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Lee AA, Kim NH, Alvarez S, Ren H, DeGrandchamp JB, Lew LJN, Groves JT. Bimodality in Ras signaling originates from processivity of the Ras activator SOS without deterministic bistability. SCIENCE ADVANCES 2024; 10:eadi0707. [PMID: 38905351 PMCID: PMC11192083 DOI: 10.1126/sciadv.adi0707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 05/15/2024] [Indexed: 06/23/2024]
Abstract
Ras is a small GTPase that is central to important functional decisions in diverse cell types. An important aspect of Ras signaling is its ability to exhibit bimodal or switch-like activity. We describe the total reconstitution of a receptor-mediated Ras activation-deactivation reaction catalyzed by SOS and p120-RasGAP on supported lipid membrane microarrays. The results reveal a bimodal Ras activation response, which is not a result of deterministic bistability but is rather driven by the distinct processivity of the Ras activator, SOS. Furthermore, the bimodal response is controlled by the condensation state of the scaffold protein, LAT, to which SOS is recruited. Processivity-driven bimodality leads to stochastic bursts of Ras activation even under strongly deactivating conditions. This behavior contrasts deterministic bistability and may be more resistant to pharmacological inhibition.
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Affiliation(s)
- Albert A. Lee
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Neil H. Kim
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Steven Alvarez
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA
| | - He Ren
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | | | - L. J. Nugent Lew
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Jay T. Groves
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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2
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Manohar SM. Shedding Light on Intracellular Proteins using Flow Cytometry. Cell Biochem Biophys 2024:10.1007/s12013-024-01338-1. [PMID: 38831173 DOI: 10.1007/s12013-024-01338-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2024] [Indexed: 06/05/2024]
Abstract
Intracellular protein abundance is routinely measured in mammalian cells using population-based techniques such as western blotting which fail to capture single cell protein levels or using fluorescence microscopy which is although suitable for single cell protein detection but not for rapid analysis of large no. of cells. Flow cytometry offers rapid, high-throughput, multiparameter-based analysis of intracellular protein expression in statistically significant no. of cells at single cell resolution. In past few decades, customized assays have been developed for flow cytometric detection of specific intracellular proteins. This review discusses the scope of flow cytometry for intracellular protein detection in mammalian cells along with specific applications. Technological advancements to overcome the limitations of traditional flow cytometry for the same are also discussed.
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Affiliation(s)
- Sonal M Manohar
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be) University, Vile Parle (West), Mumbai, 400056, India.
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3
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Takayama M, Maeda S, Watanabe D, Takebayashi K, Hiroshima M, Ueda M. Cholesterol suppresses spontaneous activation of EGFR-mediated signal transduction. Biochem Biophys Res Commun 2024; 704:149673. [PMID: 38401305 DOI: 10.1016/j.bbrc.2024.149673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 01/30/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Epidermal growth factor receptor (EGFR)-mediated signal transduction controls cell growth and proliferation. The signaling pathway is regulated so that it is activated only by external EGF stimuli, but the mechanisms that prevent EGF-independent spontaneous activation of EGFR-mediated signaling are unknown. Here we report cholesterol depletion activates EGFR-mediated signaling without EGF. We applied automated single-molecule imaging to EGFR and characterized the lateral diffusion and cluster formation on cholesterol-depleted and cholesterol-supplemented membranes. In cells in which cholesterol was depleted by methyl-β-cyclodextrin (MβCD) treatment, EGFR exhibited a reduction in lateral diffusion, an acceleration of cluster formation, and autophosphorylation without EGF. Concurrently, extracellular signal-regulated kinase (ERK), which is regulated by EGFR-mediated signaling, exhibited phosphorylation and nuclear translocation without EGF. These cholesterol depletion-induced changes were similar, albeit less efficient, to those that occurred with EGF stimulation in normal cells without MβCD, indicating the spontaneous activation of EGFR signaling. The exogenous supplementation of cholesterol suppressed the MβCD-induced spontaneous activation of EGFR and ERK nuclear translocation. Single-molecule imaging of EGFR in a large number of cells revealed cell-to-cell heterogeneity, with a sub-population showing a high ability for spontaneous activation. These results provide evidence that EGFR-mediated signaling is properly regulated by cholesterol metabolism to prevent uncontrolled spontaneous activation.
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Affiliation(s)
- Miri Takayama
- Laboratory of Single Molecular Biology, Graduate School of Science and Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, BDR (Biosystems and Dynamics Research Center), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Sakura Maeda
- Laboratory of Single Molecular Biology, Graduate School of Science and Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, BDR (Biosystems and Dynamics Research Center), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Daisuke Watanabe
- Laboratory of Single Molecular Biology, Graduate School of Science and Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, BDR (Biosystems and Dynamics Research Center), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Kazutoshi Takebayashi
- Laboratory of Single Molecular Biology, Graduate School of Science and Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, BDR (Biosystems and Dynamics Research Center), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Michio Hiroshima
- Laboratory of Single Molecular Biology, Graduate School of Science and Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, BDR (Biosystems and Dynamics Research Center), RIKEN, Suita, Osaka, 565-0874, Japan.
| | - Masahiro Ueda
- Laboratory of Single Molecular Biology, Graduate School of Science and Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, BDR (Biosystems and Dynamics Research Center), RIKEN, Suita, Osaka, 565-0874, Japan.
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4
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Zhang J, Joshua AM, Li Y, O'Meara CH, Morris MJ, Khachigian LM. Targeted therapy, immunotherapy, and small molecules and peptidomimetics as emerging immunoregulatory agents for melanoma. Cancer Lett 2024; 586:216633. [PMID: 38281663 DOI: 10.1016/j.canlet.2024.216633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024]
Abstract
Primary cutaneous melanoma is the most lethal of all skin neoplasms and its incidence is increasing. Clinical management of advanced melanoma in the last decade has been revolutionised by the availability of immunotherapies and targeted therapies, used alone and in combination. This article summarizes advances in the treatment of late-stage melanoma including use of protein kinase inhibitors, antibody-based immune checkpoint inhibitors, adoptive immunotherapy, vaccines and more recently, small molecules and peptidomimetics as emerging immunoregulatory agents.
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Affiliation(s)
- Jingwen Zhang
- Vascular Biology and Translational Research, Department of Pathology, School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Anthony M Joshua
- Kinghorn Cancer Centre, St Vincent's Hospital, Garvan Institute of Medical Research, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Yue Li
- Vascular Biology and Translational Research, Department of Pathology, School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Connor H O'Meara
- Department of Otorhinolaryngology, Head & Neck Surgery, ANU Medical School and Canberra Health Services, Australian National University, Acton, Canberra, ACT, Australia
| | - Margaret J Morris
- Department of Pharmacology, School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Levon M Khachigian
- Vascular Biology and Translational Research, Department of Pathology, School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia.
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5
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Lee AA, Kim NH, Alvarez S, Ren H, DeGrandchamp JB, Lew LJN, Groves JT. Bimodality in Ras signaling originates from processivity of the Ras activator SOS without classic kinetic bistability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549263. [PMID: 37503094 PMCID: PMC10370109 DOI: 10.1101/2023.07.17.549263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Ras is a small GTPase that is central to important functional decisions in diverse cell types. An important aspect of Ras signaling is its ability to exhibit bimodal, or switch-like activity. We describe the total reconstitution of a receptor-mediated Ras activation-deactivation reaction catalyzed by SOS and p120-RasGAP on supported lipid membrane microarrays. The results reveal a bimodal Ras activation response, which is not a result of classic kinetic bistability, but is rather driven by the distinct processivity of the Ras activator, SOS. Furthermore, the bimodal response is controlled by the condensation state of the scaffold protein, LAT, to which SOS is recruited. Processivity-driven bimodality leads to stochastic bursts of Ras activation even under strongly deactivating conditions. This behavior contrasts classic kinetic bistability and is distinctly more resistant to pharmacological inhibition.
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6
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Wang L, Li S, Cai K, Xiao Y, Ye L. TLR7 Agonists Modulate the Activation of Human Conjunctival Epithelial Cells Induced by IL-1β via the ERK1/2 Signaling Pathway. Inflammation 2023:10.1007/s10753-023-01818-1. [PMID: 37154978 DOI: 10.1007/s10753-023-01818-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 05/10/2023]
Abstract
Conjunctival epithelia cells play an important role in the development of allergic reactions. TLR7 agonists have been shown in studies to increase the body's immunological tolerance by controlling the proportion of Th1/Th2 cells, although it is still unknown what impact this has on conjunctival epithelial cells. In this study, we examined the effect of TLR7 agonists on the inflammatory-activation of conjunctival epithelial cells induced by IL-1β. Quantitative PCR and ELISA analysis confirmed that TLR7 agonists could impair the proinflammatory cytokines released by the epithelia cells, whereas pro-inflammatory cytokines led to subsequent reactive oxygen species and neutrophil chemotaxis. Phosphorylation analysis and nucleocytoplasmic separation further confirmed that TLR7 agonists inhibit IL-1β-induced epithelia cells activation and ATP depletion via modulating the cytoplasmic residence of ERK1/2. Our finding indicated that TLR7 of conjunctival epithelia cells could be as a potent anti-inflammatory target for the ocular surface. And TLR7 agonists may become potential new drug for the treatment of allergic conjunctivitis.
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Affiliation(s)
- Ling Wang
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen, China
| | - Shixu Li
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen, China
| | - Kaihong Cai
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen, China
| | - Yu Xiao
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Lin Ye
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen, China.
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7
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Liang S, Wang Q, Wen Y, Wang Y, Li M, Wang Q, Peng J, Guo L. Ligand-independent EphA2 contributes to chemoresistance in small-cell lung cancer by enhancing PRMT1-mediated SOX2 methylation. Cancer Sci 2023; 114:921-936. [PMID: 36377249 PMCID: PMC9986087 DOI: 10.1111/cas.15653] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
Chemoresistance is the crux of clinical treatment failure of small-cell lung cancer (SCLC). Cancer stem cells play a critical role in therapeutic resistance of malignant tumors. Studies have shown that the role of erythropoietin-producing hepatocellular A2 (EphA2) in tumors is complex. This study aimed to test the hypothesis that ligand-independent activation of EphA2 modulates chemoresistance by enhancing stemness in SCLC. We verified that EphA2 was activated in chemoresistance sublines in a ligand-independent manner rather than a ligand-dependent manner. Ligand-independent EphA2 enhanced the expression of stemness-associated biomarkers (CD44, Myc, and SOX2), accelerated epithelial-mesenchymal transition (EMT) and reinforced self-renewal to drive the chemoresistance of SCLC, while the P817H mutant EphA2 neutralized intrinsic function. Co-immunoprecipitation (co-IP) and GST-pull down experiments were conducted to verify that EphA2 directly interacted with PRMT1. Moreover, EphA2 increased the expression and activity of PRMT1. Whereafter, PRMT1 interacted with and methylated SOX2 to induce stemness and chemoresistance in SCLC. Pharmacological inhibition of EphA2 showed a synergistic anti-tumor effect with chemotherapy in preclinical models, including patient-derived xenograft (PDX) models. These findings highlight, for the first time, that the EphA2/PRMT1/SOX2 pathway induces chemoresistance in SCLC by promoting stemness. EphA2 is a potential therapeutic target in SCLC treatment.
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Affiliation(s)
- Shumei Liang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Qiuping Wang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yang Wen
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yu Wang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Man Li
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Qiongyao Wang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Juan Peng
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
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8
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Dynamic Distribution of ASIC1a Channels and Other Proteins within Cells Detected through Fractionation. MEMBRANES 2022; 12:membranes12040389. [PMID: 35448360 PMCID: PMC9027401 DOI: 10.3390/membranes12040389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
Proteins in eukaryotic cells reside in different cell compartments. Many studies require the specific localization of proteins and the detection of any dynamic changes in intracellular protein distribution. There are several methods available for this purpose that rely on the fractionation of the different cell compartments. Fractionation protocols have evolved since the first use of a centrifuge to isolate organelles. In this study, we described a simple method that involves the use of a tabletop centrifuge and different detergents to obtain cell fractions enriched in cytosolic (Cyt), plasma membrane (PM), membranous organelle (MO), and nuclear (Nu) proteins and identify the proteins in each fraction. This method serves to identify transmembrane proteins such as channel subunits as well as PM-embedded or weakly associated proteins. This protocol uses a minute amount of cell material and typical equipment present in laboratories, and it takes approximately 3 h. The process was validated using endogenous and exogenous proteins expressed in the HEK293T cell line that were targeted to each compartment. Using a specific stimulus as a trigger, we showed and quantified the shuttling of a protein channel (ASIC1a, acid sensing ion channel) from the MO fraction to the PM fraction and the shuttling of a kinase from a cytosolic location to a nuclear location.
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9
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Identification and validation of new ERK substrates by phosphoproteomic technologies including Phos-tag SDS-PAGE. J Proteomics 2022; 258:104543. [DOI: 10.1016/j.jprot.2022.104543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022]
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10
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Liu D, Xue D, Lu W, Yang Z, Li L, Xia B, Wei J, Chen X, Yang Y, Wang X, Lin G. BDE-47 induced PC-12 cell differentiation via TrkA downstream pathways and caused the loss of hippocampal neurons in BALB/c mice. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126850. [PMID: 34419847 DOI: 10.1016/j.jhazmat.2021.126850] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
As the most abundant congener of polybrominated diphenyl ethers (PBDEs) detected in environment and human biotic samples, 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47) has been found to accumulate in brain and induce neurotoxicity, however, the detailed mechanism has not been clearly elucidated. To investigate the neurotoxicity of BDE-47, undifferentiated PC-12 cells were exposed to different doses of BDE-47, and BDE-47 dissolved in corn oil was orally administered to mice for 8 consecutive weeks. Our data showed that BDE-47 obviously changed cell morphology, altered cell viability, promoted cell apoptosis, and induced reactive oxygen species (ROS) production. BDE-47 promoted the differentiation of PC-12 cells by enhancing the expression of TrkA receptor and the phosphorylation levels of ERK and Akt. Moreover, BDE-47-induced differentiation of PC-12 cells was suppressed by inhibitors of corresponding pathways (MAPK/ERK and PI3K/Akt). H&E staining of brain showed neurons in DG and CA1 areas of hippocampus decreased after BDE-47 exposure. Transcriptome sequencing of brain tissue suggested that multiple signaling pathways related to neuron death and nerve function were significantly regulated. In conclusion, these results provided new evidence for revealing the neurotoxicity of BDE-47, and offered important experimental basis for environmental controlling and post-exposure health risk assessment of BDE-47.
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Affiliation(s)
- Dongmeng Liu
- School of Public Health, Health Science Center, Shenzhen University, Shenzhen, China; School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Dahui Xue
- School of Public Health, Health Science Center, Shenzhen University, Shenzhen, China; School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Wencan Lu
- Department of Spine Surgery, Shenzhen University General Hospital, Shenzhen, China
| | - Zhuochun Yang
- School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Li Li
- School of Public Health, Health Science Center, Shenzhen University, Shenzhen, China
| | - Beibei Xia
- School of Public Health, Health Science Center, Shenzhen University, Shenzhen, China; School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Jinhua Wei
- School of Public Health, Health Science Center, Shenzhen University, Shenzhen, China; School of Pharmacy, Health Science Center, Shenzhen University, Shenzhen, China
| | - Xianxiong Chen
- School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Yi Yang
- School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Xiaomei Wang
- School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Guimiao Lin
- School of Public Health, Health Science Center, Shenzhen University, Shenzhen, China; School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, China.
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11
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Yang JM, Chi WY, Liang J, Takayanagi S, Iglesias PA, Huang CH. Deciphering cell signaling networks with massively multiplexed biosensor barcoding. Cell 2021; 184:6193-6206.e14. [PMID: 34838160 PMCID: PMC8686192 DOI: 10.1016/j.cell.2021.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 09/27/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022]
Abstract
Genetically encoded fluorescent biosensors are powerful tools for monitoring biochemical activities in live cells, but their multiplexing capacity is limited by the available spectral space. We overcome this problem by developing a set of barcoding proteins that can generate over 100 barcodes and are spectrally separable from commonly used biosensors. Mixtures of barcoded cells expressing different biosensors are simultaneously imaged and analyzed by deep learning models to achieve massively multiplexed tracking of signaling events. Importantly, different biosensors in cell mixtures show highly coordinated activities, thus facilitating the delineation of their temporal relationship. Simultaneous tracking of multiple biosensors in the receptor tyrosine kinase signaling network reveals distinct mechanisms of effector adaptation, cell autonomous and non-autonomous effects of KRAS mutations, as well as complex interactions in the network. Biosensor barcoding presents a scalable method to expand multiplexing capabilities for deciphering the complexity of signaling networks and their interactions between cells.
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Affiliation(s)
- Jr-Ming Yang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA.
| | - Wei-Yu Chi
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Jessica Liang
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Saki Takayanagi
- XDBio Graduate Program, Johns Hopkins School of Medicine, MD 21205, USA
| | - Pablo A Iglesias
- Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chuan-Hsiang Huang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA.
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12
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Krause HB, Bondarowicz H, Karls AL, McClean MN, Kreeger PK. Design and implementation of a microfluidic device capable of temporal growth factor delivery reveal filtering capabilities of the EGFR/ERK pathway. APL Bioeng 2021; 5:046101. [PMID: 34765858 PMCID: PMC8566012 DOI: 10.1063/5.0059011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/15/2021] [Indexed: 12/30/2022] Open
Abstract
Utilizing microfluidics to mimic the dynamic temporal changes of growth factor and cytokine concentrations in vivo has greatly increased our understanding of how signal transduction pathways are structured to encode extracellular stimuli. To date, these devices have focused on delivering pulses of varying frequency, and there are limited cell culture models for delivering slowly increasing concentrations of stimuli that cells may experience in vivo. To examine this setting, we developed and validated a microfluidic device that can deliver increasing concentrations of growth factor over periods ranging from 6 to 24 h. Using this device and a fluorescent biosensor of extracellular-regulated kinase (ERK) activity, we delivered a slowly increasing concentration of epidermal growth factor (EGF) to human mammary epithelial cells and surprisingly observed minimal ERK activation, even at concentrations that stimulate robust activity in bolus delivery. The cells remained unresponsive to subsequent challenges with EGF, and immunocytochemistry suggested that the loss of an epidermal growth factor receptor was responsible. Cells were then challenged with faster rates of change of EGF, revealing an increased ERK activity as a function of rate of change. Specifically, both the fraction of cells that responded and the length of ERK activation time increased with the rate of change. This microfluidic device fills a gap in the current repertoire of in vitro microfluidic devices and demonstrates that slower, more physiological changes in growth factor presentation can reveal new regulatory mechanisms for how signal transduction pathways encode changes in the extracellular growth factor milieu.
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Affiliation(s)
- Harris B Krause
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Hanna Bondarowicz
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Alexis L Karls
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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13
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Williaume G, de Buyl S, Sirour C, Haupaix N, Bettoni R, Imai KS, Satou Y, Dupont G, Hudson C, Yasuo H. Cell geometry, signal dampening, and a bimodal transcriptional response underlie the spatial precision of an ERK-mediated embryonic induction. Dev Cell 2021; 56:2966-2979.e10. [PMID: 34672970 DOI: 10.1016/j.devcel.2021.09.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 07/16/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Precise control of lineage segregation is critical for the development of multicellular organisms, but our quantitative understanding of how variable signaling inputs are integrated to activate lineage-specific gene programs remains limited. Here, we show how precisely two out of eight ectoderm cells adopt neural fates in response to ephrin and FGF signals during ascidian neural induction. In each ectoderm cell, FGF signals activate ERK to a level that mirrors its cell contact surface with FGF-expressing mesendoderm cells. This gradual interpretation of FGF inputs is followed by a bimodal transcriptional response of the immediate early gene, Otx, resulting in its activation specifically in the neural precursors. At low levels of ERK, Otx is repressed by an ETS family transcriptional repressor, ERF2. Ephrin signals are critical for dampening ERK activation levels across ectoderm cells so that only neural precursors exhibit above-threshold levels, evade ERF repression, and "switch on" Otx transcription.
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Affiliation(s)
- Géraldine Williaume
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Sophie de Buyl
- Applied Physics Research Group, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, 1050 Brussels, Belgium
| | - Cathy Sirour
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Nicolas Haupaix
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Rossana Bettoni
- Applied Physics Research Group, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, 1050 Brussels, Belgium; Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Geneviève Dupont
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium.
| | - Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France.
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France.
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14
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Xia Y, Yu W, Cheng F, Rao T, Ruan Y, Yuan R, Ning J, Zhou X, Lin F, Zheng D. Photobiomodulation With Blue Laser Inhibits Bladder Cancer Progression. Front Oncol 2021; 11:701122. [PMID: 34733776 PMCID: PMC8558536 DOI: 10.3389/fonc.2021.701122] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/30/2021] [Indexed: 01/22/2023] Open
Abstract
Blue lasers are becoming more widely used in the diagnosis and treatment of bladder cancer; however, their photobiomodulation effects on bladder cancer cells remains unclear. The purpose of the current study was to explore the photobiomodulation effect of blue laser irradiation on bladder cancer progression and the associated mechanisms. The human uroepithelial cell line SV-HUC-1 and human bladder cancer cell lines T24 and EJ were exposed to blue laser irradiation (450 nm) at various energy densities, and cell proliferation, migration, invasion, epithelial-mesenchymal transition (EMT), and the levels of the proteins associated with the MAPK pathway proteins were determined. A significant decrease in cell viability was observed in a density-dependent manner after blue laser irradiation at > 4 J/cm2 in both bladder cancer cell lines. However, the blue laser did not reduce cell viability in SV-HUC-1 cells until the energy density exceeded 16 J/cm2. Meanwhile, Ki67 levels, reflecting cell proliferation and senescence, were also significantly decreased after blue laser irradiation at 4 J/cm2 and 8 J/cm2 in the absence of cell cycle arrest. Moreover, blue laser irradiation at 4 J/cm2 and 8 J/cm2 caused a reduction in cell migration and invasion and also reduced the expression levels of MMP-2, MMP-9, Snail, N-cadherin, phospho-MEK and phospho-ERK, and elevated the expression levels of E-cadherin. Meanwhile ERK activator(tBHQ) significantly reversed the irradiation-induced suppression of proliferation, migration and invasion in T24 and EJ cell lines. The present study showed that blue laser irradiation inhibited bladder cancer proliferation in a density-dependent manner and inhibited bladder cancer progression by suppressing migration, invasion, and the EMT process in T24 and EJ cell lines. This inhibition was possibly mediated via suppression of the MAPK/MEK/ERK pathway. Thus, the use of a low-energy blue laser in the diagnosis and treatment of bladder cancer is possibly safe and may have an anti-tumor effect.
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Affiliation(s)
- Yuqi Xia
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weimin Yu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fan Cheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ting Rao
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuan Ruan
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Run Yuan
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jinzhuo Ning
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiangjun Zhou
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fangyou Lin
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Di Zheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
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15
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Salinas Castellanos LC, Uchitel OD, Weissmann C. Signaling Pathways in Proton and Non-proton ASIC1a Activation. Front Cell Neurosci 2021; 15:735414. [PMID: 34675777 PMCID: PMC8523820 DOI: 10.3389/fncel.2021.735414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Acid-sensing ion channels (ASICs) regulate synaptic activities and play important roles in neurodegenerative diseases as well as pain conditions. Classically, ASICs are described as transiently activated by a reduced pH, followed by desensitization; the activation allows sodium influx, and in the case of ASIC1a-composed channels, also calcium to some degree. Several factors are emerging and extensively analyzed as modulators, activating, inhibiting, and potentiating specific channel subunits. However, the signaling pathways triggered by channel activation are only starting to be revealed.The channel has been recently shown to be activated through a mechanism other than proton-mediated. Indeed, the large extracellular loop of these channels opens the possibility that other non-proton ligands might exist. One such molecule discovered was a toxin present in the Texas coral snake venom. The finding was associated with the activation of the channel at neutral pH via the toxin and causing intense and unremitting pain.By using different pharmacological tools, we analyzed the downstream signaling pathway triggered either by the proton and non-proton activation for human, mouse, and rat ASIC1a-composed channels in in vitro models. We show that for all species analyzed, the non-protonic mode of activation determines the activation of the ERK signaling cascade at a higher level and duration compared to the proton mode.This study adds to the growing evidence of the important role ASIC1a channels play in different physiological and pathological conditions and also hints at a possible pathological mechanism for a sustained effect.
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Affiliation(s)
| | | | - Carina Weissmann
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE—UBA CONICET), Facultad de Ciencias, Exactas y Naturales de la Universidad de Buenos Aires, Buenos Aires, Argentina
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16
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Jurado M, Castaño Ó, Zorzano A. Stochastic modulation evidences a transitory EGF-Ras-ERK MAPK activity induced by PRMT5. Comput Biol Med 2021; 133:104339. [PMID: 33910125 DOI: 10.1016/j.compbiomed.2021.104339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/06/2021] [Accepted: 03/10/2021] [Indexed: 02/07/2023]
Abstract
The extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK) pathway involves a three-step cascade of kinases that transduce signals and promote processes such as cell growth, development, and apoptosis. An aberrant response of this pathway is related to the proliferation of cell diseases and tumors. By using simulation modeling, we document that the protein arginine methyltransferase 5 (PRMT5) modulates the MAPK pathway and thus avoids an aberrant behavior. PRMT5 methylates the Raf kinase, reducing its catalytic activity and thereby, reducing the activation of ERK in time and amplitude. Two minimal computational models of the epidermal growth factor (EGF)-Ras-ERK MAPK pathway influenced by PRMT5 were proposed: a first model in which PRMT5 is activated by EGF and a second one in which PRMT5 is stimulated by the cascade response. The reported results show that PRMT5 reduces the time duration and the expression of the activated ERK in both cases, but only in the first model PRMT5 limits the EGF range that generates an ERK activation. Based on our data, we propose the protein PRMT5 as a regulatory factor to develop strategies to fight against an excessive activity of the MAPK pathway, which could be of use in chronic diseases and cancer.
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Affiliation(s)
- Manuel Jurado
- Biotechnology Ph.D. Programme, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Óscar Castaño
- Electronics and Biomedical Engineering, University of Barcelona, Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain; CIBER in Bioengineering, Biomaterials and Nanomedicine, CIBER-BBN, Madrid, Spain; Bioelectronics Unit and Nanobioengineering Lab., Institute for Nanoscience and Nanotechnology of the University of Barcelona (IN2UB), Barcelona, Spain.
| | - Antonio Zorzano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; CIBER of Diabetes and Associated Metabolic Diseases, Barcelona, Spain; Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
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17
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Nasu M, Esumi S, Hatakeyama J, Tamamaki N, Shimamura K. Two-Phase Lineage Specification of Telencephalon Progenitors Generated From Mouse Embryonic Stem Cells. Front Cell Dev Biol 2021; 9:632381. [PMID: 33937233 PMCID: PMC8086603 DOI: 10.3389/fcell.2021.632381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/09/2021] [Indexed: 12/16/2022] Open
Abstract
Proper brain development requires precisely controlled phases of stem cell proliferation, lineage specification, differentiation, and migration. Lineage specification depends partly on concentration gradients of chemical cues called morphogens. However, the rostral brain (telencephalon) expands prominently during embryonic development, dynamically altering local morphogen concentrations, and telencephalic subregional properties develop with a time lag. Here, we investigated how progenitor specification occurs under these spatiotemporally changing conditions using a three-dimensional in vitro differentiation model. We verified the critical contributions of three signaling factors for the lineage specification of subregional tissues in the telencephalon, ventralizing sonic hedgehog (Shh) and dorsalizing bone morphogenetic proteins (BMPs) and WNT proteins (WNTs). We observed that a short-lasting signal is sufficient to induce subregional progenitors and that the timing of signal exposure for efficient induction is specific to each lineage. Furthermore, early and late progenitors possess different Shh signal response capacities. This study reveals a novel developmental mechanism for telencephalon patterning that relies on the interplay of dose- and time-dependent signaling, including a time lag for specification and a temporal shift in cellular Shh sensitivity. This delayed fate choice through two-phase specification allows tissues with marked size expansion, such as the telencephalon, to compensate for the changing dynamics of morphogen signals.
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Affiliation(s)
- Makoto Nasu
- Department of Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Shigeyuki Esumi
- Department of Anatomy and Neurobiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jun Hatakeyama
- Department of Brain Morphogenesis, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Nobuaki Tamamaki
- Department of Morphological Neural Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kenji Shimamura
- Department of Brain Morphogenesis, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
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18
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Shindo Y, Amodeo AA. Excess histone H3 is a competitive Chk1 inhibitor that controls cell-cycle remodeling in the early Drosophila embryo. Curr Biol 2021; 31:2633-2642.e6. [PMID: 33848457 DOI: 10.1016/j.cub.2021.03.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/08/2021] [Accepted: 03/10/2021] [Indexed: 12/31/2022]
Abstract
The DNA damage checkpoint is crucial to protect genome integrity.1,2 However, the early embryos of many metazoans sacrifice this safeguard to allow for rapid cleavage divisions that are required for speedy development. At the mid-blastula transition (MBT), embryos switch from rapid cleavage divisions to slower, patterned divisions with the addition of gap phases and acquisition of DNA damage checkpoints. The timing of the MBT is dependent on the nuclear-to-cytoplasmic (N/C ratio)3-7 and the activation of the checkpoint kinase, Chk1.8-17 How Chk1 activity is coupled to the N/C ratio has remained poorly understood. Here, we show that dynamic changes in histone H3 availability in response to the increasing N/C ratio control Chk1 activity and thus time the MBT in the Drosophila embryo. We show that excess H3 in the early cycles interferes with cell-cycle slowing independent of chromatin incorporation. We find that the N-terminal tail of H3 acts as a competitive inhibitor of Chk1 in vitro and reduces Chk1 activity in vivo. Using a H3-tail mutant that has reduced Chk1 inhibitor activity, we show that the amount of available Chk1 sites in the H3 pool controls the dynamics of cell-cycle progression. Mathematical modeling quantitatively supports a mechanism where titration of H3 during early cleavage cycles regulates Chk1-dependent cell-cycle slowing. This study defines Chk1 regulation by H3 as a key mechanism that coordinates cell-cycle remodeling with developmental progression.
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Affiliation(s)
- Yuki Shindo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Amanda A Amodeo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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19
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Rombouts J, Gelens L. Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions. PLoS Comput Biol 2021; 17:e1008231. [PMID: 33411761 PMCID: PMC7817062 DOI: 10.1371/journal.pcbi.1008231] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/20/2021] [Accepted: 11/18/2020] [Indexed: 02/06/2023] Open
Abstract
Bistability is a common mechanism to ensure robust and irreversible cell cycle transitions. Whenever biological parameters or external conditions change such that a threshold is crossed, the system abruptly switches between different cell cycle states. Experimental studies have uncovered mechanisms that can make the shape of the bistable response curve change dynamically in time. Here, we show how such a dynamically changing bistable switch can provide a cell with better control over the timing of cell cycle transitions. Moreover, cell cycle oscillations built on bistable switches are more robust when the bistability is modulated in time. Our results are not specific to cell cycle models and may apply to other bistable systems in which the bistable response curve is time-dependent. Many systems in nature show bistability, which means they can evolve to one of two stable steady states under exactly the same conditions. Which state they evolve to depends on where the system comes from. Such bistability underlies the switching behavior that is essential for cells to progress in the cell division cycle. A quick switch happens when the cell jumps from one steady state to another steady state. Typical of this switching behavior is its robustness and irreversibility. In this paper, we expand this viewpoint of the dynamics of the cell cycle by considering bistable switches which themselves are changing in time. This gives the cell an extra layer of control over transitions both in time and in space, and can make those transitions more robust. Such dynamically changing bistability can appear very naturally. We show this in a model of mitotic entry, in which we include a nuclear and cytoplasmic compartment. The activity of a crucial cell cycle protein follows a bistable switch in each compartment, but the shape of its response is changing in time as proteins are imported into and exported from the nucleus.
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Affiliation(s)
- Jan Rombouts
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven (KU Leuven), B-3000 Leuven, Belgium
- * E-mail: (J.R.); (L.G.)
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven (KU Leuven), B-3000 Leuven, Belgium
- * E-mail: (J.R.); (L.G.)
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20
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Yang Z, Zou W, Pan Y, Yong KT, Li L, Wang X, Liu D, Chen T, Xue D, Lin G. PEGylated CuInS 2/ZnS quantum dots inhibit neurite outgrowth by downregulating the NGF/p75 NTR/MAPK pathway. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111378. [PMID: 33022524 DOI: 10.1016/j.ecoenv.2020.111378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
The widespread application of cadmium-free CuInS2/ZnS QDs has raised great concern regarding their potential toxicity to humans. To date, toxicological data related to CuInS2/ZnS QDs are scarce. Neurons play extraordinary roles in regulating the activities of organs and systems, and serious consequences occur when neurons are damaged. Currently, the potential toxicity of CuInS2/ZnS QDs on neurons has not been fully elucidated. Here, we investigate the neurotoxicity of PEGylated CuInS2/ZnS (CuInS2/ZnS-PEG) QDs on neuron-like PC12 cells. We found that CuInS2/ZnS-PEG QDs were taken up by PC12 cells, but at a concentration range from 0 to 100 μg/mL, they did not affect the survival rate of the PC12 cells. In addition, we found that CuInS2/ZnS-PEG QDs significantly inhibited neurite outgrowth from and the differentiation of PC12 cells in the presence of NGF, while COOH-modified CuInS2/ZnS QDs or free PEG did not have a similar effect. Further studies showed that CuInS2/ZnS-PEG QDs obviously downregulated the expression of low-affinity NGF receptor (p75NTR) and subsequently negatively regulated the downstream MAPK cascade by dephosphorylating ERK1/2 and AKT. Taken together, these results suggest that CuInS2/ZnS-PEG QDs disturb NGF signal transduction from external stimuli to relevant internal signals, thus affecting normal biological processes such as neurite outgrowth and cell differentiation.
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Affiliation(s)
- Zhiwen Yang
- Base for International Science and Technology Cooperation: Carson Cancer Stem Cell Vaccines R&D Center, Shenzhen Key Lab of Synthetic Biology, Department of Physiology, School of Basic Medical Sciences Shenzhen University, Shenzhen, 518055, China
| | - Wenyi Zou
- Base for International Science and Technology Cooperation: Carson Cancer Stem Cell Vaccines R&D Center, Shenzhen Key Lab of Synthetic Biology, Department of Physiology, School of Basic Medical Sciences Shenzhen University, Shenzhen, 518055, China
| | - Yongning Pan
- Department of Disease Prevention and Control, Shenzhen Baoan District Health Bureau, Shenzhen, China
| | - Ken-Tye Yong
- School of Electrical and Electronic Engineering, Nanyang Technological University, 639798, Singapore
| | - Li Li
- Base for International Science and Technology Cooperation: Carson Cancer Stem Cell Vaccines R&D Center, Shenzhen Key Lab of Synthetic Biology, Department of Physiology, School of Basic Medical Sciences Shenzhen University, Shenzhen, 518055, China
| | - Xiaomei Wang
- Base for International Science and Technology Cooperation: Carson Cancer Stem Cell Vaccines R&D Center, Shenzhen Key Lab of Synthetic Biology, Department of Physiology, School of Basic Medical Sciences Shenzhen University, Shenzhen, 518055, China
| | - Dongmeng Liu
- Base for International Science and Technology Cooperation: Carson Cancer Stem Cell Vaccines R&D Center, Shenzhen Key Lab of Synthetic Biology, Department of Physiology, School of Basic Medical Sciences Shenzhen University, Shenzhen, 518055, China
| | - Tingting Chen
- Base for International Science and Technology Cooperation: Carson Cancer Stem Cell Vaccines R&D Center, Shenzhen Key Lab of Synthetic Biology, Department of Physiology, School of Basic Medical Sciences Shenzhen University, Shenzhen, 518055, China
| | - Dahui Xue
- Base for International Science and Technology Cooperation: Carson Cancer Stem Cell Vaccines R&D Center, Shenzhen Key Lab of Synthetic Biology, Department of Physiology, School of Basic Medical Sciences Shenzhen University, Shenzhen, 518055, China
| | - Guimiao Lin
- Base for International Science and Technology Cooperation: Carson Cancer Stem Cell Vaccines R&D Center, Shenzhen Key Lab of Synthetic Biology, Department of Physiology, School of Basic Medical Sciences Shenzhen University, Shenzhen, 518055, China.
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21
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The Role of Protein Disorder in Nuclear Transport and in Its Subversion by Viruses. Cells 2020; 9:cells9122654. [PMID: 33321790 PMCID: PMC7764567 DOI: 10.3390/cells9122654] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
The transport of host proteins into and out of the nucleus is key to host function. However, nuclear transport is restricted by nuclear pores that perforate the nuclear envelope. Protein intrinsic disorder is an inherent feature of this selective transport barrier and is also a feature of the nuclear transport receptors that facilitate the active nuclear transport of cargo, and the nuclear transport signals on the cargo itself. Furthermore, intrinsic disorder is an inherent feature of viral proteins and viral strategies to disrupt host nucleocytoplasmic transport to benefit their replication. In this review, we highlight the role that intrinsic disorder plays in the nuclear transport of host and viral proteins. We also describe viral subversion mechanisms of the host nuclear transport machinery in which intrinsic disorder is a feature. Finally, we discuss nuclear import and export as therapeutic targets for viral infectious disease.
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22
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Miao T, Little AC, Aronshtam A, Marquis T, Fenn SL, Hristova M, Krementsov DN, van der Vliet A, Spees JL, Oldinski RA. Internalized FGF-2-Loaded Nanoparticles Increase Nuclear ERK1/2 Content and Result in Lung Cancer Cell Death. NANOMATERIALS 2020; 10:nano10040612. [PMID: 32230722 PMCID: PMC7221911 DOI: 10.3390/nano10040612] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 12/15/2022]
Abstract
Innovative cancer treatments, which improve adjuvant therapy and reduce adverse events, are desperately needed. Nanoparticles provide controlled intracellular biomolecule delivery in the absence of activating external cell surface receptors. Prior reports suggest that intracrine signaling, following overexpression of basic fibroblast growth factor (FGF-2) after viral transduction, has a toxic effect on diseased cells. Herein, the research goals were to (1) encapsulate recombinant FGF-2 within stable, alginate-based nanoparticles (ABNs) for non-specific cellular uptake, and (2) determine the effects of ABN-mediated intracellular delivery of FGF-2 on cancer cell proliferation/survival. In culture, human alveolar adenocarcinoma basal epithelial cell line (A549s) and immortalized human bronchial epithelial cell line (HBE1s) internalized ABNs through non-selective endocytosis. Compared to A549s exposed to empty (i.e., blank) ABNs, the intracellular delivery of FGF-2 via ABNs significantly increased the levels of lactate dehydrogenase, indicating that FGF-2-ABN treatment decreased the transformed cell integrity. Noticeably, the nontransformed cells were not significantly affected by FGF-2-loaded ABN treatment. Furthermore, FGF-2-loaded ABNs significantly increased nuclear levels of activated-extracellular signal-regulated kinase ½ (ERK1/2) in A549s but had no significant effect on HBE1 nuclear ERK1/2 expression. Our novel intracellular delivery method of FGF-2 via nanoparticles resulted in increased cancer cell death via increased nuclear ERK1/2 activation.
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Affiliation(s)
- Tianxin Miao
- Bioengineering Program, College of Engineering and Mathematical Sciences, Larner College of Medicine, College of Engineering and Mathematical Sciences, University of Vermont, Burlington, VT 05405, USA (S.L.F.)
| | - Andrew C. Little
- Cellular, Molecular and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA; (A.C.L.); (A.v.d.V.)
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
| | - Alexander Aronshtam
- Department of Medicine, Stem Cell Core, Larner College of Medicine, University of Vermont, Colchester, VT 05446, USA; (A.A.); (T.M.)
| | - Taylor Marquis
- Department of Medicine, Stem Cell Core, Larner College of Medicine, University of Vermont, Colchester, VT 05446, USA; (A.A.); (T.M.)
| | - Spencer L. Fenn
- Bioengineering Program, College of Engineering and Mathematical Sciences, Larner College of Medicine, College of Engineering and Mathematical Sciences, University of Vermont, Burlington, VT 05405, USA (S.L.F.)
| | - Milena Hristova
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
| | - Dimitry N. Krementsov
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT 05405, USA;
| | - Albert van der Vliet
- Cellular, Molecular and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA; (A.C.L.); (A.v.d.V.)
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
| | - Jeffrey L. Spees
- Cellular, Molecular and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA; (A.C.L.); (A.v.d.V.)
- Department of Medicine, Stem Cell Core, Larner College of Medicine, University of Vermont, Colchester, VT 05446, USA; (A.A.); (T.M.)
- Correspondence: (J.L.S.); (R.A.O.); Tel.: +1-802-656-2388 (J.L.S.); +1-802-656-3338 (R.A.O.); Fax: +1-802-656-8932 (J.L.S.); +1-802-656-3358 (R.A.O.)
| | - Rachael A. Oldinski
- Bioengineering Program, College of Engineering and Mathematical Sciences, Larner College of Medicine, College of Engineering and Mathematical Sciences, University of Vermont, Burlington, VT 05405, USA (S.L.F.)
- Department of Mechanical Engineering, College of Engineering and Mathematical Sciences, University of Vermont, Burlington, VT 05405, USA
- Department of Electrical and Biomedical Engineering, College of Engineering and Mathematical Sciences, University of Vermont, Burlington, VT 05405, USA
- Materials Science Program, College of Engineering and Mathematical Sciences, University of Vermont, Burlington, VT 05405, USA
- Correspondence: (J.L.S.); (R.A.O.); Tel.: +1-802-656-2388 (J.L.S.); +1-802-656-3338 (R.A.O.); Fax: +1-802-656-8932 (J.L.S.); +1-802-656-3358 (R.A.O.)
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23
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Chen H, Lin W, Lin P, Zheng M, Lai Y, Chen M, Zhang Y, Chen J, Lin X, Lin L, Lan Q, Yuan Q, Chen R, Jiang X, Xiao Y, Liu N. IL-10 produces a dual effect on OGD-induced neuronal apoptosis of cultured cortical neurons via the NF-κB pathway. Aging (Albany NY) 2019; 11:10796-10813. [PMID: 31801113 PMCID: PMC6932931 DOI: 10.18632/aging.102411] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/19/2019] [Indexed: 12/15/2022]
Abstract
As a classic immunoregulatory cytokine, interleukin-10 (IL-10) can provide in vivo and in vitro neuroprotection respectively during cerebral ischemia and after the oxygen-glucose deprivation (OGD)-induced injury. However, its role in cortical neuronal survival at different post-ischemic phases remains unclear. The current study found that IL-10 had distinct effects on the neuronal apoptosis at different OGD stages: at an early stage after OGD, IL-10 promoted the OGD-induced neuronal apoptosis in the cultured primary cortical neurons by activating p65 subunit, which up-regulated Bax expression and down-regulated Bcl-xL expression; at a late OGD stage, however, it attenuated the OGD-induced neuronal apoptosis by activating c-Rel, which up-regulated Bcl-xL expression and down-regulated Bax expression. The early-stage pro-apoptosis and late-stage anti-apoptosis were both partly abolished by PDTC, an NF-κB inhibitor, and promoted by PMA, an NF-κB activator. The optimal anti-apoptotic effect appeared when the cultured neurons were treated with IL-10 at 9-24 h after OGD. Taken together, our findings suggest that IL-10 exerts a dual effect on the survival of the cultured neurons by activating the NF-κB pathway at different stages after OGD injury and that PMA treatment at a late stage can facilitate the IL-10-conferred neuroprotection against OGD-induced neuronal injury.
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Affiliation(s)
- Hongbin Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Wei Lin
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Peiqiang Lin
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Mouwei Zheng
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Yongxing Lai
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Manli Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Yixian Zhang
- Department of Rehabilitation, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Jianhao Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Xiaohui Lin
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Longzai Lin
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Quan Lan
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China.,Department of Neurology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Qilin Yuan
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Ronghua Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Xinhong Jiang
- Department of Rehabilitation, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Yingchun Xiao
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Nan Liu
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China.,Department of Rehabilitation, Fujian Medical University Union Hospital, Fuzhou, China.,Institute of Cerebral Vascular Diseases of Fujian Province, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
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24
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Courtney TM, Deiters A. Optical control of protein phosphatase function. Nat Commun 2019; 10:4384. [PMID: 31558717 PMCID: PMC6763421 DOI: 10.1038/s41467-019-12260-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 08/28/2019] [Indexed: 12/12/2022] Open
Abstract
Protein phosphatases are involved in embryonic development, metabolic homeostasis, stress response, cell cycle transitions, and many other essential biological mechanisms. Unlike kinases, protein phosphatases remain understudied and less characterized. Traditional genetic and biochemical methods have contributed significantly to our understanding; however, these methodologies lack precise and acute spatiotemporal control. Here, we report the development of a light-activated protein phosphatase, the dual specificity phosphatase 6 (DUSP6 or MKP3). Through genetic code expansion, MKP3 is placed under optical control via two different approaches: (i) incorporation of a caged cysteine into the active site for controlling catalytic activity and (ii) incorporation of a caged lysine into the kinase interaction motif for controlling the protein-protein interaction between the phosphatase and its substrate. Both strategies are expected to be applicable to the engineering of a wide range of light-activated phosphatases. Applying the optogenetically controlled MKP3 in conjunction with live cell reporters, we discover that ERK nuclear translocation is regulated in a graded manner in response to increasing MKP3 activity.
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Affiliation(s)
- Taylor M Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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25
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Chen Z, Zhang W, Zhang N, Zhou Y, Hu G, Xue M, Liu J, Li Y. Down-regulation of insulin-like growth factor binding protein 5 is involved in intervertebral disc degeneration via the ERK signalling pathway. J Cell Mol Med 2019; 23:6368-6377. [PMID: 31290273 PMCID: PMC6714225 DOI: 10.1111/jcmm.14525] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 12/27/2022] Open
Abstract
It is obvious that epigenetic processes influence the evolution of intervertebral disc degeneration (IDD). However, its molecular mechanisms are poorly understood. Therefore, we tested the hypothesis that IGFBP5, a potential regulator of IDD, modulates IDD via the ERK signalling pathway. We showed that IGFBP5 mRNA was significantly down-regulated in degenerative nucleus pulposus (NP) tissues. IGFBP5 was shown to significantly promote NP cell proliferation and inhibit apoptosis in vitro, which was confirmed by MTT, flow cytometry and colony formation assays. Furthermore, IGFBP5 was shown to exert its effects by inhibiting the ERK signalling pathway. The effects induced by IGFBP5 overexpression on NP cells were similar to those induced by treatment with an ERK pathway inhibitor (PD98059). Moreover, qRT-PCR and Western blot analyses were performed to examine the levels of apoptosis-related factors, including Bax, caspase-3 and Bcl2. The silencing of IGFBP5 up-regulated the levels of Bax and caspase-3 and down-regulated the level of Bcl2, thereby contributing to the development of human IDD. Furthermore, these results were confirmed in vivo using an IDD rat model, which showed that the induction of Igfbp5 mRNA expression abrogated the effects of IGFBP5 silencing on intervertebral discs. Overall, our findings elucidate the role of IGFBP5 in the pathogenesis of IDD and provide a potential novel therapeutic target for IDD.
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Affiliation(s)
- Zhonghui Chen
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
| | - Weibing Zhang
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
| | - Nu Zhang
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
| | - Yan Zhou
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
| | - Geliang Hu
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
| | - Mingdi Xue
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
| | - Junhua Liu
- Orthopedic SurgeryChibi Third Renmin HospitalChibiChina
| | - Yaming Li
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
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26
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Xuan ZB, Wang YJ, Xie J. ANO6 promotes cell proliferation and invasion in glioma through regulating the ERK signaling pathway. Onco Targets Ther 2019; 12:6721-6731. [PMID: 31692479 PMCID: PMC6708391 DOI: 10.2147/ott.s211725] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
Purpose Anoctamin6 (ANO6) plays a crucial role in several cancers, whereas the specific role of ANO6 in glioblastoma is unclear. Methods Kaplan-Meier survival analysis was used to analysis the correlation between ANO6 and survival rate of patients with glioblastoma. Univariate Cox regression analysis was used to analysis the correlation among ANO6 expression level,and age, gender, WHO and overall survival rate. Immunohistocemical technique, RT-PCR and western blot were used to dected the ANO6 expression. CCK8, colony formation and transwell were used to detected cell viability, cell proliferation and cell invasion in glioblastoma cells transfected with sh-ANO6 and ANO6 overexpression. In addition, after SHG-44 cells trasfected with ANO6 overexpression were ERK inhibitor (PD98059), CCK8, colony formation and transwell were used to detected cell viability, cell proliferation and cell invasion. Western blot was used to detected ERK protein level and the phosphorylation level of ERK in T89G and U87MG cells tranfected wih sh-ANO6. Results The results indicated that the ANO6 expression level was significantly associated with patients' age and tumor stage. Univariate Cox regression analysis showed that the ANO6 expression level, age, gender and tumor stage were not related to the overall survival rate. ANO6 inhibition significantly suppressed the viability, invasion and the ability of colony formation in glioma cells, while ANO6 overexpression led to the opposite results in SHG-44 cells. ANO6 knockdown strongly inhibits the phosphorylation level and nuclear translocation of extracellular signal-regulated kinase (ERK) protein to inhibit ERK signaling. ERK inhibitor significantly decreased the cell proliferation and invasion in SHG-44 cells transfected with sh-ANO6. Conclusion This study revealed that ANO6 activited ERK signaling pathway through promoting the nuclear translocation of ERK to increase the proliferation and invasion of glioblastoma cells.
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Affiliation(s)
- Zhao-Bo Xuan
- Department of Neurosurgery, The First Hospital Affiliated to Jiamusi University, Jiamusi City, Heilongjiang Province 154002, People's Republic of China
| | - Ye-Ji Wang
- Department of Neurosurgery, Shanxian Haijiya Hospital, Heze City, Shandong Province 274300, People's Republic of China
| | - Jun Xie
- Department of Neurosurgery, Tongchuan People's Hospital, Tongchuan City, Shaanxi Province 727000, People's Republic of China
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27
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Mclaurin JD, Weiner OD. Multiple sources of signal amplification within the B-cell Ras/MAPK pathway. Mol Biol Cell 2019; 30:1610-1620. [PMID: 31042097 PMCID: PMC6727637 DOI: 10.1091/mbc.e18-09-0560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Ras-Map kinase (MAPK) cascade underlies functional decisions in a wide range of cell types and organisms. In B-cells, positive feedback-driven Ras activation is the proposed source of the digital (all or none) MAPK responses following antigen stimulation. However, an inability to measure endogenous Ras activity in living cells has hampered our ability to test this model directly. Here we leverage biosensors of endogenous Ras and ERK activity to revisit this question. We find that B-cell receptor (BCR) ligation drives switch-like Ras activation and that lower BCR signaling output is required for the maintenance versus the initiation of Ras activation. Surprisingly, digital ERK responses persist in the absence of positive feedback-mediated Ras activation, and digital ERK is observed at a threshold level of Ras activation. These data suggest an independent analogue-to-digital switch downstream of Ras activation and reveal that multiple sources of signal amplification exist within the Ras-ERK module of the BCR pathway.
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Affiliation(s)
- Justin D Mclaurin
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
| | - Orion D Weiner
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
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28
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Sammons RM, Ghose R, Tsai KY, Dalby KN. Targeting ERK beyond the boundaries of the kinase active site in melanoma. Mol Carcinog 2019; 58:1551-1570. [PMID: 31190430 DOI: 10.1002/mc.23047] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/14/2022]
Abstract
Extracellular signal-regulated kinase 1/2 (ERK1/2) constitute a point of convergence for complex signaling events that regulate essential cellular processes, including proliferation and survival. As such, dysregulation of the ERK signaling pathway is prevalent in many cancers. In the case of BRAF-V600E mutant melanoma, ERK inhibition has emerged as a viable clinical approach to abrogate signaling through the ERK pathway, even in cases where MEK and Raf inhibitor treatments fail to induce tumor regression due to resistance mechanisms. Several ERK inhibitors that target the active site of ERK have reached clinical trials, however, many critical ERK interactions occur at other potentially druggable sites on the protein. Here we discuss the role of ERK signaling in cell fate, in driving melanoma, and in resistance mechanisms to current BRAF-V600E melanoma treatments. We explore targeting ERK via a distinct site of protein-protein interaction, known as the D-recruitment site (DRS), as an alternative or supplementary mode of ERK pathway inhibition in BRAF-V600E melanoma. Targeting the DRS with inhibitors in melanoma has the potential to not only disrupt the catalytic apparatus of ERK but also its noncatalytic functions, which have significant impacts on spatiotemporal signaling dynamics and cell fate.
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Affiliation(s)
- Rachel M Sammons
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York
| | - Kenneth Y Tsai
- Departments of Anatomic Pathology and Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas.,Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
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29
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Automated FRET quantification shows distinct subcellular ERK activation kinetics in response to graded EGFR signaling in
Drosophila. Genes Cells 2019; 24:297-306. [DOI: 10.1111/gtc.12679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/07/2019] [Accepted: 02/12/2019] [Indexed: 12/19/2022]
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30
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The Effect of FG-Nup Phosphorylation on NPC Selectivity: A One-Bead-Per-Amino-Acid Molecular Dynamics Study. Int J Mol Sci 2019; 20:ijms20030596. [PMID: 30704069 PMCID: PMC6387328 DOI: 10.3390/ijms20030596] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/16/2023] Open
Abstract
Nuclear pore complexes (NPCs) are large protein complexes embedded in the nuclear envelope separating the cytoplasm from the nucleoplasm in eukaryotic cells. They function as selective gates for the transport of molecules in and out of the nucleus. The inner wall of the NPC is coated with intrinsically disordered proteins rich in phenylalanine-glycine repeats (FG-repeats), which are responsible for the intriguing selectivity of NPCs. The phosphorylation state of the FG-Nups is controlled by kinases and phosphatases. In the current study, we extended our one-bead-per-amino-acid (1BPA) model for intrinsically disordered proteins to account for phosphorylation. With this, we performed molecular dynamics simulations to probe the effect of phosphorylation on the Stokes radius of isolated FG-Nups, and on the structure and transport properties of the NPC. Our results indicate that phosphorylation causes a reduced attraction between the residues, leading to an extension of the FG-Nups and the formation of a significantly less dense FG-network inside the NPC. Furthermore, our simulations show that upon phosphorylation, the transport rate of inert molecules increases, while that of nuclear transport receptors decreases, which can be rationalized in terms of modified hydrophobic, electrostatic, and steric interactions. Altogether, our models provide a molecular framework to explain how extensive phosphorylation of FG-Nups decreases the selectivity of the NPC.
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31
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Phosphoproteomic identification and functional characterization of protein kinase substrates by 2D-DIGE and Phos-tag PAGE. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:57-61. [DOI: 10.1016/j.bbapap.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/22/2022]
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32
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Chen Y, Li X, Li B, Wang H, Li M, Huang S, Sun Y, Chen G, Si X, Huang C, Liao W, Liao Y, Bin J. Long Non-coding RNA ECRAR Triggers Post-natal Myocardial Regeneration by Activating ERK1/2 Signaling. Mol Ther 2018; 27:29-45. [PMID: 30528086 PMCID: PMC6319349 DOI: 10.1016/j.ymthe.2018.10.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 10/21/2018] [Accepted: 10/26/2018] [Indexed: 01/02/2023] Open
Abstract
Reactivating post-natal myocardial regeneration potential may be a feasible strategy to regenerate the injured adult heart. Long non-coding RNAs (lncRNAs) have been implicated in regulating cellular differentiation, but whether they can elicit a regenerative response in the post-natal heart remains unknown. In this study, by characterizing the lncRNA transcriptome in human hearts during the fetal-to-adult transition, we found that 3,092 lncRNAs were differentially expressed, and we further identified a novel upregulated fetal lncRNA that we called endogenous cardiac regeneration-associated regulator (ECRAR), which promoted DNA synthesis, mitosis, and cytokinesis in post-natal day 7 and adult rat cardiomyocytes (CMs). Overexpression of ECRAR markedly stimulated myocardial regeneration and induced recovery of cardiac function after myocardial infarction (MI). Knockdown of ECRAR inhibited post-natal day 1 CM proliferation and prevented post-MI recovery. ECRAR was transcriptionally upregulated by E2F transcription factor 1 (E2F1). In addition, ECRAR directly bound to and promoted the phosphorylation of extracellular signal-regulated kinases 1 and 2 (ERK1/2), resulting in downstream targets of cyclin D1 and cyclin E1 activation, which, in turn, activated E2F1. The E2F1-ECRAR-ERK1/2 signaling formed a positive feedback loop to drive cell cycle progression, and, therefore, it promoted CM proliferation. These findings indicated that our newly discovered ECRAR may be a valuable therapeutic target for heart failure.
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Affiliation(s)
- Yanmei Chen
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xinzhong Li
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Bing Li
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - He Wang
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Cardiology, the Second Affiliated Hospital of Nanchang University, Jiangxi 330006, China
| | - MengSha Li
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Senlin Huang
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yili Sun
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Guojun Chen
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xiaoyun Si
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Chixiong Huang
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Wangjun Liao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yulin Liao
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jianping Bin
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
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Manohar S, Shah P, Biswas S, Mukadam A, Joshi M, Viswanathan G. Combining fluorescent cell barcoding and flow cytometry‐based phospho‐ERK1/2 detection at short time scales in adherent cells. Cytometry A 2018; 95:192-200. [DOI: 10.1002/cyto.a.23602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/09/2018] [Accepted: 08/20/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Sonal Manohar
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Prachi Shah
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Sharmila Biswas
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Anam Mukadam
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Madhura Joshi
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Ganesh Viswanathan
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
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Fitting mathematical models of biochemical pathways to steady state perturbation response data without simulating perturbation experiments. Sci Rep 2018; 8:11679. [PMID: 30076370 PMCID: PMC6076289 DOI: 10.1038/s41598-018-30118-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/18/2018] [Indexed: 11/09/2022] Open
Abstract
Fitting Ordinary Differential Equation (ODE) models of signal transduction networks (STNs) to experimental data is a challenging problem. Computational parameter fitting algorithms simulate a model many times with different sets of parameter values until the simulated STN behaviour match closely with experimental data. This process can be slow when the model is fitted to measurements of STN responses to numerous perturbations, since this requires simulating the model as many times as the number of perturbations for each set of parameter values. Here, I propose an approach that avoids simulating perturbation experiments when fitting ODE models to steady state perturbation response (SSPR) data. Instead of fitting the model directly to SSPR data, it finds model parameters which provides a close match between the scaled Jacobian matrices (SJM) of the model, which are numerically calculated using the model's rate equations and estimated from SSPR data using modular response analysis (MRA). The numerical estimation of SJM of an ODE model does not require simulating perturbation experiments, saving significant computation time. The effectiveness of this approach is demonstrated by fitting ODE models of the Mitogen Activated Protein Kinase (MAPK) pathway using simulated and real SSPR data.
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35
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Inferring a nonlinear biochemical network model from a heterogeneous single-cell time course data. Sci Rep 2018; 8:6790. [PMID: 29717206 PMCID: PMC5931614 DOI: 10.1038/s41598-018-25064-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 04/09/2018] [Indexed: 12/30/2022] Open
Abstract
Mathematical modeling and analysis of biochemical reaction networks are key routines in computational systems biology and biophysics; however, it remains difficult to choose the most valid model. Here, we propose a computational framework for data-driven and systematic inference of a nonlinear biochemical network model. The framework is based on the expectation-maximization algorithm combined with particle smoother and sparse regularization techniques. In this method, a “redundant” model consisting of an excessive number of nodes and regulatory paths is iteratively updated by eliminating unnecessary paths, resulting in an inference of the most likely model. Using artificial single-cell time-course data showing heterogeneous oscillatory behaviors, we demonstrated that this algorithm successfully inferred the true network without any prior knowledge of network topology or parameter values. Furthermore, we showed that both the regulatory paths among nodes and the optimal number of nodes in the network could be systematically determined. The method presented in this study provides a general framework for inferring a nonlinear biochemical network model from heterogeneous single-cell time-course data.
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36
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Eblen ST. Extracellular-Regulated Kinases: Signaling From Ras to ERK Substrates to Control Biological Outcomes. Adv Cancer Res 2018; 138:99-142. [PMID: 29551131 DOI: 10.1016/bs.acr.2018.02.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The extracellular-regulated kinases ERK1 and ERK2 are evolutionarily conserved, ubiquitous serine-threonine kinases that are involved in regulating cellular signaling in both normal and pathological conditions. Their expression is critical for development and their hyperactivation is a major factor in cancer development and progression. Since their discovery as one of the major signaling mediators activated by mitogens and Ras mutation, we have learned much about their regulation, including their activation, binding partners and substrates. In this review I will discuss some of what has been discovered about the members of the Ras to ERK pathway, including regulation of their activation by growth factors and cell adhesion pathways. Looking downstream of ERK activation I will also highlight some of the many ERK substrates that have been discovered, including those involved in feedback regulation, cell migration and cell cycle progression through the control of transcription, pre-mRNA splicing and protein synthesis.
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Affiliation(s)
- Scott T Eblen
- Medical University of South Carolina, Charleston, SC, United States.
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37
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Ochab-Marcinek A, Jędrak J, Tabaka M. Hill kinetics as a noise filter: the role of transcription factor autoregulation in gene cascades. Phys Chem Chem Phys 2018; 19:22580-22591. [PMID: 28809965 DOI: 10.1039/c7cp00743d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An intuition based on deterministic models of chemical kinetics is that population heterogeneity of transcription factor levels in cells is transmitted unchanged downstream to the target genes. We use a stochastic model of a two-gene cascade with a self-regulating upstream gene to show that, counter to the intuition, there is no simple mapping (bimodal to bimodal, unimodal to unimodal) between the shapes of the distributions of transcription factor numbers and target protein numbers in cells. Due to the presence of the two regulations, the system contains two nonlinear transfer functions, defined by the Hill kinetics of transcription factor binding. The transfer function of the regulator can "interfere" with the transfer function of the target, converting the bimodal input into a unimodal output or vice versa. We show that this effect can be predicted by a geometric construction. As an example application of the method, we present a case study of a system of several downstream genes of different sensitivities, controlled by a common transcription factor which also regulates its own transcription. We show that a single regulator can induce qualitatively different patterns (binary or graded) of responses to a signal in different downstream genes, depending on whether the sensitivity regions of the transfer functions of the upstream and downstream genes overlap or not. Alternatively, the same model can be interpreted as describing a single downstream gene that has different sensitivities in different cell lines due to mutations. Our model shows, therefore, a possible kinetic mechanism by which different genes can interpret the same biological signal in a different manner.
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Affiliation(s)
- Anna Ochab-Marcinek
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Jakub Jędrak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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Lipan O, Ferwerda C. Hill functions for stochastic gene regulatory networks from master equations with split nodes and time-scale separation. Phys Rev E 2018; 97:022413. [PMID: 29548212 DOI: 10.1103/physreve.97.022413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Indexed: 06/08/2023]
Abstract
The deterministic Hill function depends only on the average values of molecule numbers. To account for the fluctuations in the molecule numbers, the argument of the Hill function needs to contain the means, the standard deviations, and the correlations. Here we present a method that allows for stochastic Hill functions to be constructed from the dynamical evolution of stochastic biocircuits with specific topologies. These stochastic Hill functions are presented in a closed analytical form so that they can be easily incorporated in models for large genetic regulatory networks. Using a repressive biocircuit as an example, we show by Monte Carlo simulations that the traditional deterministic Hill function inaccurately predicts time of repression by an order of two magnitudes. However, the stochastic Hill function was able to capture the fluctuations and thus accurately predicted the time of repression.
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Affiliation(s)
- Ovidiu Lipan
- Department of Physics, University of Richmond, 28 Westhampton Way, Richmond, Virginia 23173, USA
| | - Cameron Ferwerda
- Department of Mathematics, King's College London, Strand, London WC2R 2LS, United Kingdom
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39
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Yapo C, Nair AG, Hellgren Kotaleski J, Vincent P, Castro LRV. Switch-like PKA responses in the nucleus of striatal neurons. J Cell Sci 2018; 131:jcs.216556. [DOI: 10.1242/jcs.216556] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/25/2018] [Indexed: 12/25/2022] Open
Abstract
Although it is known that Protein Kinase A (PKA) in the nucleus regulates gene expression, the specificities of nuclear PKA signaling remain poorly understood. Here, we combined computational modeling and live-cell imaging of PKA-dependent phosphorylation in mouse brain slices to investigate how transient dopamine signals are translated into nuclear PKA activity in cortical pyramidal neurons and striatal medium spiny neurons. We observed that the nuclear PKA signal in striatal neurons featured an ultrasensitive responsiveness, associated with fast, all or none responses, which is not consistent with the commonly accepted theory of a slow and passive diffusion of catalytic PKA in the nucleus. Our numerical model suggests that a positive feed-forward mechanism inhibiting nuclear phosphatase activity - possibly mediated by DARPP-32 - could be responsible for this non-linear pattern of nuclear PKA response, allowing for a better detection of the transient dopamine signals that are often associated with reward-mediated learning.
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Affiliation(s)
- Cédric Yapo
- Sorbonne Université, CNRS, Biological Adaptation and Ageing, F-75005 Paris, France
- Member of the Bio-Psy Labex, France
| | - Anu G. Nair
- Science for Life Laboratory, School of Computer Science and Communication, KTH Royal Institute of Technology, Stockholm, 10044, Sweden
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
- Manipal University, Manipal, India
| | - Jeanette Hellgren Kotaleski
- Science for Life Laboratory, School of Computer Science and Communication, KTH Royal Institute of Technology, Stockholm, 10044, Sweden
- Department of Neuroscience, Karolinska Institutet, Solna, 17177, Sweden
| | - Pierre Vincent
- Sorbonne Université, CNRS, Biological Adaptation and Ageing, F-75005 Paris, France
- Member of the Bio-Psy Labex, France
| | - Liliana R. V. Castro
- Sorbonne Université, CNRS, Biological Adaptation and Ageing, F-75005 Paris, France
- Member of the Bio-Psy Labex, France
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40
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Zhu Y. PRMT1 mediates podocyte injury and glomerular fibrosis through phosphorylation of ERK pathway. Biochem Biophys Res Commun 2017; 495:828-838. [PMID: 29129692 DOI: 10.1016/j.bbrc.2017.11.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 11/08/2017] [Indexed: 12/21/2022]
Abstract
Diabetic nephropathy (DN) is characterized by a change of glomerular structure and dysfunction of filtration barrier, which significantly accompanied by podocytes apoptosis and glomerular fibrosis. Angiotensin Ⅱ(Ang Ⅱ) induced activation of ERK1/2 signaling plays important roles in causing apoptosis of podocytes in DN kidneys. Previous studies have shown that PRMT1 have a pro-inflammatory function through activating ERK1/2 signaling pathway during development of chronic pulmonary disease, however, its role in DN development has not been investigated. Here, we detected a higher expression of PRMT1 in podocytes of kidneys from DN patients compared with normal kidneys. High glucose administration induced elevation of PRMT1 expression in podocytes, accompanied with higher phosphorylation of ERK and cleaved caspase-3. AMI-1, a selective inhibitor for PRMT1, could block these effects caused by glucose treatment. Administration of AMI-1 also attenuated apoptosis of podocytes during DN development of high-fatty diet-induced diabetic mice. Epithelial to mesenchymal transition during DN development, which characterized by extracellular matrix deposition in podocytes, was also restrained by AMI-1 treatment. Collectively, this study firstly demonstrated that PRMT1 exert podocyte-injury effects in mouse glomerulus through Ang Ⅱ/ERK pathway, which reveals a potential therapeutic target for DN.
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Affiliation(s)
- Yu Zhu
- Tongji University School of Medicine (First Unit), Department of Nephrology, Shanghai East Hospital (Second Unit), Shanghai, China
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41
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Xian H, Xie W, Yang S, Liu Q, Xia X, Jin S, Sun T, Cui J. Stratified ubiquitination of RIG-I creates robust immune response and induces selective gene expression. SCIENCE ADVANCES 2017; 3:e1701764. [PMID: 28948228 PMCID: PMC5609842 DOI: 10.1126/sciadv.1701764] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/01/2017] [Indexed: 05/12/2023]
Abstract
The activation of retinoic acid-inducible gene I (RIG-I), an indispensable viral RNA sensor in mammals, is subtly regulated by ubiquitination. Although multiple ubiquitination sites at the amino terminus of RIG-I have been identified, their functional allocations in RIG-I activation remain elusive. We identified a stratified model for RIG-I amino-terminal ubiquitination, in which initiation at either Lys164 or Lys172 allows subsequent ubiquitination at other lysines, to trigger and amplify RIG-I activation. Experimental and mathematical modeling showed that multisite ubiquitination provides robustness in RIG-I-mediated type I interferon (IFN) signaling. Furthermore, the flexibly controlled ultrasensitivity and IFN activation intensity determine the specificity of the IFN-stimulated gene transcription and manipulate cell fate in antiviral immune response. Our work demonstrates that tunable type I IFN signaling can be regulated through multisite RIG-I ubiquitination and elucidates a new paradigm for dynamic regulation in RIG-I-mediated antiviral signaling.
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Affiliation(s)
- Huifang Xian
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Weihong Xie
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shuai Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Qingxiang Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiaojun Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shouheng Jin
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Tingzhe Sun
- School of Life Sciences, Anqing Normal University, Anqing 246011, China
| | - Jun Cui
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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42
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Kang M, Garg V, Hadjantonakis AK. Lineage Establishment and Progression within the Inner Cell Mass of the Mouse Blastocyst Requires FGFR1 and FGFR2. Dev Cell 2017; 41:496-510.e5. [PMID: 28552559 DOI: 10.1016/j.devcel.2017.05.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 04/17/2017] [Accepted: 04/30/2017] [Indexed: 11/29/2022]
Abstract
Fibroblast growth factor 4 (FGF4) is the key signal driving specification of primitive endoderm (PrE) versus pluripotent epiblast (EPI) within the inner cell mass (ICM) of the mouse blastocyst. To gain insight into the receptor(s) responding to FGF4 within ICM cells, we combined single-cell-resolution quantitative imaging with single-cell transcriptomics of wild-type and Fgf receptor (Fgfr) mutant embryos. Despite the PrE-specific expression of FGFR2, it is FGFR1, expressed by all ICM cells, that is critical for establishment of a PrE identity. Signaling through FGFR1 is also required to constrain levels of the pluripotency-associated factor NANOG in EPI cells. However, the activity of both receptors is required for lineage establishment within the ICM. Gene expression profiling of 534 single ICM cells identified distinct downstream targets associated with each receptor. These data lead us to propose a model whereby unique and additive activities of FGFR1 and FGFR2 within the ICM coordinate establishment of two distinct lineages.
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Affiliation(s)
- Minjung Kang
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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43
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Relocation sensors to quantify signaling dynamics in live single cells. Curr Opin Biotechnol 2017; 45:51-58. [PMID: 28131009 DOI: 10.1016/j.copbio.2016.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/26/2016] [Accepted: 12/01/2016] [Indexed: 11/22/2022]
Abstract
All cells are different. Even isogenic cells can possess diverse shapes, reside in different cell-cycle stages or express various sets of proteins. These variations can modulate the cell response to environmental stimuli and thereby provide key insights into the regulation of signal transduction cascades. Fluorescence microscopy allows to visualize these differences and monitor in real-time the responses of live single cells. In order to observe key cellular events, fluorescent biosensors have been developed. Among many assays, relocation reporters play an important role since they enable the quantification of the signal transduction dynamics. Fluorescently tagged endogenous proteins, as well as synthetic constructs, have allowed the measurement of kinase activity, transcription factor activation, transcription and protein expression in live single cells.
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44
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Jain R, Watson U, Saini DK. ERK activated by Histamine H1 receptor is anti-proliferative through spatial restriction in the cytosol. Eur J Cell Biol 2016; 95:623-634. [DOI: 10.1016/j.ejcb.2016.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 10/04/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022] Open
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45
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Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway. PLoS Comput Biol 2016; 12:e1005222. [PMID: 27902699 PMCID: PMC5130170 DOI: 10.1371/journal.pcbi.1005222] [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: 06/05/2016] [Accepted: 10/25/2016] [Indexed: 12/03/2022] Open
Abstract
Cellular heterogeneity, which plays an essential role in biological phenomena, such as drug resistance and migration, is considered to arise from intrinsic (i.e., reaction kinetics) and extrinsic (i.e., protein variability) noise in the cell. However, the mechanistic effects of these types of noise to determine the heterogeneity of signal responses have not been elucidated. Here, we report that the output of epidermal growth factor (EGF) signaling activity is modulated by cellular noise, particularly by extrinsic noise of particular signaling components in the pathway. We developed a mathematical model of the EGF signaling pathway incorporating regulation between extracellular signal-regulated kinase (ERK) and nuclear pore complex (NPC), which is necessary for switch-like activation of the nuclear ERK response. As the threshold of switch-like behavior is more sensitive to perturbations than the graded response, the effect of biological noise is potentially critical for cell fate decision. Our simulation analysis indicated that extrinsic noise, but not intrinsic noise, contributes to cell-to-cell heterogeneity of nuclear ERK. In addition, we accurately estimated variations in abundance of the signal proteins between individual cells by direct comparison of experimental data with simulation results using Apparent Measurement Error (AME). AME was constant regardless of whether the protein levels varied in a correlated manner, while covariation among proteins influenced cell-to-cell heterogeneity of nuclear ERK, suppressing the variation. Simulations using the estimated protein abundances showed that each protein species has different effects on cell-to-cell variation in the nuclear ERK response. In particular, variability of EGF receptor, Ras, Raf, and MEK strongly influenced cellular heterogeneity, while others did not. Overall, our results indicated that cellular heterogeneity in response to EGF is strongly driven by extrinsic noise, and that such heterogeneity results from variability of particular protein species that function as sensitive nodes, which may contribute to the pathogenesis of human diseases. Individual cell behaviors are controlled by a variety of noise, such as fluctuations in biochemical reactions, protein variability, molecular diffusion, transcriptional noise, cell-to-cell contact, temperature, and pH. Such cellular noise often interferes with signal responses from external stimuli, and such heterogeneity functions in induction of drug resistance, survival, and migration of cells. Thus, heterogeneous cellular responses have positive and negative roles. However, the regulatory mechanisms that produce cellular heterogeneity are unclear. By mathematical modeling and simulations, we investigated how heterogeneous signaling responses are evoked in the EGF signaling pathway and influence the switch-like activation of nuclear ERK. This study demonstrated that cellular heterogeneity of the EGF signaling response is evoked by cell-to-cell variation of particular signaling proteins, such as EGFR, Ras, Raf, and MEK, which act as sensitive nodes in the pathway. These results suggest that signaling responses in individual cells can be predicted from the levels of proteins of sensitive nodes. This study also suggested that proteins of sensitive nodes may serve as cell survival mechanisms.
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46
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Miao CM, Jiang XW, He K, Li PZ, Liu ZJ, Cao D, Ou ZB, Gong JP, Liu CA, Cheng Y. Bone marrow stromal cells attenuate LPS-induced mouse acute liver injury via the prostaglandin E 2-dependent repression of the NLRP3 inflammasome in Kupffer cells. Immunol Lett 2016; 179:102-113. [PMID: 27666012 DOI: 10.1016/j.imlet.2016.09.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/23/2016] [Accepted: 09/21/2016] [Indexed: 12/18/2022]
Abstract
The nucleotide-binding and oligomerization domain-like receptor 3 (NLRP3) inflammasome participates in the pathogenesis of acute liver injury during sepsis. Bone marrow mesenchymal stem cells (BMSCs) attenuate sepsis through prostaglandin E 2 (PGE2) by increasing the interleukin-10 (IL-10) production of macrophages; moreover, NLRP3 inflammasome assembly is effectively regulated by IL-10 during infection. Whether BMSCs have an effect on the activation of the NLRP3 inflammasome and its underlying mechanism is unclear. Administering of BMSCs to mice or KCs after LPS stimulating have improved liver function and reduced activation of NLRP3 inflammasome in KCs. The beneficial effect of BMSCs was enhanced by over-expression of PGE2 and eliminated by silence of PGE2. Additionally, The IL-10 levels in the serum and supernatant were increased by given BMSCs and further increase by PGE2 over-expressed BMSCs, but decreased markedly by PGE2 silenced BMSCs. Furthermore, extracellular signal-regulated kinase 1 (ERK1) inhibitor reduced IL-10 production in KCs and blocked the inhibitory effect of PGE2 on the activation of the NLRP3 inflammasome. Our data reveal a novel mechanism of BMSC-mediated suppression of the activation of KCs through the secretion of PGE2 by BMSCs, which promotes KCs to secrete IL-10, leading to the inhibition of the NLRP3 inflammasome in KCs.
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Affiliation(s)
- Chun-Mu Miao
- Chongqing Key Laboratory of Hepatobiliary Surgery and Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiao-Wei Jiang
- Chongqing Key Laboratory of Hepatobiliary Surgery and Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Kun He
- Chongqing Key Laboratory of Hepatobiliary Surgery and Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Pei-Zhi Li
- Chongqing Key Laboratory of Hepatobiliary Surgery and Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zuo-Jin Liu
- Chongqing Key Laboratory of Hepatobiliary Surgery and Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ding Cao
- Chongqing Key Laboratory of Hepatobiliary Surgery and Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Bing Ou
- Chongqing Key Laboratory of Hepatobiliary Surgery and Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jian-Ping Gong
- Chongqing Key Laboratory of Hepatobiliary Surgery and Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chang-An Liu
- Chongqing Key Laboratory of Hepatobiliary Surgery and Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Yao Cheng
- Chongqing Key Laboratory of Hepatobiliary Surgery and Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Fey D, Matallanas D, Rauch J, Rukhlenko OS, Kholodenko BN. The complexities and versatility of the RAS-to-ERK signalling system in normal and cancer cells. Semin Cell Dev Biol 2016; 58:96-107. [PMID: 27350026 DOI: 10.1016/j.semcdb.2016.06.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/18/2016] [Indexed: 12/19/2022]
Abstract
The intricate dynamic control and plasticity of RAS to ERK mitogenic, survival and apoptotic signalling has mystified researches for more than 30 years. Therapeutics targeting the oncogenic aberrations within this pathway often yield unsatisfactory, even undesired results, as in the case of paradoxical ERK activation in response to RAF inhibition. A direct approach of inhibiting single oncogenic proteins misses the dynamic network context governing the network signal processing. In this review, we discuss the signalling behaviour of RAS and RAF proteins in normal and in cancer cells, and the emerging systems-level properties of the RAS-to-ERK signalling network. We argue that to understand the dynamic complexities of this control system, mathematical models including mechanistic detail are required. Looking into the future, these dynamic models will build the foundation upon which more effective, rational approaches to cancer therapy will be developed.
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Affiliation(s)
- Dirk Fey
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
| | - David Matallanas
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jens Rauch
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Oleksii S Rukhlenko
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Boris N Kholodenko
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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48
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Buscà R, Pouysségur J, Lenormand P. ERK1 and ERK2 Map Kinases: Specific Roles or Functional Redundancy? Front Cell Dev Biol 2016; 4:53. [PMID: 27376062 PMCID: PMC4897767 DOI: 10.3389/fcell.2016.00053] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 05/17/2016] [Indexed: 12/22/2022] Open
Abstract
The MAP kinase signaling cascade Ras/Raf/MEK/ERK has been involved in a large variety of cellular and physiological processes that are crucial for life. Many pathological situations have been associated to this pathway. More than one isoform has been described at each level of the cascade. In this review we devoted our attention to ERK1 and ERK2, which are the effector kinases of the pathway. Whether ERK1 and ERK2 specify functional differences or are in contrast functionally redundant, constitutes an ongoing debate despite the huge amount of studies performed to date. In this review we compiled data on ERK1 vs. ERK2 gene structures, protein sequences, expression levels, structural and molecular mechanisms of activation and substrate recognition. We have also attempted to perform a rigorous analysis of studies regarding the individual roles of ERK1 and ERK2 by the means of morpholinos, siRNA, and shRNA silencing as well as gene disruption or gene replacement in mice. Finally, we comment on a recent study of gene and protein evolution of ERK isoforms as a distinct approach to address the same question. Our review permits the evaluation of the relevance of published studies in the field especially when measurements of global ERK activation are taken into account. Our analysis favors the hypothesis of ERK1 and ERK2 exhibiting functional redundancy and points to the concept of the global ERK quantity, and not isoform specificity, as being the essential determinant to achieve ERK function.
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Affiliation(s)
- Roser Buscà
- Centre National de la Recherche Scientifique UMR7284, Institut National de la Santé et de la Recherche Médicale, Centre A. Lacassagne, Institute for Research on Cancer and Ageing of Nice, University of Nice-Sophia Antipolis Nice, France
| | - Jacques Pouysségur
- Centre National de la Recherche Scientifique UMR7284, Institut National de la Santé et de la Recherche Médicale, Centre A. Lacassagne, Institute for Research on Cancer and Ageing of Nice, University of Nice-Sophia AntipolisNice, France; Centre Scientifique de MonacoMonaco, Monaco
| | - Philippe Lenormand
- Centre National de la Recherche Scientifique UMR7284, Institut National de la Santé et de la Recherche Médicale, Centre A. Lacassagne, Institute for Research on Cancer and Ageing of Nice, University of Nice-Sophia Antipolis Nice, France
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49
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Rubinstein BY, Mattingly HH, Berezhkovskii AM, Shvartsman SY. Long-term dynamics of multisite phosphorylation. Mol Biol Cell 2016; 27:2331-40. [PMID: 27226482 PMCID: PMC4945148 DOI: 10.1091/mbc.e16-03-0137] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/16/2016] [Indexed: 01/14/2023] Open
Abstract
A systematic framework for exploring the long-term dynamics of a reaction network is applied to a minimal model of ERK regulation that distinguishes both monophosphorylated forms and allows for nonzero enzyme processivity. Bistability and oscillations can be observed at high levels of processivity. Multisite phosphorylation cycles are ubiquitous in cell regulation systems and are studied at multiple levels of complexity, from molecules to organisms, with the ultimate goal of establishing predictive understanding of the effects of genetic and pharmacological perturbations of protein phosphorylation in vivo. Achieving this goal is essentially impossible without mathematical models, which provide a systematic framework for exploring dynamic interactions of multiple network components. Most of the models studied to date do not discriminate between the distinct partially phosphorylated forms and focus on two limiting reaction regimes, distributive and processive, which differ in the number of enzyme–substrate binding events needed for complete phosphorylation or dephosphorylation. Here we use a minimal model of extracellular signal-related kinase regulation to explore the dynamics of a reaction network that includes all essential phosphorylation forms and arbitrary levels of reaction processivity. In addition to bistability, which has been studied extensively in distributive mechanisms, this network can generate periodic oscillations. Both bistability and oscillations can be realized at high levels of reaction processivity. Our work provides a general framework for systematic analysis of dynamics in multisite phosphorylation systems.
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Affiliation(s)
| | - Henry H Mattingly
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Alexander M Berezhkovskii
- Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892
| | - Stanislav Y Shvartsman
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
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