 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-alpha-induced NF-kappaB 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.
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Affiliation(s)
- Savaş Tay
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
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111
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Paszek P, Ryan S, Ashall L, Sillitoe K, Harper CV, Spiller DG, Rand DA, White MRH. Population robustness arising from cellular heterogeneity. Proc Natl Acad Sci U S A 2010; 107:11644-9. [PMID: 20534546 PMCID: PMC2895068 DOI: 10.1073/pnas.0913798107] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Heterogeneity between individual cells is a common feature of dynamic cellular processes, including signaling, transcription, and cell fate; yet the overall tissue level physiological phenotype needs to be carefully controlled to avoid fluctuations. Here we show that in the NF-kappaB signaling system, the precise timing of a dual-delayed negative feedback motif [involving stochastic transcription of inhibitor kappaB (IkappaB)-alpha and -epsilon] is optimized to induce heterogeneous timing of NF-kappaB oscillations between individual cells. We suggest that this dual-delayed negative feedback motif enables NF-kappaB signaling to generate robust single cell oscillations by reducing sensitivity to key parameter perturbations. Simultaneously, enhanced cell heterogeneity may represent a mechanism that controls the overall coordination and stability of cell population responses by decreasing temporal fluctuations of paracrine signaling. It has often been thought that dynamic biological systems may have evolved to maximize robustness through cell-to-cell coordination and homogeneity. Our analyses suggest in contrast, that this cellular variation might be advantageous and subject to evolutionary selection. Alternative types of therapy could perhaps be designed to modulate this cellular heterogeneity.
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Affiliation(s)
- Pawel Paszek
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
| | - Sheila Ryan
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
| | - Louise Ashall
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
| | - Kate Sillitoe
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
| | - Claire V. Harper
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
| | - David G. Spiller
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
| | - David A. Rand
- Warwick Systems Biology and Mathematics Institute, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Michael R. H. White
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
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112
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Bartfeld S, Hess S, Bauer B, Machuy N, Ogilvie LA, Schuchhardt J, Meyer TF. High-throughput and single-cell imaging of NF-kappaB oscillations using monoclonal cell lines. BMC Cell Biol 2010; 11:21. [PMID: 20233427 PMCID: PMC2848210 DOI: 10.1186/1471-2121-11-21] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 03/16/2010] [Indexed: 12/29/2022] Open
Abstract
Background The nuclear factor-κB (NF-κB) family of transcription factors plays a role in a wide range of cellular processes including the immune response and cellular growth. In addition, deregulation of the NF-κB system has been associated with a number of disease states, including cancer. Therefore, insight into the regulation of NF-κB activation has crucial medical relevance, holding promise for novel drug target discovery. Transcription of NF-κB-induced genes is regulated by differential dynamics of single NF-κB subunits, but only a few methods are currently being applied to study dynamics. In particular, while oscillations of NF-κB activation have been observed in response to the cytokine tumor necrosis factor α (TNFα), little is known about the occurrence of oscillations in response to bacterial infections. Results To quantitatively assess NF-κB dynamics we generated human and murine monoclonal cell lines that stably express the NF-κB subunit p65 fused to GFP. Furthermore, a high-throughput assay based on automated microscopy coupled to image analysis to quantify p65-nuclear translocation was established. Using this assay, we demonstrate a stimulus- and cell line-specific temporal control of p65 translocation, revealing, for the first time, oscillations of p65 translocation in response to bacterial infection. Oscillations were detected at the single-cell level using real-time microscopy as well as at the population level using high-throughput image analysis. In addition, mathematical modeling of NF-κB dynamics during bacterial infections predicted masking of oscillations on the population level in asynchronous activations, which was experimentally confirmed. Conclusions Taken together, this simple and cost effective assay constitutes an integrated approach to infer the dynamics of NF-κB kinetics in single cells and cell populations. Using a single system, novel factors modulating NF-κB can be identified and analyzed, providing new possibilities for a wide range of applications from therapeutic discovery and understanding of disease to host-pathogen interactions.
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Affiliation(s)
- Sina Bartfeld
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Berlin, Germany
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113
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Yaffe MB, VanHook AM. Science Signaling
Podcast: 5 January 2010. Sci Signal 2010. [DOI: 10.1126/scisignal.3103pc1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Chief Scientific Editor Michael Yaffe reviews the year in
Science Signaling
.
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Affiliation(s)
- Michael B. Yaffe
- Chief Scientific Editor of Science Signaling, American Association for the Advancement of Science, 1200 New York Avenue, N.W., Washington, DC 20005, USA
- Koch Institute for Integrative Cancer Research, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Annalisa M. VanHook
- Associate Online Editor of Science Signaling, American Association for the Advancement of Science, 1200 New York Avenue, N.W., Washington, DC 20005, USA
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