201
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Muta Y, Matsuda M, Imajo M. Dynamic ERK signaling regulation in intestinal tumorigenesis. Mol Cell Oncol 2018; 5:e1506684. [PMID: 30263947 PMCID: PMC6154845 DOI: 10.1080/23723556.2018.1506684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 07/23/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
Extracellular signal-regulated kinase (ERK) plays a critical role in tissue homeostasis and tumorigenesis. By utilizing live imaging approaches, we recently uncovered ERK activity dynamics in the intestinal epithelium. Notably, we showed that ERK activity dynamics are defined by composite regulation from two distinct upstream receptors, and alteration of their functional balance underlies tumor cell-specific traits. Here, we discuss these findings.
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Affiliation(s)
- Yu Muta
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Michiyuki Matsuda
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Masamichi Imajo
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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202
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Mitra T, Menon SN, Sinha S. Emergent memory in cell signaling: Persistent adaptive dynamics in cascades can arise from the diversity of relaxation time-scales. Sci Rep 2018; 8:13230. [PMID: 30185923 PMCID: PMC6125488 DOI: 10.1038/s41598-018-31626-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/23/2018] [Indexed: 12/13/2022] Open
Abstract
The mitogen-activated protein kinase (MAPK) signaling cascade, an evolutionarily conserved motif present in all eukaryotic cells, is involved in coordinating crucial cellular functions. While the asymptotic dynamical behavior of the pathway stimulated by a time-invariant signal is relatively well-understood, we show using a computational model that it exhibits a rich repertoire of transient adaptive responses to changes in stimuli. When the signal is switched on, the response is characterized by long-lived modulations in frequency as well as amplitude. On withdrawing the stimulus, the activity decays over long timescales, exhibiting reverberations characterized by repeated spiking in the activated MAPK concentration. The long-term persistence of such post-stimulus activity suggests that the cascade retains memory of the signal for a significant duration following its removal. The molecular mechanism underlying the reverberatory activity is related to the existence of distinct relaxation rates for the different cascade components. This results in the imbalance of fluxes between different layers of the cascade, with the reuse of activated kinases as enzymes when they are released from sequestration in complexes. The persistent adaptive response, indicative of a cellular “short-term” memory, suggests that this ubiquitous signaling pathway plays an even more central role in information processing by eukaryotic cells.
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Affiliation(s)
- Tanmay Mitra
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai, 600113, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Shakti N Menon
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai, 600113, India
| | - Sitabhra Sinha
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai, 600113, India. .,Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
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203
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Wolff SC, Kedziora KM, Dumitru R, Dungee CD, Zikry TM, Beltran AS, Haggerty RA, Cheng J, Redick MA, Purvis JE. Inheritance of OCT4 predetermines fate choice in human embryonic stem cells. Mol Syst Biol 2018; 14:e8140. [PMID: 30177503 PMCID: PMC6120590 DOI: 10.15252/msb.20178140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 07/28/2018] [Accepted: 07/30/2018] [Indexed: 01/21/2023] Open
Abstract
It is well known that clonal cells can make different fate decisions, but it is unclear whether these decisions are determined during, or before, a cell's own lifetime. Here, we engineered an endogenous fluorescent reporter for the pluripotency factor OCT4 to study the timing of differentiation decisions in human embryonic stem cells. By tracking single-cell OCT4 levels over multiple cell cycle generations, we found that the decision to differentiate is largely determined before the differentiation stimulus is presented and can be predicted by a cell's preexisting OCT4 signaling patterns. We further quantified how maternal OCT4 levels were transmitted to, and distributed between, daughter cells. As mother cells underwent division, newly established OCT4 levels in daughter cells rapidly became more predictive of final OCT4 expression status. These results imply that the choice between developmental cell fates can be largely predetermined at the time of cell birth through inheritance of a pluripotency factor.
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Affiliation(s)
- Samuel C Wolff
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Katarzyna M Kedziora
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Raluca Dumitru
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Cierra D Dungee
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Tarek M Zikry
- Department of Biostatistics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Adriana S Beltran
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Rachel A Haggerty
- Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - JrGang Cheng
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Margaret A Redick
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
- Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
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204
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Doldán-Martelli V, Míguez DG. Drug treatment efficiency depends on the initial state of activation in nonlinear pathways. Sci Rep 2018; 8:12495. [PMID: 30131510 PMCID: PMC6104077 DOI: 10.1038/s41598-018-30913-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/03/2018] [Indexed: 11/28/2022] Open
Abstract
An accurate prediction of the outcome of a given drug treatment requires quantitative values for all parameters and concentrations involved as well as a detailed characterization of the network of interactions where the target molecule is embedded. Here, we present a high-throughput in silico screening of all potential networks of three interacting nodes to study the effect of the initial conditions of the network in the efficiency of drug inhibition. Our study shows that most network topologies can induce multiple dose-response curves, where the treatment has an enhanced, reduced or even no effect depending on the initial conditions. The type of dual response observed depends on how the potential bistable regimes interplay with the inhibition of one of the nodes inside a nonlinear pathway architecture. We propose that this dependence of the strength of the drug on the initial state of activation of the pathway may be affecting the outcome and the reproducibility of drug studies and clinical trials.
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Affiliation(s)
| | - David G Míguez
- Centro de Biología Molecular Severo Ochoa, Depto. de Física de la Materia Condensada, Instituto Nicolás Cabrera and IFIMAC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28046, Madrid, Spain.
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205
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Intratumor MAPK and PI3K signaling pathway heterogeneity in glioblastoma tissue correlates with CREB signaling and distinct target gene signatures. Exp Mol Pathol 2018; 105:23-31. [DOI: 10.1016/j.yexmp.2018.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 05/26/2018] [Indexed: 11/20/2022]
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206
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Nett IR, Mulas C, Gatto L, Lilley KS, Smith A. Negative feedback via RSK modulates Erk-dependent progression from naïve pluripotency. EMBO Rep 2018; 19:e45642. [PMID: 29895711 PMCID: PMC6073214 DOI: 10.15252/embr.201745642] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 01/08/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) signalling is implicated in initiation of embryonic stem (ES) cell differentiation. The pathway is subject to complex feedback regulation. Here, we examined the ERK-responsive phosphoproteome in ES cells and identified the negative regulator RSK1 as a prominent target. We used CRISPR/Cas9 to create combinatorial mutations in RSK family genes. Genotypes that included homozygous null mutations in Rps6ka1, encoding RSK1, resulted in elevated ERK phosphorylation. These RSK-depleted ES cells exhibit altered kinetics of transition into differentiation, with accelerated downregulation of naïve pluripotency factors, precocious expression of transitional epiblast markers and early onset of lineage specification. We further show that chemical inhibition of RSK increases ERK phosphorylation and expedites ES cell transition without compromising multilineage potential. These findings demonstrate that the ERK activation profile influences the dynamics of pluripotency progression and highlight the role of signalling feedback in temporal control of cell state transitions.
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Affiliation(s)
- Isabelle Re Nett
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Carla Mulas
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Laurent Gatto
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
- Computational Proteomics Unit, Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Austin Smith
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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207
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Ogura Y, Wen FL, Sami MM, Shibata T, Hayashi S. A Switch-like Activation Relay of EGFR-ERK Signaling Regulates a Wave of Cellular Contractility for Epithelial Invagination. Dev Cell 2018; 46:162-172.e5. [PMID: 29983336 DOI: 10.1016/j.devcel.2018.06.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/27/2018] [Accepted: 06/06/2018] [Indexed: 01/24/2023]
Abstract
The dynamics of extracellular signal-regulated kinase (ERK) signaling underlies its versatile functions in cell differentiation, cell proliferation, and cell motility. Classical studies in Drosophila established that a gradient of epidermal growth factor receptor (EGFR)-ERK signaling is essential for these cellular responses. However, we challenge this view by the real-time monitoring of ERK activation; we show that a switch-like ERK activation is essential for the invagination movement of the Drosophila tracheal placode. This switch-like ERK activation stems from the positive feedback regulation of the EGFR-ERK signaling and a resultant relay of EGFR-ERK signaling among tracheal cells. A key transcription factor Trachealess (Trh) permissively regulates the iteration of the relay, and the ERK activation becomes graded in trh mutant. A mathematical model based on these observations and a molecular link between ERK activation dynamics and myosin shows that the relay mechanism efficiently promotes epithelial invagination while the gradient mechanism does not.
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Affiliation(s)
- Yosuke Ogura
- Laboratory for Morphogenetic Signaling, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Fu-Lai Wen
- Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Mustafa M Sami
- Laboratory for Morphogenetic Signaling, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Tatsuo Shibata
- Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Shigeo Hayashi
- Laboratory for Morphogenetic Signaling, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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208
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Sampattavanich S, Steiert B, Kramer BA, Gyori BM, Albeck JG, Sorger PK. Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases. Cell Syst 2018; 6:664-678.e9. [PMID: 29886111 DOI: 10.1016/j.cels.2018.05.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/19/2017] [Accepted: 05/04/2018] [Indexed: 02/05/2023]
Abstract
Extracellular growth factors signal to transcription factors via a limited number of cytoplasmic kinase cascades. It remains unclear how such cascades encode ligand identities and concentrations. In this paper, we use live-cell imaging and statistical modeling to study FOXO3, a transcription factor regulating diverse aspects of cellular physiology that is under combinatorial control. We show that FOXO3 nuclear-to-cytosolic translocation has two temporally distinct phases varying in magnitude with growth factor identity and cell type. These phases comprise synchronous translocation soon after ligand addition followed by an extended back-and-forth shuttling; this shuttling is pulsatile and does not have a characteristic frequency, unlike a simple oscillator. Early and late dynamics are differentially regulated by Akt and ERK and have low mutual information, potentially allowing the two phases to encode different information. In cancer cells in which ERK and Akt are dysregulated by oncogenic mutation, the diversity of states is lower.
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Affiliation(s)
- Somponnat Sampattavanich
- HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, WAB Room 438, 200 Longwood Avenue, Boston, MA 02115, USA; Siriraj Laboratory for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, 12th Floor Srisavarindhira Building, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand.
| | - Bernhard Steiert
- HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, WAB Room 438, 200 Longwood Avenue, Boston, MA 02115, USA; Institute of Physics, University of Freiburg, Freiburg, Germany; Freiburg Center for Systems Biology, University of Freiburg, Freiburg, Germany
| | - Bernhard A Kramer
- HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, WAB Room 438, 200 Longwood Avenue, Boston, MA 02115, USA; Division of Systems Biology of Signal Transduction, German Cancer Research Center, Heidelberg, Germany
| | - Benjamin M Gyori
- HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, WAB Room 438, 200 Longwood Avenue, Boston, MA 02115, USA
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Peter K Sorger
- HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, WAB Room 438, 200 Longwood Avenue, Boston, MA 02115, USA.
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209
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Muta Y, Fujita Y, Sumiyama K, Sakurai A, Taketo MM, Chiba T, Seno H, Aoki K, Matsuda M, Imajo M. Composite regulation of ERK activity dynamics underlying tumour-specific traits in the intestine. Nat Commun 2018; 9:2174. [PMID: 29872037 PMCID: PMC5988836 DOI: 10.1038/s41467-018-04527-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 05/02/2018] [Indexed: 02/07/2023] Open
Abstract
Acting downstream of many growth factors, extracellular signal-regulated kinase (ERK) plays a pivotal role in regulating cell proliferation and tumorigenesis, where its spatiotemporal dynamics, as well as its strength, determine cellular responses. Here, we uncover the ERK activity dynamics in intestinal epithelial cells (IECs) and their association with tumour characteristics. Intravital imaging identifies two distinct modes of ERK activity, sustained and pulse-like activity, in IECs. The sustained and pulse-like activities depend on ErbB2 and EGFR, respectively. Notably, activation of Wnt signalling, the earliest event in intestinal tumorigenesis, augments EGFR signalling and increases the frequency of ERK activity pulses through controlling the expression of EGFR and its regulators, rendering IECs sensitive to EGFR inhibition. Furthermore, the increased pulse frequency is correlated with increased cell proliferation. Thus, ERK activity dynamics are defined by composite inputs from EGFR and ErbB2 signalling in IECs and their alterations might underlie tumour-specific sensitivity to pharmacological EGFR inhibition. The ERK signalling pathway regulates homeostasis of the intestinal epithelium. Here the authors identify two modes of ERK activity generated independently from EGFR and ErbB2 receptor and whose balance in cancer is shifted by Wnt pathway activation, resulting in enhanced sensitivity to EGFR inhibitors.
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Affiliation(s)
- Yu Muta
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, 606-8051, Japan.,Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Yoshihisa Fujita
- Department of Systems Science, Graduate School of Informatics, Kyoto University, Kyoto, 606-8501, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, Quantitative Biology Center, RIKEN, Osaka, 565-0874, Japan
| | - Atsuro Sakurai
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - M Mark Taketo
- Division of Experimental Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Tsutomu Chiba
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan.,Kansai Electric Power Hospital, Osaka, 553-0003, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Kazuhiro Aoki
- Division of Quantitative Biology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan.,Department of Basic Biology, Faculty of Life Science, SOKENDAI (Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Michiyuki Matsuda
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, 606-8051, Japan.,Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Masamichi Imajo
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
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210
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Bratt JM, Chang KY, Rabowsky M, Franzi LM, Ott SP, Filosto S, Goldkorn T, Arif M, Last JA, Kenyon NJ, Zeki AA. Farnesyltransferase Inhibition Exacerbates Eosinophilic Inflammation and Airway Hyperreactivity in Mice with Experimental Asthma: The Complex Roles of Ras GTPase and Farnesylpyrophosphate in Type 2 Allergic Inflammation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2018; 200:3840-3856. [PMID: 29703864 PMCID: PMC5964018 DOI: 10.4049/jimmunol.1601317] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 03/14/2018] [Indexed: 12/13/2022]
Abstract
Ras, a small GTPase protein, is thought to mediate Th2-dependent eosinophilic inflammation in asthma. Ras requires cell membrane association for its biological activity, and this requires the posttranslational modification of Ras with an isoprenyl group by farnesyltransferase (FTase) or geranylgeranyltransferase (GGTase). We hypothesized that inhibition of FTase using FTase inhibitor (FTI)-277 would attenuate allergic asthma by depleting membrane-associated Ras. We used the OVA mouse model of allergic inflammation and human airway epithelial (HBE1) cells to determine the role of FTase in inflammatory cell recruitment. BALB/c mice were first sensitized then exposed to 1% OVA aerosol or filtered air, and half were injected daily with FTI-277 (20 mg/kg per day). Treatment of mice with FTI-277 had no significant effect on lung membrane-anchored Ras, Ras protein levels, or Ras GTPase activity. In OVA-exposed mice, FTI-277 treatment increased eosinophilic inflammation, goblet cell hyperplasia, and airway hyperreactivity. Human bronchial epithelial (HBE1) cells were pretreated with 5, 10, or 20 μM FTI-277 prior to and during 12 h IL-13 (20 ng/ml) stimulation. In HBE1 cells, FTase inhibition with FTI-277 had no significant effect on IL-13-induced STAT6 phosphorylation, eotaxin-3 peptide secretion, or Ras translocation. However, addition of exogenous FPP unexpectedly augmented IL-13-induced STAT6 phosphorylation and eotaxin-3 secretion from HBE1 cells without affecting Ras translocation. Pharmacological inhibition of FTase exacerbates allergic asthma, suggesting a protective role for FTase or possibly Ras farnesylation. FPP synergistically augments epithelial eotaxin-3 secretion, indicating a novel Ras-independent farnesylation mechanism or direct FPP effect that promotes epithelial eotaxin-3 production in allergic asthma.
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Affiliation(s)
- Jennifer M Bratt
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA 95817
- Department of Internal Medicine, Center for Comparative Respiratory Biology and Medicine, University of California, Davis, Davis, CA 95817; and
| | - Kevin Y Chang
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA 95817
| | - Michelle Rabowsky
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA 95817
| | - Lisa M Franzi
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA 95817
- Department of Internal Medicine, Center for Comparative Respiratory Biology and Medicine, University of California, Davis, Davis, CA 95817; and
| | - Sean P Ott
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA 95817
- Department of Internal Medicine, Center for Comparative Respiratory Biology and Medicine, University of California, Davis, Davis, CA 95817; and
| | - Simone Filosto
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA 95817
- Department of Internal Medicine, Center for Comparative Respiratory Biology and Medicine, University of California, Davis, Davis, CA 95817; and
- Department of Internal Medicine, Respiratory Signal Transduction, Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA 95616
| | - Tzipora Goldkorn
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA 95817
- Department of Internal Medicine, Center for Comparative Respiratory Biology and Medicine, University of California, Davis, Davis, CA 95817; and
- Department of Internal Medicine, Respiratory Signal Transduction, Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA 95616
| | - Muhammad Arif
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA 95817
- Department of Internal Medicine, Center for Comparative Respiratory Biology and Medicine, University of California, Davis, Davis, CA 95817; and
| | - Jerold A Last
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA 95817
- Department of Internal Medicine, Center for Comparative Respiratory Biology and Medicine, University of California, Davis, Davis, CA 95817; and
| | - Nicholas J Kenyon
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA 95817
- Department of Internal Medicine, Center for Comparative Respiratory Biology and Medicine, University of California, Davis, Davis, CA 95817; and
| | - Amir A Zeki
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA 95817;
- Department of Internal Medicine, Center for Comparative Respiratory Biology and Medicine, University of California, Davis, Davis, CA 95817; and
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211
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Zhang J, Tian XJ, Chen YJ, Wang W, Watkins S, Xing J. Pathway crosstalk enables cells to interpret TGF-β duration. NPJ Syst Biol Appl 2018; 4:18. [PMID: 29872541 PMCID: PMC5972147 DOI: 10.1038/s41540-018-0060-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/28/2018] [Accepted: 05/07/2018] [Indexed: 02/07/2023] Open
Abstract
The detection and transmission of the temporal quality of intracellular and extracellular signals is an essential cellular mechanism. It remains largely unexplored how cells interpret the duration information of a stimulus. In this paper, we performed an integrated quantitative and computational analysis on TGF-β induced activation of SNAIL1, a key transcription factor that regulates several subsequent cell fate decisions such as apoptosis and epithelial-to-mesenchymal transition. We demonstrate that crosstalk among multiple TGF-β activated pathways forms a relay from SMAD to GLI1 that initializes and maintains SNAILl expression, respectively. SNAIL1 functions as a key integrator of information from TGF-β signaling distributed through upstream divergent pathways. The intertwined network serves as a temporal checkpoint, so that cells can generate a transient or sustained expression of SNAIL1 depending on TGF-β duration. Furthermore, we observed that TGF-β treatment leads to an unexpected accumulation of GSK3 molecules in an enzymatically active tyrosine phosphorylation form in Golgi apparatus and ER, followed by accumulation of GSK3 molecules in an enzymatically inhibitive serine phosphorylation in the nucleus. Subsequent model analysis and inhibition experiments revealed that the initial localized increase of GSK3 enzymatic activity couples to the positive feedback loop of the substrate Gli1 to form a network motif with multi-objective functions. That is, the motif is robust against stochastic fluctuations, and has a narrow distribution of response time that is insensitive to initial conditions. Specifically for TGF-β signaling, the motif ensures a smooth relay from SMAD to GLI1 on regulating SNAIL1 expression.
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Affiliation(s)
- Jingyu Zhang
- 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Xiao-Jun Tian
- 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 USA.,4Present Address: School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287 USA
| | - Yi-Jiun Chen
- 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Weikang Wang
- 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Simon Watkins
- 2Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Jianhua Xing
- 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 USA.,3UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232 USA
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212
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Kovary KM, Taylor B, Zhao ML, Teruel MN. Expression variation and covariation impair analog and enable binary signaling control. Mol Syst Biol 2018; 14:e7997. [PMID: 29759982 PMCID: PMC5951153 DOI: 10.15252/msb.20177997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 03/26/2018] [Accepted: 04/05/2018] [Indexed: 11/09/2022] Open
Abstract
Due to noise in the synthesis and degradation of proteins, the concentrations of individual vertebrate signaling proteins were estimated to vary with a coefficient of variation (CV) of approximately 25% between cells. Such high variation is beneficial for population-level regulation of cell functions but abolishes accurate single-cell signal transmission. Here, we measure cell-to-cell variability of relative protein abundance using quantitative proteomics of individual Xenopus laevis eggs and cultured human cells and show that variation is typically much lower, in the range of 5-15%, compatible with accurate single-cell transmission. Focusing on bimodal ERK signaling, we show that variation and covariation in MEK and ERK expression improves controllability of the percentage of activated cells, demonstrating how variation and covariation in expression enables population-level control of binary cell-fate decisions. Together, our study argues for a control principle whereby low expression variation enables accurate control of analog single-cell signaling, while increased variation, covariation, and numbers of pathway components are required to widen the stimulus range over which external inputs regulate binary cell activation to enable precise control of the fraction of activated cells in a population.
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Affiliation(s)
- Kyle M Kovary
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Brooks Taylor
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Michael L Zhao
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Mary N Teruel
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
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213
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Davies AE, Albeck JG. Microenvironmental Signals and Biochemical Information Processing: Cooperative Determinants of Intratumoral Plasticity and Heterogeneity. Front Cell Dev Biol 2018; 6:44. [PMID: 29732370 PMCID: PMC5921997 DOI: 10.3389/fcell.2018.00044] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/03/2018] [Indexed: 12/25/2022] Open
Abstract
Intra-tumor cellular heterogeneity is a major challenge in cancer therapy. Tumors are composed of multiple phenotypic subpopulations that vary in their ability to initiate metastatic tumors and in their sensitivity to chemotherapy. In many cases, cells can transition between these subpopulations, not by genetic mutation, but instead through reversible changes in signal transduction or gene expression programs. This plasticity begins at the level of the microenvironment where local autocrine and paracrine signals, exosomes, tumor–stroma interactions, and extracellular matrix (ECM) composition create a signaling landscape that varies over space and time. The integration of this complex array of signals engages signaling pathways that control gene expression. The resulting modulation of gene expression programs causes individual cells to sample a wide array of phenotypic states that support tumor growth, dissemination, and therapeutic resistance. In this review, we discuss how information flows dynamically within the microenvironmental landscape to inform cell state decisions and to create intra-tumoral heterogeneity. We address the role of plasticity in the acquisition of transient and prolonged drug resistant states and discuss how targeted pharmacological modification of the signaling landscape may be able to constrain phenotypic plasticity, leading to improved treatment responses.
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Affiliation(s)
- Alexander E Davies
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
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214
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Chatterjee M, Acar M. Heritable stress response dynamics revealed by single-cell genealogy. SCIENCE ADVANCES 2018; 4:e1701775. [PMID: 29675464 PMCID: PMC5906080 DOI: 10.1126/sciadv.1701775] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
Cells often respond to environmental stimuli by activating specific transcription factors. Upon exposure to glucose limitation stress, it is known that yeast Saccharomyces cerevisiae cells dephosphorylate the general stress response factor Msn2, leading to its nuclear localization, which in turn activates the expression of many genes. However, the precise dynamics of Msn2 nucleocytoplasmic translocations and whether they are inherited over multiple generations in a stress-dependent manner are not well understood. Tracking Msn2 localization events in yeast lineages grown on a microfluidic chip, here we report how cells modulate the amplitude, duration, frequency, and dynamic pattern of the localization events in response to glucose limitation stress. Single yeast cells were found to modulate the amplitude and frequency of Msn2 nuclear localization, but not its duration. Moreover, the Msn2 localization frequency was epigenetically inherited in descendants of mother cells, leading to a decrease in cell-to-cell variation in localization frequency. An analysis of the time dynamic patterns of nuclear localizations between genealogically related cell pairs using an information theory approach found that the magnitude of pattern similarity increased with stress intensity and was strongly inherited by the descendant cells at the highest stress level. By dissecting how general stress response dynamics is contributed by different modulation schemes over long time scales, our work provides insight into which scheme evolution might have acted on to optimize fitness in stressful environments.
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Affiliation(s)
- Meenakshi Chatterjee
- Department of Electrical Engineering, Yale University, 10 Hillhouse Avenue, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Murat Acar
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06511, USA
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT 06511, USA
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215
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Bouhaddou M, Barrette AM, Stern AD, Koch RJ, DiStefano MS, Riesel EA, Santos LC, Tan AL, Mertz AE, Birtwistle MR. A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens. PLoS Comput Biol 2018; 14:e1005985. [PMID: 29579036 PMCID: PMC5886578 DOI: 10.1371/journal.pcbi.1005985] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 04/05/2018] [Accepted: 01/16/2018] [Indexed: 01/02/2023] Open
Abstract
Most cancer cells harbor multiple drivers whose epistasis and interactions with expression context clouds drug and drug combination sensitivity prediction. We constructed a mechanistic computational model that is context-tailored by omics data to capture regulation of stochastic proliferation and death by pan-cancer driver pathways. Simulations and experiments explore how the coordinated dynamics of RAF/MEK/ERK and PI-3K/AKT kinase activities in response to synergistic mitogen or drug combinations control cell fate in a specific cellular context. In this MCF10A cell context, simulations suggest that synergistic ERK and AKT inhibitor-induced death is likely mediated by BIM rather than BAD, which is supported by prior experimental studies. AKT dynamics explain S-phase entry synergy between EGF and insulin, but simulations suggest that stochastic ERK, and not AKT, dynamics seem to drive cell-to-cell proliferation variability, which in simulations is predictable from pre-stimulus fluctuations in C-Raf/B-Raf levels. Simulations suggest MEK alteration negligibly influences transformation, consistent with clinical data. Tailoring the model to an alternate cell expression and mutation context, a glioma cell line, allows prediction of increased sensitivity of cell death to AKT inhibition. Our model mechanistically interprets context-specific landscapes between driver pathways and cell fates, providing a framework for designing more rational cancer combination therapy. Cancer is a complex and diverse disease. Two people with the same cancer type often respond differently to the same treatment. These differences are primarily driven by the fact that two type-matched tumors can possess distinct sets of mutations and gene expression profiles, provoking differential sensitivity to drugs. Over the past few decades, we have seen a shift away from more broadly cytotoxic drugs to more targeted molecules therapies; but how to match a patient with a specific drug or drug cocktail remains a difficult problem. Here, we build a mechanistic ordinary differential equation model describing the interactions between commonly mutated pan-cancer signaling pathways—receptor tyrosine kinases, Ras/RAF/ERK, PI3K/AKT, mTOR, cell cycle, DNA damage, and apoptosis. We develop methods for how to tailor the model to multi-omics data from a specific biological context, devise a novel stochastic algorithm to induce non-genetic cell-to-cell fluctuations in mRNA and protein quantities over time, and train the model against a wealth of biochemical and cell fate data to gain insight into the systems-level, context-specific control of proliferation and death. One day, we hope models of this kind could be tailored to patient-derived tumor mRNA sequencing data and used to prioritize patient-specific drug regimens.
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Affiliation(s)
- Mehdi Bouhaddou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Anne Marie Barrette
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Alan D. Stern
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Rick J. Koch
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Matthew S. DiStefano
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Eric A. Riesel
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Luis C. Santos
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Annie L. Tan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Alex E. Mertz
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Marc R. Birtwistle
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States of America
- * E-mail:
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216
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Network Motifs Capable of Decoding Transcription Factor Dynamics. Sci Rep 2018; 8:3594. [PMID: 29483553 PMCID: PMC5827039 DOI: 10.1038/s41598-018-21945-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/13/2018] [Indexed: 11/08/2022] Open
Abstract
Transcription factors (TFs) can encode the information of upstream signal in terms of its temporal activation dynamics. However, it remains unclear how different types of TF dynamics are decoded by downstream signalling networks. In this work, we studied all three-node transcriptional networks for their ability to distinguish two types of TF dynamics: amplitude modulation (AM), where the TF is activated with a constant amplitude, and frequency modulation (FM), where the TF activity displays an oscillatory behavior. We found two sets of network topologies: one set can differentially respond to AM TF signal but not to FM; the other set to FM signal but not to AM. Interestingly, there is little overlap between the two sets. We identified the prevalent topological features in each set and gave a mechanistic explanation as to why they can differentially respond to only one type of TF signal. We also found that some network topologies have a weak (not robust) ability to differentially respond to both AM and FM input signals by using different values of parameters for AM and FM cases. Our results provide a novel network mechanism for decoding different TF dynamics.
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217
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Ambrogio C, Köhler J, Zhou ZW, Wang H, Paranal R, Li J, Capelletti M, Caffarra C, Li S, Lv Q, Gondi S, Hunter JC, Lu J, Chiarle R, Santamaría D, Westover KD, Jänne PA. KRAS Dimerization Impacts MEK Inhibitor Sensitivity and Oncogenic Activity of Mutant KRAS. Cell 2018; 172:857-868.e15. [DOI: 10.1016/j.cell.2017.12.020] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/19/2017] [Accepted: 12/15/2017] [Indexed: 01/10/2023]
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218
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Abstract
In their native environment, cells are immersed in a complex milieu of biochemical and biophysical cues. These cues may include growth factors, the extracellular matrix, cell-cell contacts, stiffness, and topography, and they are responsible for regulating cellular behaviors such as adhesion, proliferation, migration, apoptosis, and differentiation. The decision-making process used to convert these extracellular inputs into actions is highly complex and sensitive to changes both in the type of individual cue (e.g., growth factor dose/level, timing) and in how these individual cues are combined (e.g., homotypic/heterotypic combinations). In this review, we highlight recent advances in the development of engineering-based approaches to study the cellular decision-making process. Specifically, we discuss the use of biomaterial platforms that enable controlled and tailored delivery of individual and combined cues, as well as the application of computational modeling to analyses of the complex cellular decision-making networks.
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Affiliation(s)
- Pamela K Kreeger
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , .,Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health , Madison, Wisconsin 53705, USA.,Department of Obstetrics and Gynecology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, USA.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53792, USA
| | - Laura E Strong
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; ,
| | - Kristyn S Masters
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , .,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53792, USA.,Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53792, USA
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219
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Varusai TM, Nguyen LK. Dynamic modelling of the mTOR signalling network reveals complex emergent behaviours conferred by DEPTOR. Sci Rep 2018; 8:643. [PMID: 29330362 PMCID: PMC5766521 DOI: 10.1038/s41598-017-18400-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/01/2017] [Indexed: 01/10/2023] Open
Abstract
The mechanistic Target of Rapamycin (mTOR) signalling network is an evolutionarily conserved network that controls key cellular processes, including cell growth and metabolism. Consisting of the major kinase complexes mTOR Complex 1 and 2 (mTORC1/2), the mTOR network harbours complex interactions and feedback loops. The DEP domain-containing mTOR-interacting protein (DEPTOR) was recently identified as an endogenous inhibitor of both mTORC1 and 2 through direct interactions, and is in turn degraded by mTORC1/2, adding an extra layer of complexity to the mTOR network. Yet, the dynamic properties of the DEPTOR-mTOR network and the roles of DEPTOR in coordinating mTORC1/2 activation dynamics have not been characterised. Using computational modelling, systems analysis and dynamic simulations we show that DEPTOR confers remarkably rich and complex dynamic behaviours to mTOR signalling, including abrupt, bistable switches, oscillations and co-existing bistable/oscillatory responses. Transitions between these distinct modes of behaviour are enabled by modulating DEPTOR expression alone. We characterise the governing conditions for the observed dynamics by elucidating the network in its vast multi-dimensional parameter space, and develop strategies to identify core network design motifs underlying these dynamics. Our findings provide new systems-level insights into the complexity of mTOR signalling contributed by DEPTOR.
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Affiliation(s)
- Thawfeek M Varusai
- European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.,Systems Biology Ireland, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Lan K Nguyen
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia. .,Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, 3800, Australia. .,Systems Biology Ireland, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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220
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Efficacy of the combination of MEK and CDK4/6 inhibitors in vitro and in vivo in KRAS mutant colorectal cancer models. Oncotarget 2018; 7:39595-39608. [PMID: 27167191 PMCID: PMC5129956 DOI: 10.18632/oncotarget.9153] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 04/16/2016] [Indexed: 02/06/2023] Open
Abstract
Purpose Though the efficacy of MEK inhibitors is being investigated in KRAS-mutant colorectal cancers (CRC), early clinical trials of MEK inhibitor monotherapy did not reveal significant antitumor activity. Resistance to MEK inhibitor monotherapy developed through a variety of mechanisms converging in ERK reactivation. Since ERK increases cyclin D expression and increases entry into the cell cycle, we hypothesized that the combination of MEK inhibitors and CDK4/6 inhibitors would have synergistic antitumor activity and cause tumor regression in vivo. Results The combination of MEK and CDK4/6 inhibitors synergistically inhibited cancer cell growth in vitro and caused tumor regression in vivo in cell line and patient-derived xenograft models. Combination therapy markedly decreased levels of phosphorylated ribosomal protein S6 both in vitro and in vivo and decreased Ki67 staining in vivo. Experimental Design We performed in vitro proliferation, colony formation, apoptosis, and senescence assays, and Western blots, on a panel of 11 KRAS mutant CRC cell lines treated with the MEK inhibitor MEK162, the CDK4/6 inhibitor palbociclib, or the combination. We also treated 4 KRAS mutant CRC cell line and patient-derived xenografts with the MEK inhibitor trametinib, the CDK4/6 inhibitor palbociclib, or the combination, and performed immunohistochemical and reverse phase protein array analysis. Conclusions Combined inhibition of both MEK and CDK4/6 is effective in preclinical models of KRAS mutant CRC and justifies a planned phase II clinical trial in patients with refractory KRAS-mutant CRC. Efficacy of the combination of MEK and CDK4/6 inhibitors in vitro and in vivo in KRAS mutant colorectal cancer models.
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221
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Behinaein B, Rudie K, Sangrar W. Petri net siphon analysis and graph theoretic measures for identifying combination therapies in cancer. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:231-243. [PMID: 28113516 DOI: 10.1109/tcbb.2016.2614301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Epidermal Growth Factor Receptor (EGFR) signaling to the Ras-MAPK pathway is implicated in the development and progression of cancer and is a major focus of targeted combination therapies. Physiochemical models have been used for identifying and testing the signal-inhibiting potential of targeted therapies, however, their application to larger multi-pathway networks is limited by the availability of experimentally-determined rate and concentration parameters. An alternate strategy for identifying and evaluating drug-targetable nodes is proposed. A physiochemical model of EGFR-Ras-MAPK signaling is implemented and calibrated to experimental data. Essential topological features of the model are converted into a Petri net and nodes that behave as siphons-a structural property of Petri nets-are identified. Siphons represent potential drug-targets since they are unrecoverable if their values fall below a threshold. Centrality measures are then used to prioritize siphons identified as candidate drug-targets. Single and multiple drug-target combinations are identified which correspond to clinically relevant drug targets and exhibit inhibition synergy in physiochemical simulations of EGF-induced EGFR-Ras-MAPK signaling. Taken together, these studies suggest that siphons and centrality analyses are a promising computational strategy to identify and rank drug-targetable nodes in larger networks as they do not require knowledge of the dynamics of the system, but rely solely on topology.
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222
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Decoding Signal Processing at the Single-Cell Level. Cell Syst 2017; 5:542-543. [PMID: 29284127 DOI: 10.1016/j.cels.2017.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The feedforward circuitry regulating ERK-dependent early response genes acts as a signal integrator rather than a signal persistence detector.
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223
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Saidak Z, Giacobbi AS, Morisse MC, Mammeri Y, Galmiche A. [Mathematical modeling: an essential tool for the study of therapeutic targeting in solid tumors]. Med Sci (Paris) 2017; 33:1055-1062. [PMID: 29261493 DOI: 10.1051/medsci/20173312012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recent progress in biology has made the study of the medical treatment of cancer more effective, but it has also revealed the large complexity of carcinogenesis and cell signaling. For many types of cancer, several therapeutic targets are known and in some cases drugs against these targets exist. Unfortunately, the target proteins often work in networks, resulting in functional adaptation and the development of resilience/resistance to medical treatment. The use of mathematical modeling makes it possible to carry out system-level analyses for improved study of therapeutic targeting in solid tumours. We present the main types of mathematical models used in cancer research and we provide examples illustrating the relevance of these approaches in molecular oncobiology.
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Affiliation(s)
- Zuzana Saidak
- Laboratoire d'oncobiologie moléculaire, Centre de biologie humaine (CBH), CHU Amiens Sud, Amiens, France
| | - Anne-Sophie Giacobbi
- Laboratoire amiénois de mathématique fondamentale et appliquée (LAMFA), CNRS UMR7352, UFR des sciences, Université de Picardie Jules Verne, Amiens, France
| | - Mony Chenda Morisse
- Laboratoire de biochimie, Centre de biologie humaine (CBH), CHU Amiens Sud, Amiens, France
| | - Youcef Mammeri
- Laboratoire amiénois de mathématique fondamentale et appliquée (LAMFA), CNRS UMR7352, UFR des sciences, Université de Picardie Jules Verne, Amiens, France
| | - Antoine Galmiche
- Laboratoire de biochimie, Centre de biologie humaine (CBH), CHU Amiens Sud, Amiens, France - Équipe CHIMERE (Chirurgie et extrémité céphalique, caractérisation morphologique et fonctionnelle), Université de Picardie Jules Verne, Amiens, France
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224
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Pinilla-Macua I, Grassart A, Duvvuri U, Watkins SC, Sorkin A. EGF receptor signaling, phosphorylation, ubiquitylation and endocytosis in tumors in vivo. eLife 2017; 6. [PMID: 29268862 PMCID: PMC5741375 DOI: 10.7554/elife.31993] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/14/2017] [Indexed: 12/11/2022] Open
Abstract
Despite a well-established role for the epidermal growth factor receptor (EGFR) in tumorigenesis, EGFR activities and endocytosis in tumors in vivo have not been studied. We labeled endogenous EGFR with GFP by genome-editing of human oral squamous cell carcinoma cells, which were used to examine EGFR-GFP behavior in mouse tumor xenografts in vivo. Intravital multiphoton imaging, confocal imaging of cryosections and biochemical analysis revealed that localization and trafficking patterns, as well as levels of phosphorylation and ubiquitylation of EGFR in tumors in vivo closely resemble patterns and levels observed in the same cells treated with 20–200 pM EGF in vitro. Consistent with the prediction of low ligand concentrations in tumors, EGFR endocytosis was kinase-dependent and blocked by inhibitors of clathrin-mediated internalization; and EGFR activity was insensitive to Cbl overexpression. Collectively, our data suggest that a small pool of active EGFRs is sufficient to drive tumorigenesis by signaling primarily through the Ras-MAPK pathway.
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Affiliation(s)
- Itziar Pinilla-Macua
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Alexandre Grassart
- Department of Molecular Microbial Pathogenesis, Institute Pasteur, Paris, France
| | - Umamaheswar Duvvuri
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Alexander Sorkin
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States
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225
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Live-cell measurements of kinase activity in single cells using translocation reporters. Nat Protoc 2017; 13:155-169. [PMID: 29266096 DOI: 10.1038/nprot.2017.128] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although kinases are important regulators of many cellular processes, measuring their activity in live cells remains challenging. We have developed kinase translocation reporters (KTRs), which enable multiplexed measurements of the dynamics of kinase activity at a single-cell level. These KTRs are composed of an engineered construct in which a kinase substrate is fused to a bipartite nuclear localization signal (bNLS) and nuclear export signal (NES), as well as to a fluorescent protein for microscopy-based detection of its localization. The negative charge introduced by phosphorylation of the substrate is used to directly modulate nuclear import and export, thereby regulating the reporter's distribution between the cytoplasm and nucleus. The relative cytoplasmic versus nuclear fluorescence of the KTR construct (the C/N ratio) is used as a proxy for the kinase activity in living, single cells. Multiple KTRs can be studied in the same cell by fusing them to different fluorescent proteins. Here, we present a protocol to execute and analyze live-cell microscopy experiments using KTRs. We describe strategies for development of new KTRs and procedures for lentiviral expression of KTRs in a cell line of choice. Cells are then plated in a 96-well plate, from which multichannel fluorescent images are acquired with automated time-lapse microscopy. We provide detailed guidance for a computational analysis and parameterization pipeline. The entire procedure, from virus production to data analysis, can be completed in ∼10 d.
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226
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Smith GA, Taunton J, Weiss A. IL-2Rβ abundance differentially tunes IL-2 signaling dynamics in CD4 + and CD8 + T cells. Sci Signal 2017; 10:10/510/eaan4931. [PMID: 29259099 DOI: 10.1126/scisignal.aan4931] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Interleukin-2 (IL-2) stimulates both activated CD4+ and CD8+ T cells to proliferate. IL-2 signals through an identical receptor complex and promotes the same dose-dependent phosphorylation of the canonical transcription factor STAT5 in both cell types. Despite this, CD8+ T cells enter the S phase earlier and proliferate to a greater extent than do CD4+ T cells in response to IL-2. We identified distinct IL-2 signaling dynamics in CD4+ and CD8+ T cells. In IL-2-stimulated CD8+ T cells, STAT5 phosphorylation increased rapidly and was sustained for 6 hours. In contrast, CD4+ T cells had a biphasic response, with maxima at 15 min and 2 to 4 hours after stimulation. Both cell types required vesicular trafficking, but only CD4+ T cells required new protein synthesis to maintain high phosphorylation of STAT5. Two subunits of the IL-2 receptor, IL-2Rβ and IL-2Rγ, were twice as abundant in CD8+ T cells than in CD4+ T cells. Reduction of IL-2Rβ abundance by 50% was sufficient to convert CD8+ T cells to a CD4+ T cell-like signaling pattern and delay S phase entry. These results suggest that the larger pool of IL-2Rβ chains in CD8+ T cells is required to sustain IL-2 signaling and contributes to the quantitatively greater proliferative response to IL-2 relative to that of CD4+ T cells. This cell type-specific difference in IL-2Rβ abundance appears to tune responses, potentially preventing extensive, autoimmune proliferation of CD4+ T cells, while still enabling sufficient proliferation of CD8+ T cells to control viral infections.
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Affiliation(s)
- Geoffrey A Smith
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA.,Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Arthur Weiss
- Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA. .,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
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227
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Hung YP, Teragawa C, Kosaisawe N, Gillies TE, Pargett M, Minguet M, Distor K, Rocha-Gregg BL, Coloff JL, Keibler MA, Stephanopoulos G, Yellen G, Brugge JS, Albeck JG. Akt regulation of glycolysis mediates bioenergetic stability in epithelial cells. eLife 2017; 6:27293. [PMID: 29239720 PMCID: PMC5730373 DOI: 10.7554/elife.27293] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 12/05/2017] [Indexed: 12/26/2022] Open
Abstract
Cells use multiple feedback controls to regulate metabolism in response to nutrient and signaling inputs. However, feedback creates the potential for unstable network responses. We examined how concentrations of key metabolites and signaling pathways interact to maintain homeostasis in proliferating human cells, using fluorescent reporters for AMPK activity, Akt activity, and cytosolic NADH/NAD+ redox. Across various conditions, including glycolytic or mitochondrial inhibition or cell proliferation, we observed distinct patterns of AMPK activity, including both stable adaptation and highly dynamic behaviors such as periodic oscillations and irregular fluctuations that indicate a failure to reach a steady state. Fluctuations in AMPK activity, Akt activity, and cytosolic NADH/NAD+ redox state were temporally linked in individual cells adapting to metabolic perturbations. By monitoring single-cell dynamics in each of these contexts, we identified PI3K/Akt regulation of glycolysis as a multifaceted modulator of single-cell metabolic dynamics that is required to maintain metabolic stability in proliferating cells.
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Affiliation(s)
- Yin P Hung
- Department of Cell Biology, Harvard Medical School, Boston, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States.,Department of Pathology, Brigham and Women's Hospital, Boston, United States
| | - Carolyn Teragawa
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Nont Kosaisawe
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Taryn E Gillies
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Marta Minguet
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Kevin Distor
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Briana L Rocha-Gregg
- Department of Molecular and Cellular Biology, University of California, Davis, United States
| | - Jonathan L Coloff
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Mark A Keibler
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Gary Yellen
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, United States
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228
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Eich C, Arlt J, Vink CS, Solaimani Kartalaei P, Kaimakis P, Mariani SA, van der Linden R, van Cappellen WA, Dzierzak E. In vivo single cell analysis reveals Gata2 dynamics in cells transitioning to hematopoietic fate. J Exp Med 2017; 215:233-248. [PMID: 29217535 PMCID: PMC5748852 DOI: 10.1084/jem.20170807] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/12/2017] [Accepted: 10/31/2017] [Indexed: 01/07/2023] Open
Abstract
Eich et al. reveal the dynamic expression of the Gata2 transcription factor in single aortic cells transitioning to hematopoietic fate by vital imaging of Gata2Venus mouse embryos. Pulsatile expression level changes highlight an unstable genetic state during hematopoietic cell generation. Cell fate is established through coordinated gene expression programs in individual cells. Regulatory networks that include the Gata2 transcription factor play central roles in hematopoietic fate establishment. Although Gata2 is essential to the embryonic development and function of hematopoietic stem cells that form the adult hierarchy, little is known about the in vivo expression dynamics of Gata2 in single cells. Here, we examine Gata2 expression in single aortic cells as they establish hematopoietic fate in Gata2Venus mouse embryos. Time-lapse imaging reveals rapid pulsatile level changes in Gata2 reporter expression in cells undergoing endothelial-to-hematopoietic transition. Moreover, Gata2 reporter pulsatile expression is dramatically altered in Gata2+/− aortic cells, which undergo fewer transitions and are reduced in hematopoietic potential. Our novel finding of dynamic pulsatile expression of Gata2 suggests a highly unstable genetic state in single cells concomitant with their transition to hematopoietic fate. This reinforces the notion that threshold levels of Gata2 influence fate establishment and has implications for transcription factor–related hematologic dysfunctions.
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Affiliation(s)
- Christina Eich
- Department of Cell Biology, Erasmus Stem Cell Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Jochen Arlt
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Chris S Vink
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, Scotland, UK
| | | | - Polynikis Kaimakis
- Department of Cell Biology, Erasmus Stem Cell Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Samanta A Mariani
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Reinier van der Linden
- Department of Cell Biology, Erasmus Stem Cell Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Wiggert A van Cappellen
- Department of Pathology, Erasmus Optical Imaging Centre, Erasmus Medical Center, Rotterdam, Netherlands
| | - Elaine Dzierzak
- Department of Cell Biology, Erasmus Stem Cell Institute, Erasmus Medical Center, Rotterdam, Netherlands .,Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, Scotland, UK
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229
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Illuminating information transfer in signaling dynamics by optogenetics. Curr Opin Cell Biol 2017; 49:9-15. [DOI: 10.1016/j.ceb.2017.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/06/2017] [Indexed: 11/18/2022]
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230
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Tsuchiya T, Fujii M, Matsuda N, Kunida K, Uda S, Kubota H, Konishi K, Kuroda S. System identification of signaling dependent gene expression with different time-scale data. PLoS Comput Biol 2017; 13:e1005913. [PMID: 29281625 PMCID: PMC5760096 DOI: 10.1371/journal.pcbi.1005913] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 01/09/2018] [Accepted: 12/01/2017] [Indexed: 01/11/2023] Open
Abstract
Cells decode information of signaling activation at a scale of tens of minutes by downstream gene expression with a scale of hours to days, leading to cell fate decisions such as cell differentiation. However, no system identification method with such different time scales exists. Here we used compressed sensing technology and developed a system identification method using data of different time scales by recovering signals of missing time points. We measured phosphorylation of ERK and CREB, immediate early gene expression products, and mRNAs of decoder genes for neurite elongation in PC12 cell differentiation and performed system identification, revealing the input-output relationships between signaling and gene expression with sensitivity such as graded or switch-like response and with time delay and gain, representing signal transfer efficiency. We predicted and validated the identified system using pharmacological perturbation. Thus, we provide a versatile method for system identification using data with different time scales.
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Affiliation(s)
- Takaho Tsuchiya
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Masashi Fujii
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Molecular Genetics Research Laboratory, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Naoki Matsuda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Katsuyuki Kunida
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Laboratory of Computational Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shinsuke Uda
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Kubota
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Katsumi Konishi
- Department of Computer Science, Faculty of Informatics, Kogakuin University, Tokyo, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Corporation, Tokyo, Japan
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231
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Gillies TE, Pargett M, Minguet M, Davies AE, Albeck JG. Linear Integration of ERK Activity Predominates over Persistence Detection in Fra-1 Regulation. Cell Syst 2017; 5:549-563.e5. [PMID: 29199017 DOI: 10.1016/j.cels.2017.10.019] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 08/29/2017] [Accepted: 10/27/2017] [Indexed: 12/14/2022]
Abstract
ERK signaling regulates the expression of target genes, but it is unclear how ERK activity dynamics are interpreted. Here, we investigate this question using simultaneous, live, single-cell imaging of two ERK activity reporters and expression of Fra-1, a target gene controlling epithelial cell identity. We find that Fra-1 is expressed in proportion to the amplitude and duration of ERK activity. In contrast to previous "persistence detector" and "selective filter" models in which Fra-1 expression only occurs when ERK activity persists beyond a threshold duration, our observations demonstrate that the network regulating Fra-1 expression integrates total ERK activity and responds to it linearly. However, exploration of a generalized mathematical model of the Fra-1 coherent feedforward loop demonstrates that it can perform either linear integration or persistence detection, depending on the basal mRNA production rate and protein production delays. Our data indicate that significant basal expression and short delays cause Fra-1 to respond linearly to integrated ERK activity.
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Affiliation(s)
- Taryn E Gillies
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Marta Minguet
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Alex E Davies
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.
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232
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Tudelska K, Markiewicz J, Kochańczyk M, Czerkies M, Prus W, Korwek Z, Abdi A, Błoński S, Kaźmierczak B, Lipniacki T. Information processing in the NF-κB pathway. Sci Rep 2017; 7:15926. [PMID: 29162874 PMCID: PMC5698458 DOI: 10.1038/s41598-017-16166-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/08/2017] [Indexed: 02/07/2023] Open
Abstract
The NF-κB pathway is known to transmit merely 1 bit of information about stimulus level. We combined experimentation with mathematical modeling to elucidate how information about TNF concentration is turned into a binary decision. Using Kolmogorov-Smirnov distance, we quantified the cell’s ability to discern 8 TNF concentrations at each step of the NF-κB pathway, to find that input discernibility decreases as signal propagates along the pathway. Discernibility of low TNF concentrations is restricted by noise at the TNF receptor level, whereas discernibility of high TNF concentrations it is restricted by saturation/depletion of downstream signaling components. Consequently, signal discernibility is highest between 0.03 and 1 ng/ml TNF. Simultaneous exposure to TNF or LPS and a translation inhibitor, cycloheximide, leads to prolonged NF-κB activation and a marked increase of transcript levels of NF-κB inhibitors, IκBα and A20. The impact of cycloheximide becomes apparent after the first peak of nuclear NF-κB translocation, meaning that the NF-κB network not only relays 1 bit of information to coordinate the all-or-nothing expression of early genes, but also over a longer time course integrates information about other stimuli. The NF-κB system should be thus perceived as a feedback-controlled decision-making module rather than a simple information transmission channel.
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Affiliation(s)
- Karolina Tudelska
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Markiewicz
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Marek Kochańczyk
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Maciej Czerkies
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Wiktor Prus
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Zbigniew Korwek
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Ali Abdi
- Department of Biological Sciences and Department of Electrical and Computer Engineering, New Jersey Institute of Technology, New Jersey, United States of America
| | - Sławomir Błoński
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Bogdan Kaźmierczak
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Lipniacki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland.
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233
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Li Y, Roberts J, AkhavanAghdam Z, Hao N. Mitogen-activated protein kinase (MAPK) dynamics determine cell fate in the yeast mating response. J Biol Chem 2017; 292:20354-20361. [PMID: 29123025 DOI: 10.1074/jbc.ac117.000548] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/05/2017] [Indexed: 12/21/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, the exposure to mating pheromone activates a prototypic mitogen-activated protein kinase (MAPK) cascade and triggers a dose-dependent differentiation response. Whereas a high pheromone dose induces growth arrest and formation of a shmoo-like morphology in yeast cells, lower pheromone doses elicit elongated cell growth. Previous population-level analysis has revealed that the MAPK Fus3 plays an important role in mediating this differentiation switch. To further investigate how Fus3 controls the fate decision process at the single-cell level, we developed a specific translocation-based reporter for monitoring Fus3 activity in individual live cells. Using this reporter, we observed strikingly different dynamic patterns of Fus3 activation in single cells differentiated into distinct fates. Cells committed to growth arrest and shmoo formation exhibited sustained Fus3 activation. In contrast, most cells undergoing elongated growth showed either a delayed gradual increase or pulsatile dynamics of Fus3 activity. Furthermore, we found that chemically perturbing Fus3 dynamics with a specific inhibitor could effectively redirect the mating differentiation, confirming the causative role of Fus3 dynamics in driving cell fate decisions. MAPKs mediate proliferation and differentiation signals in mammals and are therapeutic targets in many cancers. Our results highlight the importance of MAPK dynamics in regulating single-cell responses and open up the possibility that MAPK signaling dynamics could be a pharmacological target in therapeutic interventions.
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Affiliation(s)
- Yang Li
- From the Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093
| | - Julie Roberts
- From the Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093
| | - Zohreh AkhavanAghdam
- From the Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093
| | - Nan Hao
- From the Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093
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234
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BCL-X L directly modulates RAS signalling to favour cancer cell stemness. Nat Commun 2017; 8:1123. [PMID: 29066722 PMCID: PMC5654832 DOI: 10.1038/s41467-017-01079-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 08/16/2017] [Indexed: 11/08/2022] Open
Abstract
In tumours, accumulation of chemoresistant cells that express high levels of anti-apoptotic proteins such as BCL-XL is thought to result from the counter selection of sensitive, low expresser clones during progression and/or initial treatment. We herein show that BCL-XL expression is selectively advantageous to cancer cell populations even in the absence of pro-apoptotic pressure. In transformed human mammary epithelial cells BCL-XL favours full activation of signalling downstream of constitutively active RAS with which it interacts in a BH4-dependent manner. Comparative proteomic analysis and functional assays indicate that this is critical for RAS-induced expression of stemness regulators and maintenance of a cancer initiating cell (CIC) phenotype. Resistant cancer cells thus arise from a positive selection driven by BCL-XL modulation of RAS-induced self-renewal, and during which apoptotic resistance is not necessarily the directly selected trait. BCL-XL provides a survival advantage to cancer cells even in the absence of apoptotic pressures. In this study, the authors show that BCL-XL interacts with RAS in a BH4-dependent manner and regulates RAS-mediated activation of pathways involved in the stemness feature of breast cancer cells.
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235
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Li Y, Jin M, O'Laughlin R, Bittihn P, Tsimring LS, Pillus L, Hasty J, Hao N. Multigenerational silencing dynamics control cell aging. Proc Natl Acad Sci U S A 2017; 114:11253-11258. [PMID: 29073021 PMCID: PMC5651738 DOI: 10.1073/pnas.1703379114] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cellular aging plays an important role in many diseases, such as cancers, metabolic syndromes, and neurodegenerative disorders. There has been steady progress in identifying aging-related factors such as reactive oxygen species and genomic instability, yet an emerging challenge is to reconcile the contributions of these factors with the fact that genetically identical cells can age at significantly different rates. Such complexity requires single-cell analyses designed to unravel the interplay of aging dynamics and cell-to-cell variability. Here we use microfluidic technologies to track the replicative aging of single yeast cells and reveal that the temporal patterns of heterochromatin silencing loss regulate cellular life span. We found that cells show sporadic waves of silencing loss in the heterochromatic ribosomal DNA during the early phases of aging, followed by sustained loss of silencing preceding cell death. Isogenic cells have different lengths of the early intermittent silencing phase that largely determine their final life spans. Combining computational modeling and experimental approaches, we found that the intermittent silencing dynamics is important for longevity and is dependent on the conserved Sir2 deacetylase, whereas either sustained silencing or sustained loss of silencing shortens life span. These findings reveal that the temporal patterns of a key molecular process can directly influence cellular aging, and thus could provide guidance for the design of temporally controlled strategies to extend life span.
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Affiliation(s)
- Yang Li
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Meng Jin
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093
- The San Diego Center for Systems Biology, La Jolla, CA 92093
| | - Richard O'Laughlin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Philip Bittihn
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093
- The San Diego Center for Systems Biology, La Jolla, CA 92093
| | - Lev S Tsimring
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093
- The San Diego Center for Systems Biology, La Jolla, CA 92093
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093
| | - Jeff Hasty
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093
- The San Diego Center for Systems Biology, La Jolla, CA 92093
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093;
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093
- The San Diego Center for Systems Biology, La Jolla, CA 92093
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236
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Merchant M, Moffat J, Schaefer G, Chan J, Wang X, Orr C, Cheng J, Hunsaker T, Shao L, Wang SJ, Wagle MC, Lin E, Haverty PM, Shahidi-Latham S, Ngu H, Solon M, Eastham-Anderson J, Koeppen H, Huang SMA, Schwarz J, Belvin M, Kirouac D, Junttila MR. Combined MEK and ERK inhibition overcomes therapy-mediated pathway reactivation in RAS mutant tumors. PLoS One 2017; 12:e0185862. [PMID: 28982154 PMCID: PMC5628883 DOI: 10.1371/journal.pone.0185862] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/20/2017] [Indexed: 12/19/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) pathway dysregulation is implicated in >30% of all cancers, rationalizing the development of RAF, MEK and ERK inhibitors. While BRAF and MEK inhibitors improve BRAF mutant melanoma patient outcomes, these inhibitors had limited success in other MAPK dysregulated tumors, with insufficient pathway suppression and likely pathway reactivation. In this study we show that inhibition of either MEK or ERK alone only transiently inhibits the MAPK pathway due to feedback reactivation. Simultaneous targeting of both MEK and ERK nodes results in deeper and more durable suppression of MAPK signaling that is not achievable with any dose of single agent, in tumors where feedback reactivation occurs. Strikingly, combined MEK and ERK inhibition is synergistic in RAS mutant models but only additive in BRAF mutant models where the RAF complex is dissociated from RAS and thus feedback productivity is disabled. We discovered that pathway reactivation in RAS mutant models occurs at the level of CRAF with combination treatment resulting in a markedly more active pool of CRAF. However, distinct from single node targeting, combining MEK and ERK inhibitor treatment effectively blocks the downstream signaling as assessed by transcriptional signatures and phospho-p90RSK. Importantly, these data reveal that MAPK pathway inhibitors whose activity is attenuated due to feedback reactivation can be rescued with sufficient inhibition by using a combination of MEK and ERK inhibitors. The MEK and ERK combination significantly suppresses MAPK pathway output and tumor growth in vivo to a greater extent than the maximum tolerated doses of single agents, and results in improved anti-tumor activity in multiple xenografts as well as in two Kras mutant genetically engineered mouse (GEM) models. Collectively, these data demonstrate that combined MEK and ERK inhibition is functionally unique, yielding greater than additive anti-tumor effects and elucidates a highly effective combination strategy in MAPK-dependent cancer, such as KRAS mutant tumors.
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Affiliation(s)
- Mark Merchant
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California, United States of America
| | - John Moffat
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Gabriele Schaefer
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California, United States of America
| | - Jocelyn Chan
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California, United States of America
| | - Xi Wang
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California, United States of America
| | - Christine Orr
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California, United States of America
| | - Jason Cheng
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California, United States of America
| | - Thomas Hunsaker
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California, United States of America
| | - Lily Shao
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California, United States of America
| | - Stephanie J. Wang
- Department of Biological Engineering, The Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Marie-Claire Wagle
- Department of Oncology Biomarker Development, Genentech, Inc., South San Francisco, California, United States of America
| | - Eva Lin
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California, United States of America
| | - Peter M. Haverty
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California, United States of America
| | - Sheerin Shahidi-Latham
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California, United States of America
| | - Hai Ngu
- Department of Pathology, Genentech, Inc., South San Francisco, California, United States of America
| | - Margaret Solon
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Jeffrey Eastham-Anderson
- Department of Pathology, Genentech, Inc., South San Francisco, California, United States of America
| | - Hartmut Koeppen
- Department of Pathology, Genentech, Inc., South San Francisco, California, United States of America
| | - Shih-Min A. Huang
- Department of Oncology Biomarker Development, Genentech, Inc., South San Francisco, California, United States of America
| | - Jacob Schwarz
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Marcia Belvin
- Department of Cancer Immunology, Genentech, Inc., South San Francisco, California, United States of America
| | - Daniel Kirouac
- Department of Pre-clinical & Translational Pharmacokinetics Genentech, Inc., South San Francisco, California, United States of America
| | - Melissa R. Junttila
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California, United States of America
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237
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Multistep phosphorelay in fungi: the enigma of multiple signals and a limited number of signaling pathways. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1342-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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238
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Zhou XX, Fan LZ, Li P, Shen K, Lin MZ. Optical control of cell signaling by single-chain photoswitchable kinases. Science 2017; 355:836-842. [PMID: 28232577 DOI: 10.1126/science.aah3605] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 11/15/2016] [Accepted: 01/23/2017] [Indexed: 12/31/2022]
Abstract
Protein kinases transduce signals to regulate a wide array of cellular functions in eukaryotes. A generalizable method for optical control of kinases would enable fine spatiotemporal interrogation or manipulation of these various functions. We report the design and application of single-chain cofactor-free kinases with photoswitchable activity. We engineered a dimeric protein, pdDronpa, that dissociates in cyan light and reassociates in violet light. Attaching two pdDronpa domains at rationally selected locations in the kinase domain, we created the photoswitchable kinases psRaf1, psMEK1, psMEK2, and psCDK5. Using these photoswitchable kinases, we established an all-optical cell-based assay for screening inhibitors, uncovered a direct and rapid inhibitory feedback loop from ERK to MEK1, and mediated developmental changes and synaptic vesicle transport in vivo using light.
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Affiliation(s)
- Xin X Zhou
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Linlin Z Fan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Pengpeng Li
- Howard Hughes Medical Institute and Department of Biology, Stanford University, Stanford, CA, USA
| | - Kang Shen
- Howard Hughes Medical Institute and Department of Biology, Stanford University, Stanford, CA, USA
| | - Michael Z Lin
- Department of Bioengineering, Stanford University, Stanford, CA, USA. .,Department of Neurobiology, Stanford University, Stanford, CA, USA
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239
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Kallenberger SM, Unger AL, Legewie S, Lymperopoulos K, Klingmüller U, Eils R, Herten DP. Correlated receptor transport processes buffer single-cell heterogeneity. PLoS Comput Biol 2017; 13:e1005779. [PMID: 28945754 PMCID: PMC5659801 DOI: 10.1371/journal.pcbi.1005779] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 10/27/2017] [Accepted: 09/19/2017] [Indexed: 11/25/2022] Open
Abstract
Cells typically vary in their response to extracellular ligands. Receptor transport processes modulate ligand-receptor induced signal transduction and impact the variability in cellular responses. Here, we quantitatively characterized cellular variability in erythropoietin receptor (EpoR) trafficking at the single-cell level based on live-cell imaging and mathematical modeling. Using ensembles of single-cell mathematical models reduced parameter uncertainties and showed that rapid EpoR turnover, transport of internalized EpoR back to the plasma membrane, and degradation of Epo-EpoR complexes were essential for receptor trafficking. EpoR trafficking dynamics in adherent H838 lung cancer cells closely resembled the dynamics previously characterized by mathematical modeling in suspension cells, indicating that dynamic properties of the EpoR system are widely conserved. Receptor transport processes differed by one order of magnitude between individual cells. However, the concentration of activated Epo-EpoR complexes was less variable due to the correlated kinetics of opposing transport processes acting as a buffering system. Cell surface receptors translate extracellular ligand concentrations to intracellular responses. Receptor transport between the plasma membrane and other cellular compartments regulates the number of accessible receptors at the plasma membrane that determines the strength of downstream pathway activation at a given ligand concentration. In cell populations, pathway activation strength and cellular responses vary between cells. Understanding origins of cell-to-cell variability is highly relevant for cancer research, motivated by the problem of fractional killing by chemotherapies and development of resistance in subpopulations of tumor cells. The erythropoietin receptor (EpoR) is a characteristic example of a receptor system that strongly depends on receptor transport processes. It is involved in several cellular processes, such as differentiation or proliferation, regulates the renewal of erythrocytes, and is expressed in several tumors. To investigate the involvement of receptor transport processes in cell-to-cell variability, we quantitatively characterized trafficking of EpoR in individual cells by combining live-cell imaging with mathematical modeling. Thereby, we found that EpoR dynamics was strongly dependent on rapid receptor transport and turnover. Interestingly, although transport processes largely differed between individual cells, receptor concentrations in cellular compartments were robust to variability in trafficking processes due to the correlated kinetics of opposing transport processes.
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Affiliation(s)
- Stefan M. Kallenberger
- Department for Bioinformatics and Functional Genomics, Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Anne L. Unger
- Cellnetworks Cluster and Institute of Physical Chemistry, BioQuant, Heidelberg University, Heidelberg, Germany
| | | | - Konstantinos Lymperopoulos
- Cellnetworks Cluster and Institute of Physical Chemistry, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Ursula Klingmüller
- Division Systems Biology of Signal Transduction, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- * E-mail: (DPH); (RE); (UK)
| | - Roland Eils
- Department for Bioinformatics and Functional Genomics, Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
- * E-mail: (DPH); (RE); (UK)
| | - Dirk-Peter Herten
- Cellnetworks Cluster and Institute of Physical Chemistry, BioQuant, Heidelberg University, Heidelberg, Germany
- * E-mail: (DPH); (RE); (UK)
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240
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de la Cova C, Townley R, Regot S, Greenwald I. A Real-Time Biosensor for ERK Activity Reveals Signaling Dynamics during C. elegans Cell Fate Specification. Dev Cell 2017; 42:542-553.e4. [PMID: 28826819 PMCID: PMC5595649 DOI: 10.1016/j.devcel.2017.07.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/19/2017] [Accepted: 07/20/2017] [Indexed: 01/06/2023]
Abstract
Kinase translocation reporters (KTRs) are genetically encoded fluorescent activity sensors that convert kinase activity into a nucleocytoplasmic shuttling equilibrium for visualizing single-cell signaling dynamics. Here, we adapt the first-generation KTR for extracellular signal-regulated kinase (ERK) to allow easy implementation in vivo. This sensor, "ERK-nKTR," allows quantitative and qualitative assessment of ERK activity by analysis of individual nuclei and faithfully reports ERK activity during development and neural function in diverse cell contexts in Caenorhabditis elegans. Analysis of ERK activity over time in the vulval precursor cells, a well-characterized paradigm of epidermal growth factor receptor (EGFR)-Ras-ERK signaling, has identified dynamic features not evident from analysis of developmental endpoints alone, including pulsatile frequency-modulated signaling associated with proximity to the EGF source. The toolkit described here will facilitate studies of ERK signaling in other C. elegans contexts, and the design features will enable implementation of this technology in other multicellular organisms.
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Affiliation(s)
- Claire de la Cova
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Biochemistry & Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Robert Townley
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Sergi Regot
- Department of Molecular Biology & Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Iva Greenwald
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Biochemistry & Molecular Biophysics, Columbia University Medical Center, New York, NY, USA.
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241
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Dessauges C, Pertz O. Developmental ERK Signaling Goes Digital. Dev Cell 2017; 42:443-444. [PMID: 28898676 DOI: 10.1016/j.devcel.2017.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reporting in Developmental Cell, de la Cova et al. (2017) present a biosensor to measure ERK activity dynamics in C. elegans larvae. They find that fate decision signaling involves frequency-modulated, digital ERK activity pulses. These findings may explain how graded morphogen signals are converted into precise and robust cell fate patterns.
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Affiliation(s)
- Coralie Dessauges
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland.
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242
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Khamo JS, Krishnamurthy VV, Sharum SR, Mondal P, Zhang K. Applications of Optobiology in Intact Cells and Multicellular Organisms. J Mol Biol 2017; 429:2999-3017. [PMID: 28882542 DOI: 10.1016/j.jmb.2017.08.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 08/26/2017] [Accepted: 08/28/2017] [Indexed: 12/25/2022]
Abstract
Temporal kinetics and spatial coordination of signal transduction in cells are vital for cell fate determination. Tools that allow for precise modulation of spatiotemporal regulation of intracellular signaling in intact cells and multicellular organisms remain limited. The emerging optobiological approaches use light to control protein-protein interaction in live cells and multicellular organisms. Optobiology empowers light-mediated control of diverse cellular and organismal functions such as neuronal activity, intracellular signaling, gene expression, cell proliferation, differentiation, migration, and apoptosis. In this review, we highlight recent developments in optobiology, focusing on new features of second-generation optobiological tools. We cover applications of optobiological approaches in the study of cellular and organismal functions, discuss current challenges, and present our outlook. Taking advantage of the high spatial and temporal resolution of light control, optobiology promises to provide new insights into the coordination of signaling circuits in intact cells and multicellular organisms.
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Affiliation(s)
- John S Khamo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Savanna R Sharum
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Payel Mondal
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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243
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Lin YL, Persaud SD, Nhieu J, Wei LN. Cellular Retinoic Acid-Binding Protein 1 Modulates Stem Cell Proliferation to Affect Learning and Memory in Male Mice. Endocrinology 2017; 158:3004-3014. [PMID: 28911165 PMCID: PMC5659671 DOI: 10.1210/en.2017-00353] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/14/2017] [Indexed: 01/05/2023]
Abstract
Retinoic acid (RA) is the active ingredient of vitamin A. It exerts its canonical activity by binding to nuclear RA receptors (RARs) to regulate gene expression. Increasingly, RA is also known to elicit nongenomic RAR-independent activities, most widely detected in activating extracellular regulated kinase (ERK)1/2. This study validated the functional role of cellular retinoic acid-binding protein 1 (Crabp1) in mediating nongenomic activity in RA, specifically activating ERK1/2 to rapidly augment the cell cycle by expanding the growth 1 phase and slowing down embryonic stem cell and neural stem cell (NSC) proliferation. The study further uncovered the physiological activity of Crabp1 in modulating NSC proliferation and animal behavior. In the Crabp1 knockout mouse hippocampus, where Crabp1 is otherwise detected in the subgranular zone, neurogenesis and NSC proliferation increased and hippocampus-dependent brain functions such as learning and memory correspondingly improved. This study established the physiological role of Crabp1 in modulating stem cell proliferation and hippocampus-dependent brain activities such as learning and memory.
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Affiliation(s)
- Yu-Lung Lin
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455
| | - Shawna D. Persaud
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jennifer Nhieu
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455
| | - Li-Na Wei
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455
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244
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Wilson MZ, Ravindran PT, Lim WA, Toettcher JE. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell 2017; 67:757-769.e5. [PMID: 28826673 DOI: 10.1016/j.molcel.2017.07.016] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/12/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
Abstract
Cell signaling networks coordinate specific patterns of protein expression in response to external cues, yet the logic by which signaling pathway activity determines the eventual abundance of target proteins is complex and poorly understood. Here, we describe an approach for simultaneously controlling the Ras/Erk pathway and monitoring a target gene's transcription and protein accumulation in single live cells. We apply our approach to dissect how Erk activity is decoded by immediate early genes (IEGs). We find that IEG transcription decodes Erk dynamics through a shared band-pass filtering circuit; repeated Erk pulses transcribe IEGs more efficiently than sustained Erk inputs. However, despite highly similar transcriptional responses, each IEG exhibits dramatically different protein-level accumulation, demonstrating a high degree of post-transcriptional regulation by combinations of multiple pathways. Our results demonstrate that the Ras/Erk pathway is decoded by both dynamic filters and logic gates to shape target gene responses in a context-specific manner.
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Affiliation(s)
- Maxwell Z Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Pavithran T Ravindran
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Wendell A Lim
- Howard Hughes Medical Institute; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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245
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Rattanasinchai C, Llewellyn BJ, Conrad SE, Gallo KA. MLK3 regulates FRA-1 and MMPs to drive invasion and transendothelial migration in triple-negative breast cancer cells. Oncogenesis 2017; 6:e345. [PMID: 28604765 PMCID: PMC5519193 DOI: 10.1038/oncsis.2017.44] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/14/2017] [Accepted: 04/17/2017] [Indexed: 02/06/2023] Open
Abstract
Mixed-lineage kinase 3 (MLK3), a mitogen-activated protein kinase kinase kinase (MAP3K), has critical roles in metastasis of triple-negative breast cancer (TNBC), in part by regulating paxillin phosphorylation and focal adhesion turnover. However the mechanisms and the distinct step(s) of the metastatic processes through which MLK3 exerts its influence are not fully understood. Here we report that in non-metastatic, estrogen receptor-positive breast cancer (ER+ BC) cells, induced MLK3 expression robustly upregulates the oncogenic transcription factor, FOS-related antigen-1 (FRA-1), which is accompanied by elevation of matrix metalloproteinases (MMPs), MMP-1 and MMP-9. MLK3-induced ER+ BC cell invasion is abrogated by FRA-1 silencing, demonstrating that MLK3 drives invasion through FRA-1. Conversely, in metastatic TNBC models, high FRA-1 levels are significantly reduced upon depletion of MLK3 by either gene silencing or by the CRISPR/Cas9n editing approach. Furthermore, ablation of MLK3 or MLK inhibitor treatment decreases expression of both MMP-1 and MMP-9. Consistent with the role of tumor cell-derived MMP-1 in endothelial permeability and transendothelial migration, both of these are reduced in MLK3-depleted TNBC cells. In addition, MLK inhibitor treatment or MLK3 depletion, which downregulates MMP-9 expression, renders TNBC cells defective in Matrigel invasion. Furthermore, circulating tumor cells derived from TNBC-bearing mice display increased levels of FRA-1 and MMP-1 compared with parental cells, supporting a role for the MLK3–FRA-1–MMP-1 signaling axis in vascular intravasation. Our results demonstrating the requirement for MLK3 in controlling the FRA-1/MMPs axis suggest that MLK3 is a promising therapeutic target for treatment of TNBC.
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Affiliation(s)
- C Rattanasinchai
- Department of Physiology, Michigan State University, East Lansing, MI, USA.,Cell and Molecular Biology Program, Michigan State University, East Lansing, MI, USA
| | - B J Llewellyn
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - S E Conrad
- Cell and Molecular Biology Program, Michigan State University, East Lansing, MI, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - K A Gallo
- Department of Physiology, Michigan State University, East Lansing, MI, USA.,Cell and Molecular Biology Program, Michigan State University, East Lansing, MI, USA
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246
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Zhang Z, Stickney Z, Duong N, Curley K, Lu B. AAV-based dual-reporter circuit for monitoring cell signaling in living human cells. J Biol Eng 2017; 11:18. [PMID: 28592991 PMCID: PMC5458475 DOI: 10.1186/s13036-017-0060-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/20/2017] [Indexed: 01/12/2023] Open
Abstract
Background High-throughput methods based on molecular reporters have greatly advanced our knowledge of cell signaling in mammalian cells. However, their ability to monitor various types of cells is markedly limited by the inefficiency of reporter gene delivery. Recombinant adeno-associated virus (AAV) vectors are efficient tools widely used for delivering and expressing transgenes in diverse animal cells in vitro and in vivo. Here we present the design, construction and validation of a novel AAV-based dual-reporter circuit that can be used to monitor and quantify cell signaling in living human cells. Results We first design and construct the AAV-based reporter system. We then validate the versatility and specificity of this system in monitoring and quantifying two important cell signaling pathways, inflammation (NFκB) and cell growth and differentiation (AP-1), in cultured HEK293 and MCF-7 cells. Our results demonstrate that the AAV reporter system is both specific and versatile, and it can be used in two common experimental protocols including transfection with plasmid DNA and transduction with packaged viruses. Importantly, this system is efficient, with a high signal-to-background noise ratio, and can be easily adapted to monitor other common signaling pathways. Conclusions The AAV-based system extends the dual-reporter technology to more cell types, allowing for cost-effective and high throughput applications. Electronic supplementary material The online version of this article (doi:10.1186/s13036-017-0060-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhiwen Zhang
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053 USA
| | - Zachary Stickney
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053 USA
| | - Natalie Duong
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053 USA
| | - Kevin Curley
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053 USA
| | - Biao Lu
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053 USA
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247
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Zahavi EE, Maimon R, Perlson E. Spatial-specific functions in retrograde neuronal signalling. Traffic 2017; 18:415-424. [DOI: 10.1111/tra.12487] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/16/2017] [Accepted: 04/05/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Eitan Erez Zahavi
- Department of Physiology and Pharmacology; Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv Israel
| | - Roy Maimon
- Department of Physiology and Pharmacology; Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv Israel
| | - Eran Perlson
- Department of Physiology and Pharmacology; Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv Israel
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248
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Cooper S, Bakal C. Accelerating Live Single-Cell Signalling Studies. Trends Biotechnol 2017; 35:422-433. [PMID: 28161141 DOI: 10.1016/j.tibtech.2017.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/24/2016] [Accepted: 01/06/2017] [Indexed: 12/21/2022]
Abstract
The dynamics of signalling networks that couple environmental conditions with cellular behaviour can now be characterised in exquisite detail using live single-cell imaging experiments. Recent improvements in our abilities to introduce fluorescent sensors into cells, coupled with advances in pipelines for quantifying and extracting single-cell data, mean that high-throughput systematic analyses of signalling dynamics are becoming possible. In this review, we consider current technologies that are driving progress in the scale and range of such studies. Moreover, we discuss novel approaches that are allowing us to explore how pathways respond to changes in inputs and even predict the fate of a cell based upon its signalling history and state.
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Affiliation(s)
- Sam Cooper
- The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK; Department of Computational Systems Medicine, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
| | - Chris Bakal
- The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
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249
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Mönke G, Cristiano E, Finzel A, Friedrich D, Herzel H, Falcke M, Loewer A. Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells. Sci Rep 2017; 7:46571. [PMID: 28417973 PMCID: PMC5394551 DOI: 10.1038/srep46571] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/17/2017] [Indexed: 01/07/2023] Open
Abstract
Cellular signaling systems precisely transmit information in the presence of molecular noise while retaining flexibility to accommodate the needs of individual cells. To understand design principles underlying such versatile signaling, we analyzed the response of the tumor suppressor p53 to varying levels of DNA damage in hundreds of individual cells and observed a switch between distinct signaling modes characterized by isolated pulses and sustained oscillations of p53 accumulation. Guided by dynamic systems theory we show that this requires an excitable network structure comprising positive feedback and provide experimental evidence for its molecular identity. The resulting data-driven model reproduced all features of measured signaling responses and is sufficient to explain their heterogeneity in individual cells. We present evidence that heterogeneity in the levels of the feedback regulator Wip1 sets cell-specific thresholds for p53 activation, providing means to modulate its response through interacting signaling pathways. Our results demonstrate how excitable signaling networks can provide high specificity, sensitivity and robustness while retaining unique possibilities to adjust their function to the physiology of individual cells.
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Affiliation(s)
- Gregor Mönke
- Mathematical Cell Physiology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Elena Cristiano
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Ana Finzel
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Dhana Friedrich
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité and Humboldt University, Berlin, Germany
| | - Martin Falcke
- Mathematical Cell Physiology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Alexander Loewer
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
- Department of Biology, Technische Universitaet Darmstadt, Germany
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250
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Lane K, Van Valen D, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe'er D, Boutet SC, Covert MW. Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation. Cell Syst 2017; 4:458-469.e5. [PMID: 28396000 DOI: 10.1016/j.cels.2017.03.010] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/16/2016] [Accepted: 03/15/2017] [Indexed: 02/02/2023]
Abstract
Signaling proteins display remarkable cell-to-cell heterogeneity in their dynamic responses to stimuli, but the consequences of this heterogeneity remain largely unknown. For instance, the contribution of the dynamics of the innate immune transcription factor nuclear factor κB (NF-κB) to gene expression output is disputed. Here we explore these questions by integrating live-cell imaging approaches with single-cell sequencing technologies. We used this approach to measure both the dynamics of lipopolysaccharide-induced NF-κB activation and the global transcriptional response in the same individual cell. Our results identify multiple, distinct cytokine expression patterns that are correlated with NF-κB activation dynamics, establishing a functional role for NF-κB dynamics in determining cellular phenotypes. Applications of this approach to other model systems and single-cell sequencing technologies have significant potential for discovery, as it is now possible to trace cellular behavior from the initial stimulus, through the signaling pathways, down to genome-wide changes in gene expression, all inside of a single cell.
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Affiliation(s)
- Keara Lane
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - David Van Valen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Mialy M DeFelice
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Derek N Macklin
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Takamasa Kudo
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Ariel Jaimovich
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ambrose Carr
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Dana Pe'er
- Program in Computational and Systems Biology, Sloan Kettering Institute, New York, NY 10065, USA
| | - Stéphane C Boutet
- R&D Department, Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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