1
|
Oh TJ, Krishnamurthy V, Won Han J, Zhu J, Beg Z, Mehfooz A, Gworek B, Shapiro DJ, Zhang K. Spatiotemporal control of inflammatory lytic cell death through optogenetic induction of RIPK3 oligomerization. J Mol Biol 2024:168628. [PMID: 38797430 DOI: 10.1016/j.jmb.2024.168628] [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: 03/04/2024] [Revised: 04/21/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
Necroptosis is a programmed lytic cell death involving active cytokine production and plasma membrane rupture through distinct signaling cascades. However, it remains challenging to delineate this inflammatory cell death pathway at specific signaling nodes with spatiotemporal accuracy. To address this challenge, we developed an optogenetic system, termed Light-activatable Receptor-Interacting Protein Kinase 3 or La-RIPK3, to enable ligand-free, optical induction of RIPK3 oligomerization. La-RIPK3 activation dissects RIPK3-centric lytic cell death through the induction of RIPK3-containing necrosome, which mediates cytokine production and plasma membrane rupture. Bulk RNA-Seq analysis reveals that RIPK3 oligomerization results in partially overlapped gene expression compared to pharmacological induction of necroptosis. However, La-RIPK3 activates a group of genes likely regulated by RIPK3 kinase-independent processes. Using patterned light stimulation delivered by a spatial light modulator, we demonstrate precise spatiotemporal control of necroptosis in La-RIPK3-transduced HT-29 cells. Optogenetic control of proinflammatory lytic cell death could lead to the development of innovative experimental strategies to finetune the immune landscape for disease intervention.
Collapse
Affiliation(s)
- Teak-Jung Oh
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Vishnu Krishnamurthy
- High-throughput screening center, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Jeong Won Han
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Junyao Zhu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Zayn Beg
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Amna Mehfooz
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Bryan Gworek
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - David J Shapiro
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
| |
Collapse
|
2
|
Kochel B. Negative feedback systems for modelling NF-κB transcription factor oscillatory activity. Transcription 2024:1-32. [PMID: 38739365 DOI: 10.1080/21541264.2024.2331887] [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: 10/27/2023] [Accepted: 03/13/2024] [Indexed: 05/14/2024] Open
Abstract
Low-dimensional negative feedback systems (NFSs) were developed within a signal flow model to describe the oscillatory activities of NF-κB caused by interactions with its inhibitor IκBα. The NFSs were established as 3rd- and 4th-order linear systems containing unperturbed and perturbed negative feedback (NF) loops with constant or time-varying NF strengths and a feed-forward loop. NF-related analytical solutions to the NFSs representing the time courses of NF-κB and IκBα were determined and their exact mathematical relationship was found. The NFS's parameters were determined to fit the experimental time courses of NF-κB in TNF-α-stimulated embryonic fibroblasts, rela-/- embryonic fibroblasts reconstituted with RelA, C9L cells, GFP-p65 knock-in embryonic fibroblasts and embryogenic fibroblasts lacking Iκβ and IκBε, LPS-stimulated IC-21 macrophages treated or not with DCPA, and anti-IgM-stimulated DT40 B-lymphocytes. The unperturbed and perturbed NFSs describing the above biosystems generated isochronous and non-isochronous solutions, depending on a constant or time-varying NF strength, respectively. The oscillation period of the NF-coupled solutions, the phase difference between them and the time delays in the appearance of cytoplasmic IκBα after stimulation of NF-κB were determined. A significant divergence between the IκBα solutions to the NFSs and the IκBα experimental courses led to a rejection of the NF coupling between NF-κB and IκBα in the above biosystems. It was shown that neither the linearity nor the low dimensionality of the NFSs altered the NF relationship and the divergence between the IκBα solutions to the NFS and IκBα experimental time courses. Although the NF relationship between IκBα and NF-κB was not confirmed in all the experimental data analyzed, delayed negative feedback was found in some cases.
Collapse
Affiliation(s)
- Bonawentura Kochel
- Immunotherapy Central Europe, Wroclaw Medical University, Wrocław, Poland
| |
Collapse
|
3
|
Rahman SMT, Singh A, Lowe S, Aqdas M, Jiang K, Vaidehi Narayanan H, Hoffmann A, Sung MH. Co-imaging of RelA and c-Rel reveals features of NF-κB signaling for ligand discrimination. Cell Rep 2024; 43:113940. [PMID: 38483906 PMCID: PMC11015162 DOI: 10.1016/j.celrep.2024.113940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/11/2023] [Accepted: 02/23/2024] [Indexed: 04/02/2024] Open
Abstract
Individual cell sensing of external cues has evolved through the temporal patterns in signaling. Since nuclear factor κB (NF-κB) signaling dynamics have been examined using a single subunit, RelA, it remains unclear whether more information might be transmitted via other subunits. Using NF-κB double-knockin reporter mice, we monitored both canonical NF-κB subunits, RelA and c-Rel, simultaneously in single macrophages by quantitative live-cell imaging. We show that signaling features of RelA and c-Rel convey more information about the stimuli than those of either subunit alone. Machine learning is used to predict the ligand identity accurately based on RelA and c-Rel signaling features without considering the co-activated factors. Ligand discrimination is achieved through selective non-redundancy of RelA and c-Rel signaling dynamics, as well as their temporal coordination. These results suggest a potential role of c-Rel in fine-tuning immune responses and highlight the need for approaches that will elucidate the mechanisms regulating NF-κB subunit specificity.
Collapse
Affiliation(s)
- Shah Md Toufiqur Rahman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Apeksha Singh
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sarina Lowe
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mohammad Aqdas
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kevin Jiang
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Haripriya Vaidehi Narayanan
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alexander Hoffmann
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
| |
Collapse
|
4
|
Preedy MK, White MRH, Tergaonkar V. Cellular heterogeneity in TNF/TNFR1 signalling: live cell imaging of cell fate decisions in single cells. Cell Death Dis 2024; 15:202. [PMID: 38467621 PMCID: PMC10928192 DOI: 10.1038/s41419-024-06559-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/13/2024]
Abstract
Cellular responses to TNF are inherently heterogeneous within an isogenic cell population and across different cell types. TNF promotes cell survival by activating pro-inflammatory NF-κB and MAPK signalling pathways but may also trigger apoptosis and necroptosis. Following TNF stimulation, the fate of individual cells is governed by the balance of pro-survival and pro-apoptotic signalling pathways. To elucidate the molecular mechanisms driving heterogenous responses to TNF, quantifying TNF/TNFR1 signalling at the single-cell level is crucial. Fluorescence live-cell imaging techniques offer real-time, dynamic insights into molecular processes in single cells, allowing for detection of rapid and transient changes, as well as identification of subpopulations, that are likely to be missed with traditional endpoint assays. Whilst fluorescence live-cell imaging has been employed extensively to investigate TNF-induced inflammation and TNF-induced cell death, it has been underutilised in studying the role of TNF/TNFR1 signalling pathway crosstalk in guiding cell-fate decisions in single cells. Here, we outline the various opportunities for pathway crosstalk during TNF/TNFR1 signalling and how these interactions may govern heterogenous responses to TNF. We also advocate for the use of live-cell imaging techniques to elucidate the molecular processes driving cell-to-cell variability in single cells. Understanding and overcoming cellular heterogeneity in response to TNF and modulators of the TNF/TNFR1 signalling pathway could lead to the development of targeted therapies for various diseases associated with aberrant TNF/TNFR1 signalling, such as rheumatoid arthritis, metabolic syndrome, and cancer.
Collapse
Affiliation(s)
- Marcus K Preedy
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, D3308, Dover Street, Manchester, M13 9PT, England, UK
| | - Michael R H White
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, D3308, Dover Street, Manchester, M13 9PT, England, UK.
| | - Vinay Tergaonkar
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, MD7, Singapore, 117596, Singapore.
| |
Collapse
|
5
|
Glotfelty EJ, Tovar-Y-Romo LB, Hsueh SC, Tweedie D, Li Y, Harvey BK, Hoffer BJ, Karlsson TE, Olson L, Greig NH. The RhoA-ROCK1/ROCK2 Pathway Exacerbates Inflammatory Signaling in Immortalized and Primary Microglia. Cells 2023; 12:1367. [PMID: 37408199 DOI: 10.3390/cells12101367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 07/07/2023] Open
Abstract
Neuroinflammation is a unifying factor among all acute central nervous system (CNS) injuries and chronic neurodegenerative disorders. Here, we used immortalized microglial (IMG) cells and primary microglia (PMg) to understand the roles of the GTPase Ras homolog gene family member A (RhoA) and its downstream targets Rho-associated coiled-coil-containing protein kinases 1 and 2 (ROCK1 and ROCK2) in neuroinflammation. We used a pan-kinase inhibitor (Y27632) and a ROCK1- and ROCK2-specific inhibitor (RKI1447) to mitigate a lipopolysaccharide (LPS) challenge. In both the IMG cells and PMg, each drug significantly inhibited pro-inflammatory protein production detected in media (TNF-α, IL-6, KC/GRO, and IL-12p70). In the IMG cells, this resulted from the inhibition of NF-κB nuclear translocation and the blocking of neuroinflammatory gene transcription (iNOS, TNF-α, and IL-6). Additionally, we demonstrated the ability of both compounds to block the dephosphorylation and activation of cofilin. In the IMG cells, RhoA activation with Nogo-P4 or narciclasine (Narc) exacerbated the inflammatory response to the LPS challenge. We utilized a siRNA approach to differentiate ROCK1 and ROCK2 activity during the LPS challenges and showed that the blockade of both proteins may mediate the anti-inflammatory effects of Y27632 and RKI1447. Using previously published data, we show that genes in the RhoA/ROCK signaling cascade are highly upregulated in the neurodegenerative microglia (MGnD) from APP/PS-1 transgenic Alzheimer's disease (AD) mice. In addition to illuminating the specific roles of RhoA/ROCK signaling in neuroinflammation, we demonstrate the utility of using IMG cells as a model for primary microglia in cellular studies.
Collapse
Affiliation(s)
- Elliot J Glotfelty
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Luis B Tovar-Y-Romo
- Division of Neuroscience, Institute of Cellular Physiology, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Shih-Chang Hsueh
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - David Tweedie
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yazhou Li
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Brandon K Harvey
- Molecular Mechanisms of Cellular Stress and Inflammation Unit, Integrative Neuroscience Department, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD 21224, USA
| | - Barry J Hoffer
- Department of Neurosurgery, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Tobias E Karlsson
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Lars Olson
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Nigel H Greig
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
| |
Collapse
|
6
|
Downton P, Bagnall JS, England H, Spiller DG, Humphreys NE, Jackson DA, Paszek P, White MRH, Adamson AD. Overexpression of IκB⍺ modulates NF-κB activation of inflammatory target gene expression. Front Mol Biosci 2023; 10:1187187. [PMID: 37228587 PMCID: PMC10203502 DOI: 10.3389/fmolb.2023.1187187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Cells respond to inflammatory stimuli such as cytokines by activation of the nuclear factor-κB (NF-κB) signalling pathway, resulting in oscillatory translocation of the transcription factor p65 between nucleus and cytoplasm in some cell types. We investigate the relationship between p65 and inhibitor-κB⍺ (IκBα) protein levels and dynamic properties of the system, and how this interaction impacts on the expression of key inflammatory genes. Using bacterial artificial chromosomes, we developed new cell models of IκB⍺-eGFP protein overexpression in a pseudo-native genomic context. We find that cells with high levels of the negative regulator IκBα remain responsive to inflammatory stimuli and maintain dynamics for both p65 and IκBα. In contrast, canonical target gene expression is dramatically reduced by overexpression of IκBα, but can be partially rescued by overexpression of p65. Treatment with leptomycin B to promote nuclear accumulation of IκB⍺ also suppresses canonical target gene expression, suggesting a mechanism in which nuclear IκB⍺ accumulation prevents productive p65 interaction with promoter binding sites. This causes reduced target promoter binding and gene transcription, which we validate by chromatin immunoprecipitation and in primary cells. Overall, we show how inflammatory gene transcription is modulated by the expression levels of both IκB⍺ and p65. This results in an anti-inflammatory effect on transcription, demonstrating a broad mechanism to modulate the strength of inflammatory response.
Collapse
Affiliation(s)
- Polly Downton
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James S. Bagnall
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Hazel England
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David G. Spiller
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Neil E. Humphreys
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Dean A. Jackson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Pawel Paszek
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Michael R. H. White
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Antony D. Adamson
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| |
Collapse
|
7
|
Duran CL, Karagiannis GS, Chen X, Sharma VP, Entenberg D, Condeelis JS, Oktay MH. Cooperative NF-κB and Notch1 signaling promotes macrophage-mediated MenaINV expression in breast cancer. Breast Cancer Res 2023; 25:37. [PMID: 37024946 PMCID: PMC10080980 DOI: 10.1186/s13058-023-01628-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/27/2023] [Indexed: 04/08/2023] Open
Abstract
Metastasis is a multistep process that leads to the formation of clinically detectable tumor foci at distant organs and frequently to patient demise. Only a subpopulation of breast cancer cells within the primary tumor can disseminate systemically and cause metastasis. To disseminate, cancer cells must express MenaINV, an isoform of the actin regulatory protein Mena, encoded by the ENAH gene, that endows tumor cells with transendothelial migration activity, allowing them to enter and exit the blood circulation. We have previously demonstrated that MenaINV mRNA and protein expression is induced in cancer cells by macrophage contact. In this study, we discovered the precise mechanism by which macrophages induce MenaINV expression in tumor cells. We examined the promoter of the human and mouse ENAH gene and discovered a conserved NF-κB transcription factor binding site. Using live imaging of an NF-κB activity reporter and staining of fixed tissues from mouse and human breast cancer, we further determined that for maximal induction of MenaINV in cancer cells, NF-κB needs to cooperate with the Notch1 signaling pathway. Mechanistically, Notch1 signaling does not directly increase MenaINV expression, but it enhances and sustains NF-κB signaling through retention of p65, an NF-κB transcription factor, in the nucleus of tumor cells, leading to increased MenaINV expression. In mice, these signals are augmented following chemotherapy treatment and abrogated upon macrophage depletion. Targeting Notch1 signaling in vivo decreased NF-κB signaling activation and MenaINV expression in the primary tumor and decreased metastasis. Altogether, these data uncover mechanistic targets for blocking MenaINV induction that should be explored clinically to decrease cancer cell dissemination and improve survival of patients with metastatic disease.
Collapse
Affiliation(s)
- Camille L Duran
- Department of Pathology, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - George S Karagiannis
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
- Integrated Imaging Program, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine / Montefiore Medical Center, Bronx, NY, USA
| | - Xiaoming Chen
- Department of Pathology, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Ved P Sharma
- Department of Pathology, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
- Integrated Imaging Program, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
- Bio-Imaging Resource Center, The Rockefeller University, Box 209, 1230 York Avenue, New York City, NY, 10065, USA
| | - David Entenberg
- Department of Pathology, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
- Integrated Imaging Program, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - John S Condeelis
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA.
- Integrated Imaging Program, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA.
- Department of Cell Biology, Albert Einstein College of Medicine / Montefiore Medical Center, Bronx, NY, USA.
- Department of Surgery, Albert Einstein College of Medicine / Montefiore Medical Center, Bronx, NY, USA.
| | - Maja H Oktay
- Department of Pathology, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA.
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA.
- Integrated Imaging Program, Albert Einstein College of Medicine / Montefiore Medical Center, 1301 Morris Park Avenue, Bronx, NY, 10461, USA.
| |
Collapse
|
8
|
Goldman S, Aldana M, Cluzel P. Resonant learning in scale-free networks. PLoS Comput Biol 2023; 19:e1010894. [PMID: 36809235 PMCID: PMC9983844 DOI: 10.1371/journal.pcbi.1010894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 03/03/2023] [Accepted: 01/24/2023] [Indexed: 02/23/2023] Open
Abstract
Large networks of interconnected components, such as genes or machines, can coordinate complex behavioral dynamics. One outstanding question has been to identify the design principles that allow such networks to learn new behaviors. Here, we use Boolean networks as prototypes to demonstrate how periodic activation of network hubs provides a network-level advantage in evolutionary learning. Surprisingly, we find that a network can simultaneously learn distinct target functions upon distinct hub oscillations. We term this emergent property resonant learning, as the new selected dynamical behaviors depend on the choice of the period of the hub oscillations. Furthermore, this procedure accelerates the learning of new behaviors by an order of magnitude faster than without oscillations. While it is well-established that modular network architecture can be selected through evolutionary learning to produce different network behaviors, forced hub oscillations emerge as an alternative evolutionary learning strategy for which network modularity is not necessarily required.
Collapse
Affiliation(s)
- Samuel Goldman
- Department of Molecular and Cellular Biology, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
| | - Maximino Aldana
- Instituto de Ciencias Fisicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, Mexico
- * E-mail: (MA); (PC)
| | - Philippe Cluzel
- Department of Molecular and Cellular Biology, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (MA); (PC)
| |
Collapse
|
9
|
Duran CL, Karagiannis GS, Chen X, Sharma VP, Entenberg D, Condeelis JS, Oktay MH. Cooperative NF-κB and Notch1 signaling promotes macrophage-mediated MenaINV expression in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522642. [PMID: 36711751 PMCID: PMC9881873 DOI: 10.1101/2023.01.03.522642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Metastasis is a multistep process that leads to the formation of clinically detectable tumor foci at distant organs and frequently patient demise. Only a subpopulation of breast cancer cells within the primary tumor can disseminate systemically and cause metastasis. To disseminate, cancer cells must express MenaINV, an isoform of the actin-regulatory protein Mena encoded by the ENAH gene that endows tumor cells with transendothelial migration activity allowing them to enter and exit the blood circulation. We have previously demonstrated that MenaINV mRNA and protein expression is induced in cancer cells by macrophage contact. In this study, we discovered the precise mechanism by which macrophages induce MenaINV expression in tumor cells. We examined the promoter of the human and mouse ENAH gene and discovered a conserved NF-κB transcription factor binding site. Using live imaging of an NF-κB activity reporter and staining of fixed tissues from mouse and human breast cancer we further determined that for maximal induction of MenaINV in cancer cell NF-κB needs to cooperate with the Notch1 signaling pathway. Mechanistically, Notch1 signaling does not directly increase MenaINV expression, but it enhances and sustains NF-κB signaling through retention of p65, an NF-κB transcription factor, in the nucleus of tumor cells, leading to increased MenaINV expression. In mice, these signals are augmented following chemotherapy treatment and abrogated upon macrophage depletion. Targeting Notch1 signaling in vivo decreased NF-κB signaling and MenaINV expression in the primary tumor and decreased metastasis. Altogether, these data uncover mechanistic targets for blocking MenaINV induction that should be explored clinically to decrease cancer cell dissemination and improve survival of patients with metastatic disease.
Collapse
|
10
|
Aqdas M, Sung MH. NF-κB dynamics in the language of immune cells. Trends Immunol 2023; 44:32-43. [PMID: 36473794 PMCID: PMC9811507 DOI: 10.1016/j.it.2022.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022]
Abstract
Biological discovery has been driven by advances in throughput and resolution of analysis technologies. They have also created an indelible bias for snapshot-based knowledge. Even though recent methods such as multi-omics single-cell assays have empowered immunological investigations, they still provide snapshots of cellular behaviors and thus, have inherent limitations in reconstructing unsynchronized dynamic events across individual cells. Here, we present a rationale for how NF-κB may convey specificity of contextual information through subtle quantitative features of its signaling dynamics. The next frontier of predictive understanding should involve functional characterization of NF-κB signaling dynamics and their immunological implications. This may help solve the apparent paradox that a ubiquitously activated transcription factor can shape accurate responses to different immune challenges.
Collapse
Affiliation(s)
- Mohammad Aqdas
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
| |
Collapse
|
11
|
Rahman SMT, Aqdas M, Martin EW, Tomassoni Ardori F, Songkiatisak P, Oh KS, Uderhardt S, Yun S, Claybourne QC, McDevitt RA, Greco V, Germain RN, Tessarollo L, Sung MH. Double knockin mice show NF-κB trajectories in immune signaling and aging. Cell Rep 2022; 41:111682. [DOI: 10.1016/j.celrep.2022.111682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/06/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
|
12
|
Kizilirmak C, Bianchi ME, Zambrano S. Insights on the NF-κB System Using Live Cell Imaging: Recent Developments and Future Perspectives. Front Immunol 2022; 13:886127. [PMID: 35844496 PMCID: PMC9277462 DOI: 10.3389/fimmu.2022.886127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022] Open
Abstract
The transcription factor family of nuclear factor kappa B (NF-κB) proteins is widely recognized as a key player in inflammation and the immune responses, where it plays a fundamental role in translating external inflammatory cues into precise transcriptional programs, including the timely expression of a wide variety of cytokines/chemokines. Live cell imaging in single cells showed approximately 15 years ago that the canonical activation of NF-κB upon stimulus is very dynamic, including oscillations of its nuclear localization with a period close to 1.5 hours. This observation has triggered a fruitful interdisciplinary research line that has provided novel insights on the NF-κB system: how its heterogeneous response differs between cell types but also within homogeneous populations; how NF-κB dynamics translate external cues into intracellular signals and how NF-κB dynamics affects gene expression. Here we review the main features of this live cell imaging approach to the study of NF-κB, highlighting the key findings, the existing gaps of knowledge and hinting towards some of the potential future steps of this thriving research field.
Collapse
Affiliation(s)
- Cise Kizilirmak
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco E. Bianchi
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- *Correspondence: Marco E. Bianchi, ; Samuel Zambrano,
| | - Samuel Zambrano
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- *Correspondence: Marco E. Bianchi, ; Samuel Zambrano,
| |
Collapse
|
13
|
NfκB signaling dynamics and their target genes differ between mouse blood cell types and induce distinct cell behavior. Blood 2022; 140:99-111. [PMID: 35468185 DOI: 10.1182/blood.2021012918] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 03/16/2022] [Indexed: 11/20/2022] Open
Abstract
Cells can use signaling pathway activity over time (i.e., dynamics) to control cell fates. However, little is known about the potential existence and function of signaling dynamics in primary hematopoietic stem and progenitor cells (HSPCs). Here, we use time-lapse imaging and tracking of single murine HSPCs from GFP-p65/H2BmCherry reporter mice to quantify their nuclear factor κB (NfκB) activity dynamics in response to TNFα and IL1β. We find response dynamics to be heterogeneous between individual cells, with cell type specific dynamics distributions. Transcriptome sequencing of single cells physically isolated after live dynamics quantification shows activation of different target gene programs in cells with different dynamics. Finally, artificial induction of oscillatory NfκB activity causes changes in GMP behavior. Thus, HSPC behavior can be influenced by signaling dynamics, which are tightly regulated during hematopoietic differentiation and enable cell type specific responses to the same signaling inputs.
Collapse
|
14
|
Murphy JM, Jeong K, Cioffi DL, Campbell PM, Jo H, Ahn EYE, Lim STS. Focal Adhesion Kinase Activity and Localization is Critical for TNF-α-Induced Nuclear Factor-κB Activation. Inflammation 2021; 44:1130-1144. [PMID: 33527321 PMCID: PMC8326009 DOI: 10.1007/s10753-020-01408-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
While sustained nuclear factor-κB (NF-κB) activation is critical for proinflammatory molecule expression, regulators of NF-κB activity during chronic inflammation are not known. We investigated the role of focal adhesion kinase (FAK) on sustained NF-κB activation in tumor necrosis factor-α (TNF-α)-stimulated endothelial cells (ECs) both in vitro and in vivo. We found that FAK inhibition abolished TNF-α-mediated sustained NF-κB activity in ECs by disrupting formation of TNF-α receptor complex-I (TNFRC-I). Additionally, FAK inhibition diminished recruitment of receptor-interacting serine/threonine-protein kinase 1 (RIPK1) and the inhibitor of NF-κB (IκB) kinase (IKK) complex to TNFRC-I, resulting in elevated stability of IκBα protein. In mice given TNF-α, pharmacological and genetic FAK inhibition blocked TNF-α-induced IKK-NF-κB activation in aortic ECs. Mechanistically, TNF-α activated and redistributed FAK from the nucleus to the cytoplasm, causing elevated IKK-NF-κB activation. On the other hand, FAK inhibition trapped FAK in the nucleus of ECs even upon TNF-α stimulation, leading to reduced IKK-NF-κB activity. Together, these findings support a potential use for FAK inhibitors in treating chronic inflammatory diseases.
Collapse
Affiliation(s)
- James M Murphy
- Department of Biochemistry and Molecular Biology, University of South Alabama College of Medicine, 5851 N. USA Drive, Room 2366, Mobile, AL, 36688, USA
| | - Kyuho Jeong
- Department of Biochemistry and Molecular Biology, University of South Alabama College of Medicine, 5851 N. USA Drive, Room 2366, Mobile, AL, 36688, USA
| | - Donna L Cioffi
- Department of Biochemistry and Molecular Biology, University of South Alabama College of Medicine, 5851 N. USA Drive, Room 2366, Mobile, AL, 36688, USA
| | - Pamela Moore Campbell
- Department of Pathology, University of South Alabama College of Medicine, Mobile, AL, 36617, USA
| | - Hanjoong Jo
- Wallace H. Coulter Department of Bioengineering, Emory University and Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Eun-Young Erin Ahn
- Department of Pathology, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Ssang-Taek Steve Lim
- Department of Biochemistry and Molecular Biology, University of South Alabama College of Medicine, 5851 N. USA Drive, Room 2366, Mobile, AL, 36688, USA.
| |
Collapse
|
15
|
Adelaja A, Taylor B, Sheu KM, Liu Y, Luecke S, Hoffmann A. Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses. Immunity 2021; 54:916-930.e7. [PMID: 33979588 PMCID: PMC8184127 DOI: 10.1016/j.immuni.2021.04.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 12/21/2020] [Accepted: 04/13/2021] [Indexed: 12/12/2022]
Abstract
Macrophages initiate inflammatory responses via the transcription factor NFκB. The temporal pattern of NFκB activity determines which genes are expressed and thus, the type of response that ensues. Here, we examined how information about the stimulus is encoded in the dynamics of NFκB activity. We generated an mVenus-RelA reporter mouse line to enable high-throughput live-cell analysis of primary macrophages responding to host- and pathogen-derived stimuli. An information-theoretic workflow identified six dynamical features—termed signaling codons—that convey stimulus information to the nucleus. In particular, oscillatory trajectories were a hallmark of responses to cytokine but not pathogen-derived stimuli. Single-cell imaging and RNA sequencing of macrophages from a mouse model of Sjögren’s syndrome revealed inappropriate responses to stimuli, suggestive of confusion of two NFκB signaling codons. Thus, the dynamics of NFκB signaling classify immune threats through six signaling codons, and signal confusion based on defective codon deployment may underlie the etiology of some inflammatory diseases. Adelaja and Taylor et al. use a RelA-mVenus reporter mouse to examine, at single-cell level, the NFκB activation dynamics in primary macrophages responding to different stimuli. Their findings define six dynamical features—signaling codons—that classify immune threats and further suggest that signal “confusion” may contribute to autoimmune pathology.
Collapse
Affiliation(s)
- Adewunmi Adelaja
- Institute for Quantitative and Computational Biosciences (QCBio), Molecular Biology Institute (MBI), and Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles (UCLA), 611 Charles E. Young Dr S, Los Angeles, CA 90093
| | - Brooks Taylor
- Institute for Quantitative and Computational Biosciences (QCBio), Molecular Biology Institute (MBI), and Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles (UCLA), 611 Charles E. Young Dr S, Los Angeles, CA 90093
| | - Katherine M Sheu
- Institute for Quantitative and Computational Biosciences (QCBio), Molecular Biology Institute (MBI), and Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles (UCLA), 611 Charles E. Young Dr S, Los Angeles, CA 90093
| | - Yi Liu
- Institute for Quantitative and Computational Biosciences (QCBio), Molecular Biology Institute (MBI), and Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles (UCLA), 611 Charles E. Young Dr S, Los Angeles, CA 90093
| | - Stefanie Luecke
- Institute for Quantitative and Computational Biosciences (QCBio), Molecular Biology Institute (MBI), and Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles (UCLA), 611 Charles E. Young Dr S, Los Angeles, CA 90093
| | - Alexander Hoffmann
- Institute for Quantitative and Computational Biosciences (QCBio), Molecular Biology Institute (MBI), and Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles (UCLA), 611 Charles E. Young Dr S, Los Angeles, CA 90093.
| |
Collapse
|
16
|
Clark HR, McKenney C, Livingston NM, Gershman A, Sajjan S, Chan IS, Ewald AJ, Timp W, Wu B, Singh A, Regot S. Epigenetically regulated digital signaling defines epithelial innate immunity at the tissue level. Nat Commun 2021; 12:1836. [PMID: 33758175 PMCID: PMC7988009 DOI: 10.1038/s41467-021-22070-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 02/26/2021] [Indexed: 02/08/2023] Open
Abstract
To prevent damage to the host or its commensal microbiota, epithelial tissues must match the intensity of the immune response to the severity of a biological threat. Toll-like receptors allow epithelial cells to identify microbe associated molecular patterns. However, the mechanisms that mitigate biological noise in single cells to ensure quantitatively appropriate responses remain unclear. Here we address this question using single cell and single molecule approaches in mammary epithelial cells and primary organoids. We find that epithelial tissues respond to bacterial microbe associated molecular patterns by activating a subset of cells in an all-or-nothing (i.e. digital) manner. The maximum fraction of responsive cells is regulated by a bimodal epigenetic switch that licenses the TLR2 promoter for transcription across multiple generations. This mechanism confers a flexible memory of inflammatory events as well as unique spatio-temporal control of epithelial tissue-level immune responses. We propose that epigenetic licensing in individual cells allows for long-term, quantitative fine-tuning of population-level responses.
Collapse
Affiliation(s)
- Helen R Clark
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Connor McKenney
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nathan M Livingston
- The Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Seema Sajjan
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Isaac S Chan
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew J Ewald
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Bin Wu
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Abhyudai Singh
- Electrical and Computer Engineering, University of Delaware, Newark, DE, USA
| | - Sergi Regot
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
17
|
Abstract
Since time immemorial, ginger has been widely used as a food spice, providing aromatic odor and pungent taste, and as a medicinal plant, with various therapeutic effects such as antioxidant, anti-inflammatory, and analgesic, among others. It has long been an integral constituent of most herbal medicines in Africa, China and India. Its medicinal properties are largely attributed to its outstanding amount of phenolics which include gingerols, paradols, zingerones, and many others. With consumer preference gradually and remarkably shifting from high-calorie towards low-calorie and functional beverages, the demand for ginger beer is flourishing at a faster rate. Currently, the ginger beer market is dominated by the United States. The demand for ginger beer is, however, debilitated by using artificial ingredients. Nonetheless, the use of natural ginger extract enriches beer with putative bioactive phytoconstituents such as shagaol, gingerone, zingerone, ginger flavonoids and essential oils, as well as essential nutritional components including proteins, vitamins and minerals, to promote general wellbeing of consumer. This paper presents an overview of the phytoconstituents of ginger as well as the overall biological activities they confer to the consumer. In addition, the market trend as well as the production technology of ginger beer using natural ginger extract is described here.
Collapse
|
18
|
Yan F, Liu L, Wang Q. Combinatorial dynamics of protein synthesis time delay and negative feedback loop in NF- κB signalling pathway. IET Syst Biol 2020; 14:284-291. [PMID: 33095749 DOI: 10.1049/iet-syb.2020.0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The transcription factor NF-κB links immune response and inflammatory reaction and its different oscillation patterns determine different cell fates. In this study, a mathematical model with IκBα protein synthesis time delay is developed based on the experimental evidences. The results show that time delay has the ability to drive oscillation of NF-κB via Hopf bifurcation. Meanwhile, the amplitude and period are sensitive to the time delay. Moreover, the time delay threshold is a function of four parameters characterising the negative feedback loop. Likewise, the parameters also have effects on the amplitude and period of NF-κB oscillation induced by time delay. Therefore, the oscillation patterns of NF-κB are collaborative results of time delay coupled with the negative feedback loop. These results not only enhance the understanding of NF-κB biological oscillation but also provide clues for the development of anti-inflammatory or anti-cancer drugs.
Collapse
Affiliation(s)
- Fang Yan
- Department of Mathematics, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Li Liu
- Department of Mathematics, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Qingyun Wang
- Department of Dynamics and Control, Beihang University, Beijing 100191, People's Republic of China.
| |
Collapse
|
19
|
Zambrano S, Loffreda A, Carelli E, Stefanelli G, Colombo F, Bertrand E, Tacchetti C, Agresti A, Bianchi ME, Molina N, Mazza D. First Responders Shape a Prompt and Sharp NF-κB-Mediated Transcriptional Response to TNF-α. iScience 2020; 23:101529. [PMID: 33083759 PMCID: PMC7509218 DOI: 10.1016/j.isci.2020.101529] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/05/2020] [Accepted: 09/01/2020] [Indexed: 12/01/2022] Open
Abstract
Nuclear factor (NF)-κB controls the transcriptional response to inflammatory signals by translocating into the nucleus, but we lack a single-cell characterization of the resulting transcription dynamics. Here we show that upon tumor necrosis factor (TNF)-α transcription of NF-κB target genes is heterogeneous in individual cells but results in an average nascent transcription profile that is prompt (i.e., occurs almost immediately) and sharp (i.e., increases and decreases rapidly) compared with NF-κB nuclear localization. Using an NF-κB-controlled MS2 reporter we show that the single-cell nascent transcription is more heterogeneous than NF-κB translocation dynamics, with a fraction of synchronized “first responders” that shape the average transcriptional profile and are more prone to respond to multiple TNF-α stimulations. A mathematical model combining NF-κB-mediated gene activation and a gene refractory state is able to reproduce these features. Our work shows how the expression of target genes induced by transcriptional activators can be heterogeneous across single cells and yet time resolved on average. Nascent transcription upon TNF-α is heterogeneous, with a subset of “first responders” The average nascent transcription is prompt and sharper than NF-κB response First responders do not depend on NF-κB dynamics and respond more to pulsed stimuli A model including NF-κB and a gene refractory state reproduces these observations
Collapse
Affiliation(s)
- Samuel Zambrano
- School of Medicine, Vita-Salute San Raffaele University, Milan 20132, Italy.,Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Alessia Loffreda
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Elena Carelli
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Giacomo Stefanelli
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Federica Colombo
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan 20133, Italy
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, CNRS, Montpellier 34293, France
| | - Carlo Tacchetti
- School of Medicine, Vita-Salute San Raffaele University, Milan 20132, Italy.,Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Alessandra Agresti
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Marco E Bianchi
- School of Medicine, Vita-Salute San Raffaele University, Milan 20132, Italy.,Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Nacho Molina
- Institut de Génétique et Biologie Moléculaire Cellulaire, Illkirch-Graffenstaden 67404, France
| | - Davide Mazza
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| |
Collapse
|
20
|
Martin EW, Pacholewska A, Patel H, Dashora H, Sung MH. Integrative analysis suggests cell type-specific decoding of NF-κB dynamics. Sci Signal 2020; 13:13/620/eaax7195. [PMID: 32098801 DOI: 10.1126/scisignal.aax7195] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The complex signaling dynamics of transcription factors can encode both qualitative and quantitative information about the extracellular environment, which increases the information transfer capacity and potentially supports accurate cellular decision-making. An important question is how these signaling dynamics patterns are translated into functionally appropriate gene regulation programs. To address this question for transcription factors of the nuclear factor κB (NF-κB) family, we profiled the single-cell dynamics of two major NF-κB subunits, RelA and c-Rel, induced by a panel of pathogen-derived stimuli in immune and nonimmune cellular contexts. Diverse NF-κB-activating ligands produced different patterns of RelA and c-Rel signaling dynamic features, such as variations in duration or time-integrated activity. Analysis of nascent transcripts delineated putative direct targets of NF-κB as compared to genes controlled by other transcriptional and posttranscriptional mechanisms and showed that the transcription of more than half of the induced genes was tightly linked to specific dynamic features of NF-κB signaling. Fibroblast and macrophage cell lines shared a cluster of such "NF-κB dynamics-decoding" genes, as well as cell type-specific decoding genes. Dissecting the subunit specificity of dynamics-decoding genes suggested that target genes were most often linked to both RelA and c-Rel or to RelA alone. Thus, our analysis reveals the cell type-specific interpretation of pathogenic information through the signaling dynamics of NF-κB.
Collapse
Affiliation(s)
- Erik W Martin
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Alicja Pacholewska
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Heta Patel
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Himanshu Dashora
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
| |
Collapse
|
21
|
Martin EW, Chakraborty S, Presman DM, Tomassoni Ardori F, Oh KS, Kaileh M, Tessarollo L, Sung MH. Assaying Homodimers of NF-κB in Live Single Cells. Front Immunol 2019; 10:2609. [PMID: 31787981 PMCID: PMC6853996 DOI: 10.3389/fimmu.2019.02609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/21/2019] [Indexed: 11/25/2022] Open
Abstract
NF-κB is a family of heterodimers and homodimers which are generated from subunits encoded by five genes. The predominant classical dimer RelA:p50 is presumed to operate as “NF-κB” in many contexts. However, there are several other dimer species which exist and may even be more functionally relevant in specific cell types. Accurate characterization of stimulus-specific and tissue-specific dimer repertoires is fundamentally important for understanding the downstream gene regulation by NF-κB proteins. In vitro assays such as immunoprecipitation have been widely used to analyze subunit composition, but these methods do not provide information about dimerization status within the natural intracellular environment of intact live cells. Here we apply a live single cell microscopy technique termed Number and Brightness to examine dimers translocating to the nucleus in fibroblasts after pro-inflammatory stimulation. This quantitative assay suggests that RelA:RelA homodimers are more prevalent than might be expected. We also found that the relative proportion of RelA:RelA homodimers can be perturbed by small molecule inhibitors known to disrupt the NF-κB pathway. Our findings show that Number and Brightness is a useful method for investigating NF-κB dimer species in live cells. This approach may help identify the relevant targets in pathophysiological contexts where the dimer specificity of NF-κB intervention is desired.
Collapse
Affiliation(s)
- Erik W Martin
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Sayantan Chakraborty
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Francesco Tomassoni Ardori
- Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Kyu-Seon Oh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Mary Kaileh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| |
Collapse
|
22
|
Controlling Nuclear NF-κB Dynamics by β-TrCP-Insights from a Computational Model. Biomedicines 2019; 7:biomedicines7020040. [PMID: 31137887 PMCID: PMC6631534 DOI: 10.3390/biomedicines7020040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/15/2019] [Accepted: 05/24/2019] [Indexed: 12/11/2022] Open
Abstract
The canonical nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling pathway regulates central processes in mammalian cells and plays a fundamental role in the regulation of inflammation and immunity. Aberrant regulation of the activation of the transcription factor NF-κB is associated with severe diseases such as inflammatory bowel disease and arthritis. In the canonical pathway, the inhibitor IκB suppresses NF-κB’s transcriptional activity. NF-κB becomes active upon the degradation of IκB, a process that is, in turn, regulated by the β-transducin repeat-containing protein (β-TrCP). β-TrCP has therefore been proposed as a promising pharmacological target in the development of novel therapeutic approaches to control NF-κB’s activity in diseases. This study explores the extent to which β-TrCP affects the dynamics of nuclear NF-κB using a computational model of canonical NF-κB signaling. The analysis predicts that β-TrCP influences the steady-state concentration of nuclear NF-κB, as well as changes characteristic dynamic properties of nuclear NF-κB, such as fold-change and the duration of its response to pathway stimulation. The results suggest that the modulation of β-TrCP has a high potential to regulate the transcriptional activity of NF-κB.
Collapse
|
23
|
DeFelice MM, Clark HR, Hughey JJ, Maayan I, Kudo T, Gutschow MV, Covert MW, Regot S. NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop. Sci Signal 2019; 12:12/579/eaau3568. [PMID: 31040261 DOI: 10.1126/scisignal.aau3568] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Over the last decade, multiple studies have shown that signaling proteins activated in different temporal patterns, such as oscillatory, transient, and sustained, can result in distinct gene expression patterns or cell fates. However, the molecular events that ensure appropriate stimulus- and dose-dependent dynamics are not often understood and are difficult to investigate. Here, we used single-cell analysis to dissect the mechanisms underlying the stimulus- and dose-encoding patterns in the innate immune signaling network. We found that Toll-like receptor (TLR) and interleukin-1 receptor (IL-1R) signaling dynamics relied on a dose-dependent, autoinhibitory loop that rendered cells refractory to further stimulation. Using inducible gene expression and optogenetics to perturb the network at different levels, we identified IL-1R-associated kinase 1 (IRAK1) as the dose-sensing node responsible for limiting signal flow during the innate immune response. Although the kinase activity of IRAK1 was not required for signal propagation, it played a critical role in inhibiting the nucleocytoplasmic oscillations of the transcription factor NF-κB. Thus, protein activities that may be "dispensable" from a topological perspective can nevertheless be essential in shaping the dynamic response to the external environment.
Collapse
Affiliation(s)
- Mialy M DeFelice
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Helen R Clark
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jacob J Hughey
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Inbal Maayan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Takamasa Kudo
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Miriam V Gutschow
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Sergi Regot
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. .,Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
24
|
Dorrington MG, Fraser IDC. NF-κB Signaling in Macrophages: Dynamics, Crosstalk, and Signal Integration. Front Immunol 2019; 10:705. [PMID: 31024544 PMCID: PMC6465568 DOI: 10.3389/fimmu.2019.00705] [Citation(s) in RCA: 399] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/14/2019] [Indexed: 12/12/2022] Open
Abstract
The nuclear factor-κB (NF-κB) signaling pathway is one of the best understood immune-related pathways thanks to almost four decades of intense research. NF-κB signaling is activated by numerous discrete stimuli and is a master regulator of the inflammatory response to pathogens and cancerous cells, as well as a key regulator of autoimmune diseases. In this regard, the role of NF-κB signaling in immunity is not unlike that of the macrophage. The dynamics by which NF-κB proteins shuttle between the cytoplasm and the nucleus to initiate transcription have been studied rigorously in fibroblasts and other non-hematopoietic cells, but many questions remain as to how current models of NF-κB signaling and dynamics can be translated to innate immune cells such as macrophages. In this review, we will present recent research on the dynamics of NF-κB signaling and focus especially on how these dynamics vary in different cell types, while discussing why these characteristics may be important. We will end by looking ahead to how new techniques and technologies should allow us to analyze these signaling processes with greater clarity, bringing us closer to a more complete understanding of inflammatory transcription factor dynamics and how different cellular contexts might allow for appropriate control of innate immune responses.
Collapse
Affiliation(s)
- Michael G Dorrington
- Signaling Systems Section, Laboratory of Immune System Biology, NIAID, DIR, NIH, Bethesda, MD, United States
| | - Iain D C Fraser
- Signaling Systems Section, Laboratory of Immune System Biology, NIAID, DIR, NIH, Bethesda, MD, United States
| |
Collapse
|
25
|
Brignall R, Moody AT, Mathew S, Gaudet S. Considering Abundance, Affinity, and Binding Site Availability in the NF-κB Target Selection Puzzle. Front Immunol 2019; 10:609. [PMID: 30984185 PMCID: PMC6450194 DOI: 10.3389/fimmu.2019.00609] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/07/2019] [Indexed: 12/21/2022] Open
Abstract
The NF-κB transcription regulation system governs a diverse set of responses to various cytokine stimuli. With tools from in vitro biochemical characterizations, to omics-based whole genome investigations, great strides have been made in understanding how NF-κB transcription factors control the expression of specific sets of genes. Nonetheless, these efforts have also revealed a very large number of potential binding sites for NF-κB in the human genome, and a puzzle emerges when trying to explain how NF-κB selects from these many binding sites to direct cell-type- and stimulus-specific gene expression patterns. In this review, we surmise that target gene transcription can broadly be thought of as a function of the nuclear abundance of the various NF-κB dimers, the affinity of NF-κB dimers for the regulatory sequence and the availability of this regulatory site. We use this framework to place quantitative information that has been gathered about the NF-κB transcription regulation system into context and thus consider questions it answers, and questions it raises. We end with a brief discussion of some of the future prospects that new approaches could bring to our understanding of how NF-κB transcription factors orchestrate diverse responses in different biological contexts.
Collapse
Affiliation(s)
- Ruth Brignall
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States
| | - Amy T Moody
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States.,Laboratory for Systems Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, United States.,Department of Microbiology, Tufts University School of Medicine, Boston, MA, United States
| | - Shibin Mathew
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States
| | - Suzanne Gaudet
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States
| |
Collapse
|
26
|
Lahmann I, Bröhl D, Zyrianova T, Isomura A, Czajkowski MT, Kapoor V, Griger J, Ruffault PL, Mademtzoglou D, Zammit PS, Wunderlich T, Spuler S, Kühn R, Preibisch S, Wolf J, Kageyama R, Birchmeier C. Oscillations of MyoD and Hes1 proteins regulate the maintenance of activated muscle stem cells. Genes Dev 2019; 33:524-535. [PMID: 30862660 PMCID: PMC6499323 DOI: 10.1101/gad.322818.118] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/19/2019] [Indexed: 11/25/2022]
Abstract
Lahmann et al. show that Hes1 controls the balance between proliferation and differentiation of activated muscle stem cells in both developing and regenerating muscle. Hes1 is expressed in an oscillatory manner in activated stem cells, where it drives the oscillatory expression of MyoD. The balance between proliferation and differentiation of muscle stem cells is tightly controlled, ensuring the maintenance of a cellular pool needed for muscle growth and repair. We demonstrate here that the transcriptional regulator Hes1 controls the balance between proliferation and differentiation of activated muscle stem cells in both developing and regenerating muscle. We observed that Hes1 is expressed in an oscillatory manner in activated stem cells where it drives the oscillatory expression of MyoD. MyoD expression oscillates in activated muscle stem cells from postnatal and adult muscle under various conditions: when the stem cells are dispersed in culture, when they remain associated with single muscle fibers, or when they reside in muscle biopsies. Unstable MyoD oscillations and long periods of sustained MyoD expression are observed in differentiating cells. Ablation of the Hes1 oscillator in stem cells interfered with stable MyoD oscillations and led to prolonged periods of sustained MyoD expression, resulting in increased differentiation propensity. This interfered with the maintenance of activated muscle stem cells, and impaired muscle growth and repair. We conclude that oscillatory MyoD expression allows the cells to remain in an undifferentiated and proliferative state and is required for amplification of the activated stem cell pool.
Collapse
Affiliation(s)
- Ines Lahmann
- Developmental Biology/Signal Transduction, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Dominique Bröhl
- Developmental Biology/Signal Transduction, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Tatiana Zyrianova
- Developmental Biology/Signal Transduction, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Akihiro Isomura
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Maciej T Czajkowski
- Developmental Biology/Signal Transduction, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Varun Kapoor
- Microscopy/Image Analysis, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Joscha Griger
- Developmental Biology/Signal Transduction, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Pierre-Louis Ruffault
- Developmental Biology/Signal Transduction, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Despoina Mademtzoglou
- IMRB U955-E10, Institut National de la Santé et de la Recherche Médicale (INSERM), Faculté de Medicine, Université Paris Est, 94000 Creteil, France
| | - Peter S Zammit
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom
| | - Thomas Wunderlich
- Max Planck Institute for Metabolism Research, 50931 Cologne, Germany
| | - Simone Spuler
- Muscle Research Unit, Experimental and Clinical Research Center, Max-Delbrück-Center, Charité Medical Faculty, 13125 Berlin, Germany
| | - Ralf Kühn
- Transgenic Core Facility, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany.,Berlin Institute of Health, 10178 Berlin, Germany
| | - Stephan Preibisch
- Microscopy/Image Analysis, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Jana Wolf
- Mathematical Modelling, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Carmen Birchmeier
- Developmental Biology/Signal Transduction, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| |
Collapse
|
27
|
Critical roles of IκBα and RelA phosphorylation in transitional oscillation in NF-κB signaling module. J Theor Biol 2019; 462:479-489. [DOI: 10.1016/j.jtbi.2018.11.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 11/21/2018] [Accepted: 11/26/2018] [Indexed: 11/19/2022]
|
28
|
Martin EW, Sung MH. Challenges of Decoding Transcription Factor Dynamics in Terms of Gene Regulation. Cells 2018; 7:cells7090132. [PMID: 30205475 PMCID: PMC6162420 DOI: 10.3390/cells7090132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/01/2018] [Accepted: 09/03/2018] [Indexed: 01/20/2023] Open
Abstract
Technological advances are continually improving our ability to obtain more accurate views about the inner workings of biological systems. One such rapidly evolving area is single cell biology, and in particular gene expression and its regulation by transcription factors in response to intrinsic and extrinsic factors. Regarding the study of transcription factors, we discuss some of the promises and pitfalls associated with investigating how individual cells regulate gene expression through modulation of transcription factor activities. Specifically, we discuss four leading experimental approaches, the data that can be obtained from each, and important considerations that investigators should be aware of when drawing conclusions from such data.
Collapse
Affiliation(s)
- Erik W Martin
- Transcription Systems Dynamics and Biology Unit, Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Myong-Hee Sung
- Transcription Systems Dynamics and Biology Unit, Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
| |
Collapse
|
29
|
Oh KS, Gottschalk RA, Lounsbury NW, Sun J, Dorrington MG, Baek S, Sun G, Wang Z, Krauss KS, Milner JD, Dutta B, Hager GL, Sung MH, Fraser IDC. Dual Roles for Ikaros in Regulation of Macrophage Chromatin State and Inflammatory Gene Expression. THE JOURNAL OF IMMUNOLOGY 2018; 201:757-771. [PMID: 29898962 DOI: 10.4049/jimmunol.1800158] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/15/2018] [Indexed: 12/19/2022]
Abstract
Macrophage activation by bacterial LPS leads to induction of a complex inflammatory gene program dependent on numerous transcription factor families. The transcription factor Ikaros has been shown to play a critical role in lymphoid cell development and differentiation; however, its function in myeloid cells and innate immune responses is less appreciated. Using comprehensive genomic analysis of Ikaros-dependent transcription, DNA binding, and chromatin accessibility, we describe unexpected dual repressor and activator functions for Ikaros in the LPS response of murine macrophages. Consistent with the described function of Ikaros as transcriptional repressor, Ikzf1-/- macrophages showed enhanced induction for select responses. In contrast, we observed a dramatic defect in expression of many delayed LPS response genes, and chromatin immunoprecipitation sequencing analyses support a key role for Ikaros in sustained NF-κB chromatin binding. Decreased Ikaros expression in Ikzf1+/- mice and human cells dampens these Ikaros-enhanced inflammatory responses, highlighting the importance of quantitative control of Ikaros protein level for its activator function. In the absence of Ikaros, a constitutively open chromatin state was coincident with dysregulation of LPS-induced chromatin remodeling, gene expression, and cytokine responses. Together, our data suggest a central role for Ikaros in coordinating the complex macrophage transcriptional program in response to pathogen challenge.
Collapse
Affiliation(s)
- Kyu-Seon Oh
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.,Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Rachel A Gottschalk
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Nicolas W Lounsbury
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jing Sun
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Michael G Dorrington
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Guangping Sun
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Ze Wang
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Kathleen S Krauss
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Joshua D Milner
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Bhaskar Dutta
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Iain D C Fraser
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892;
| |
Collapse
|
30
|
Temperature regulates NF-κB dynamics and function through timing of A20 transcription. Proc Natl Acad Sci U S A 2018; 115:E5243-E5249. [PMID: 29760065 PMCID: PMC5984538 DOI: 10.1073/pnas.1803609115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
NF-κB signaling plays a pivotal role in control of the inflammatory response. We investigated how the dynamics and function of NF-κB were affected by temperature within the mammalian physiological range (34 °C to 40 °C). An increase in temperature led to an increase in NF-κB nuclear/cytoplasmic oscillation frequency following Tumor Necrosis Factor alpha (TNFα) stimulation. Mathematical modeling suggested that this temperature sensitivity might be due to an A20-dependent mechanism, and A20 silencing removed the sensitivity to increased temperature. The timing of the early response of a key set of NF-κB target genes showed strong temperature dependence. The cytokine-induced expression of many (but not all) later genes was insensitive to temperature change (suggesting that they might be functionally temperature-compensated). Moreover, a set of temperature- and TNFα-regulated genes were implicated in NF-κB cross-talk with key cell-fate-controlling pathways. In conclusion, NF-κB dynamics and target gene expression are modulated by temperature and can accurately transmit multidimensional information to control inflammation.
Collapse
|
31
|
Colombo F, Zambrano S, Agresti A. NF-κB, the Importance of Being Dynamic: Role and Insights in Cancer. Biomedicines 2018; 6:biomedicines6020045. [PMID: 29673148 PMCID: PMC6027537 DOI: 10.3390/biomedicines6020045] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 12/11/2022] Open
Abstract
In this review, we aim at describing the results obtained in the past years on dynamics features defining NF-κB regulatory functions, as we believe that these developments might have a transformative effect on the way in which NF-κB involvement in cancer is studied. We will also describe technical aspects of the studies performed in this context, including the use of different cellular models, culture conditions, microscopy approaches and quantification of the imaging data, balancing their strengths and limitations and pointing out to common features and to some open questions. Our emphasis in the methodology will allow a critical overview of literature and will show how these cutting-edge approaches can contribute to shed light on the involvement of NF-κB deregulation in tumour onset and progression. We hypothesize that this “dynamic point of view” can be fruitfully applied to untangle the complex relationship between NF-κB and cancer and to find new targets to restrain cancer growth.
Collapse
Affiliation(s)
- Federica Colombo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, 20132 Milan, Italy.
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy.
| | - Samuel Zambrano
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, 20132 Milan, Italy.
- Vita-Salute San Raffaele University, 20132 Milan, Italy.
| | - Alessandra Agresti
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, 20132 Milan, Italy.
| |
Collapse
|
32
|
Ernst O, Vayttaden SJ, Fraser IDC. Measurement of NF-κB Activation in TLR-Activated Macrophages. Methods Mol Biol 2018; 1714:67-78. [PMID: 29177856 DOI: 10.1007/978-1-4939-7519-8_5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nuclear factor kappa-B (NF-κB) is a key transcription factor in the regulation of the innate immune inflammatory response in activated macrophages. NF-κB functions as a homo- or hetero-dimer derived from one or more of the five members of the NF-κB family, and is activated through a well-studied process of stimulus-dependent inhibitor degradation, post-translational modification, nuclear translocation, and chromatin binding. Its activity is subject to multiple levels of feedback control through both inhibitor protein activity and direct regulation of NF-κB components. Many methods have been developed to measure and quantify NF-κB activation. In this chapter, we summarize available methods and present a protocol for image-based measurement of NF-κB activation in macrophages activated with microbial stimuli. Using either a stably expressed GFP-tagged fusion of the RelA NF-κB protein, or direct detection of endogenous RelA by immunocytochemistry, we describe data collection and analysis to quantify NF-κB cytosol to nuclear translocation in single cells using fluorescence microscopy.
Collapse
Affiliation(s)
- Orna Ernst
- Signaling Systems Unit, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sharat J Vayttaden
- Signaling Systems Unit, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Iain D C Fraser
- Signaling Systems Unit, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
33
|
Kircher S, Schopfer P. The plant hormone auxin beats the time for oscillating, light-regulated lateral root induction. Development 2018; 145:dev.169839. [DOI: 10.1242/dev.169839] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/29/2018] [Indexed: 11/20/2022]
Abstract
The molecular mechanism underlying the periodic induction of lateral roots, a paradigmatic example of clock-driven organ formation in plant development, is presently a matter of ongoing, controversial debate. Here we provide experimental evidence that this clock is frequency-modulated by light and that auxin serves as a mediator for translating continuous light signals into discontinuous gene activation signals preceding the initiation of lateral roots in Arabidopsis seedlings. Based on this evidence, we propose a molecular model of an ultradian biological clock involving auxin-dependent degradation of an AUX/IAA-type transcription repressor as a flexible, frequency-controlling delay element. This model widens the bandwidth of biological clocks by adding a new type that allows the pace of organ formation to adapt to the changing environmental demands of the growing plant.
Collapse
Affiliation(s)
- Stefan Kircher
- Department of Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University, Schänzlestr. 1, D-79104-Freiburg, Germany
| | - Peter Schopfer
- Department of Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University, Schänzlestr. 1, D-79104-Freiburg, Germany
| |
Collapse
|
34
|
Tudelska K, Markiewicz J, Kochańczyk M, Czerkies M, Prus W, Korwek Z, Abdi A, Błoński S, Kaźmierczak B, Lipniacki T. Information processing in the NF-κB pathway. Sci Rep 2017; 7:15926. [PMID: 29162874 PMCID: PMC5698458 DOI: 10.1038/s41598-017-16166-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/08/2017] [Indexed: 02/07/2023] Open
Abstract
The NF-κB pathway is known to transmit merely 1 bit of information about stimulus level. We combined experimentation with mathematical modeling to elucidate how information about TNF concentration is turned into a binary decision. Using Kolmogorov-Smirnov distance, we quantified the cell’s ability to discern 8 TNF concentrations at each step of the NF-κB pathway, to find that input discernibility decreases as signal propagates along the pathway. Discernibility of low TNF concentrations is restricted by noise at the TNF receptor level, whereas discernibility of high TNF concentrations it is restricted by saturation/depletion of downstream signaling components. Consequently, signal discernibility is highest between 0.03 and 1 ng/ml TNF. Simultaneous exposure to TNF or LPS and a translation inhibitor, cycloheximide, leads to prolonged NF-κB activation and a marked increase of transcript levels of NF-κB inhibitors, IκBα and A20. The impact of cycloheximide becomes apparent after the first peak of nuclear NF-κB translocation, meaning that the NF-κB network not only relays 1 bit of information to coordinate the all-or-nothing expression of early genes, but also over a longer time course integrates information about other stimuli. The NF-κB system should be thus perceived as a feedback-controlled decision-making module rather than a simple information transmission channel.
Collapse
Affiliation(s)
- Karolina Tudelska
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Markiewicz
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Marek Kochańczyk
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Maciej Czerkies
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Wiktor Prus
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Zbigniew Korwek
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Ali Abdi
- Department of Biological Sciences and Department of Electrical and Computer Engineering, New Jersey Institute of Technology, New Jersey, United States of America
| | - Sławomir Błoński
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Bogdan Kaźmierczak
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Lipniacki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland.
| |
Collapse
|
35
|
Chae HS, You BH, Song J, Ko HW, Choi YH, Chin YW. Mangosteen Extract Prevents Dextran Sulfate Sodium-Induced Colitis in Mice by Suppressing NF-κB Activation and Inflammation. J Med Food 2017; 20:727-733. [DOI: 10.1089/jmf.2017.3944] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Hee-Sung Chae
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, South Korea
| | - Byoung Hoon You
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, South Korea
| | - Jieun Song
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, South Korea
| | - Hyuk Wan Ko
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, South Korea
| | - Young Hee Choi
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, South Korea
| | - Young-Won Chin
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, South Korea
| |
Collapse
|
36
|
Lane K, Van Valen D, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe'er D, Boutet SC, Covert MW. Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation. Cell Syst 2017; 4:458-469.e5. [PMID: 28396000 DOI: 10.1016/j.cels.2017.03.010] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/16/2016] [Accepted: 03/15/2017] [Indexed: 02/02/2023]
Abstract
Signaling proteins display remarkable cell-to-cell heterogeneity in their dynamic responses to stimuli, but the consequences of this heterogeneity remain largely unknown. For instance, the contribution of the dynamics of the innate immune transcription factor nuclear factor κB (NF-κB) to gene expression output is disputed. Here we explore these questions by integrating live-cell imaging approaches with single-cell sequencing technologies. We used this approach to measure both the dynamics of lipopolysaccharide-induced NF-κB activation and the global transcriptional response in the same individual cell. Our results identify multiple, distinct cytokine expression patterns that are correlated with NF-κB activation dynamics, establishing a functional role for NF-κB dynamics in determining cellular phenotypes. Applications of this approach to other model systems and single-cell sequencing technologies have significant potential for discovery, as it is now possible to trace cellular behavior from the initial stimulus, through the signaling pathways, down to genome-wide changes in gene expression, all inside of a single cell.
Collapse
Affiliation(s)
- Keara Lane
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - David Van Valen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Mialy M DeFelice
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Derek N Macklin
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Takamasa Kudo
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Ariel Jaimovich
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ambrose Carr
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Dana Pe'er
- Program in Computational and Systems Biology, Sloan Kettering Institute, New York, NY 10065, USA
| | - Stéphane C Boutet
- R&D Department, Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
37
|
NF-κB signalling and cell fate decisions in response to a short pulse of tumour necrosis factor. Sci Rep 2016; 6:39519. [PMID: 28004761 PMCID: PMC5177917 DOI: 10.1038/srep39519] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/24/2016] [Indexed: 12/22/2022] Open
Abstract
In tissues and tumours, cell behaviours are regulated by multiple time-varying signals. While in the laboratory cells are often exposed to a stimulus for the duration of the experiment, in vivo exposures may be much shorter. In this study, we monitored NF-κB and caspase signalling in human cancer cells treated with a short pulse of Tumour Necrosis Factor (TNF). TNF is an inflammatory cytokine that can induce both the pro-survival NF-κB-driven gene transcription pathway and the pro-apoptotic caspase pathway. We find that a few seconds of exposure to TNF is sufficient to activate the NF-κB pathway in HeLa cells and induce apoptotic cell death in both HeLa and Kym-1 cells. Strikingly, a 1-min pulse of TNF can be more effective at killing than a 1-hour pulse, indicating that in addition to TNF concentration, duration of exposure also coordinates cell fate decisions.
Collapse
|
38
|
Hell J, Rendall AD. Sustained oscillations in the MAP kinase cascade. Math Biosci 2016; 282:S0025-5564(16)30279-6. [PMID: 27984076 DOI: 10.1016/j.mbs.2016.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 09/23/2016] [Accepted: 10/28/2016] [Indexed: 01/07/2023]
Abstract
The MAP kinase cascade is a network of enzymatic reactions arranged in layers. In each layer occurs a multiple futile cycle of phosphorylations. The fully phosphorylated substrate then serves as an enzyme for the layer below. This paper focusses on the existence of parameters for which Hopf bifurcations occur and generate periodic orbits. Furthermore it is explained how geometric singular perturbation theory allows to generalize results from simple models to more complex ones.
Collapse
|
39
|
Ramos-Marquès E, Zambrano S, Tiérrez A, Bianchi ME, Agresti A, García-Del Portillo F. Single-cell analyses reveal an attenuated NF-κB response in the Salmonella-infected fibroblast. Virulence 2016; 8:719-740. [PMID: 27575017 DOI: 10.1080/21505594.2016.1229727] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The eukaryotic transcriptional regulator Nuclear Factor kappa B (NF-κB) plays a central role in the defense to pathogens. Despite this, few studies have analyzed NF-κB activity in single cells during infection. Here, we investigated at the single cell level how NF-κB nuclear localization - a proxy for NF-κB activity - oscillates in infected and uninfected fibroblasts co-existing in cultures exposed to Salmonella enterica serovar Typhimurium. Fibroblasts were used due to the capacity of S. Typhimurium to persist in this cell type. Real-time dynamics of NF-κB was examined in microfluidics, which prevents cytokine accumulation. In this condition, infected (ST+) cells translocate NF-κB to the nucleus at higher rate than the uninfected (ST-) cells. Surprisingly, in non-flow (static) culture conditions, ST- fibroblasts exhibited higher NF-κB nuclear translocation than the ST+ population, with these latter cells turning refractory to external stimuli such as TNF-α or a second infection. Sorting of ST+ and ST- cell populations confirmed enhanced expression of NF-κB target genes such as IL1B, NFKBIA, TNFAIP3, and TRAF1 in uninfected (ST-) fibroblasts. These observations proved that S. Typhimurium dampens the NF-κB response in the infected fibroblast. Higher expression of SOCS3, encoding a "suppressor of cytokine signaling," was also observed in the ST+ population. Intracellular S. Typhimurium subverts NF-κB activity using protein effectors translocated by the secretion systems encoded by pathogenicity islands 1 (T1) and 2 (T2). T1 is required for regulating expression of SOCS3 and all NF-κB target genes analyzed whereas T2 displayed no role in the control of SOCS3 and IL1B expression. Collectively, these data demonstrate that S. Typhimurium attenuates NF-κB signaling in fibroblasts, an effect only perceptible when ST+ and ST- populations are analyzed separately. This tune-down in a central host defense might be instrumental for S. Typhimurium to establish intracellular persistent infections.
Collapse
Affiliation(s)
- Estel Ramos-Marquès
- a Laboratory of Intracellular Bacterial Pathogens , Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC) , Madrid , Spain
| | | | - Alberto Tiérrez
- a Laboratory of Intracellular Bacterial Pathogens , Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC) , Madrid , Spain
| | - Marco E Bianchi
- c Genetics and Cell Biology Division , San Raffaele Scientific Institute , Milan , Italy
| | - Alessandra Agresti
- c Genetics and Cell Biology Division , San Raffaele Scientific Institute , Milan , Italy
| | - Francisco García-Del Portillo
- a Laboratory of Intracellular Bacterial Pathogens , Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC) , Madrid , Spain
| |
Collapse
|
40
|
Adamson A, Boddington C, Downton P, Rowe W, Bagnall J, Lam C, Maya-Mendoza A, Schmidt L, Harper CV, Spiller DG, Rand DA, Jackson DA, White MRH, Paszek P. Signal transduction controls heterogeneous NF-κB dynamics and target gene expression through cytokine-specific refractory states. Nat Commun 2016; 7:12057. [PMID: 27381163 PMCID: PMC4935804 DOI: 10.1038/ncomms12057] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 05/25/2016] [Indexed: 02/03/2023] Open
Abstract
Cells respond dynamically to pulsatile cytokine stimulation. Here we report that single, or well-spaced pulses of TNFα (>100 min apart) give a high probability of NF-κB activation. However, fewer cells respond to shorter pulse intervals (<100 min) suggesting a heterogeneous refractory state. This refractory state is established in the signal transduction network downstream of TNFR and upstream of IKK, and depends on the level of the NF-κB system negative feedback protein A20. If a second pulse within the refractory phase is IL-1β instead of TNFα, all of the cells respond. This suggests a mechanism by which two cytokines can synergistically activate an inflammatory response. Gene expression analyses show strong correlation between the cellular dynamic response and NF-κB-dependent target gene activation. These data suggest that refractory states in the NF-κB system constitute an inherent design motif of the inflammatory response and we suggest that this may avoid harmful homogenous cellular activation.
Collapse
Affiliation(s)
- Antony Adamson
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Christopher Boddington
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Polly Downton
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - William Rowe
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - James Bagnall
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Connie Lam
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Apolinar Maya-Mendoza
- The Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Lorraine Schmidt
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Claire V. Harper
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David G. Spiller
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David A. Rand
- Warwick Systems Biology and Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
| | - Dean A. Jackson
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Michael R. H. White
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Pawel Paszek
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| |
Collapse
|
41
|
Hayes JB, Sircy LM, Heusinkveld LE, Ding W, Leander RN, McClelland EE, Nelson DE. Modulation of Macrophage Inflammatory Nuclear Factor κB (NF-κB) Signaling by Intracellular Cryptococcus neoformans. J Biol Chem 2016; 291:15614-27. [PMID: 27231343 DOI: 10.1074/jbc.m116.738187] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Indexed: 01/29/2023] Open
Abstract
Cryptococcus neoformans (Cn) is a common facultative intracellular pathogen that can cause life-threatening fungal meningitis in immunocompromised individuals. Shortly after infection, Cn is detectable as both extra- and intracellular yeast particles, with Cn being capable of establishing long-lasting latent infections within host macrophages. Although recent studies have shown that shed capsular polysaccharides and intact extracellular Cn can compromise macrophage function through modulation of NF-κB signaling, it is currently unclear whether intracellular Cn also affects NF-κB signaling. Utilizing live cell imaging and computational modeling, we find that extra- and intracellular Cn support distinct modes of NF-κB signaling in cultured murine macrophages. Specifically, in RAW 264.7 murine macrophages treated with extracellular glucuronoxylomannan (GXM), the major Cn capsular polysaccharide, LPS-induced nuclear translocation of p65 is inhibited, whereas in cells with intracellular Cn, LPS-induced nuclear translocation of p65 is both amplified and sustained. Mathematical simulations and quantification of nascent protein expression indicate that this is a possible consequence of Cn-induced "translational interference," impeding IκBα resynthesis. We also show that long term Cn infection induces stable nuclear localization of p65 and IκBα proteins in the absence of additional pro-inflammatory stimuli. In this case, nuclear localization of p65 is not accompanied by TNFα or inducible NOS (iNOS) expression. These results demonstrate that capsular polysaccharides and intact intracellular yeast manipulate NF-κB via multiple distinct mechanisms and provide new insights into how Cn might modulate cellular signaling at different stages of an infection.
Collapse
Affiliation(s)
| | | | | | - Wandi Ding
- Mathematical Sciences, Middle Tennessee State University, Murfreesboro, Tennessee 37130
| | - Rachel N Leander
- Mathematical Sciences, Middle Tennessee State University, Murfreesboro, Tennessee 37130
| | | | | |
Collapse
|
42
|
Ankers JM, Awais R, Jones NA, Boyd J, Ryan S, Adamson AD, Harper CV, Bridge L, Spiller DG, Jackson DA, Paszek P, Sée V, White MR. Dynamic NF-κB and E2F interactions control the priority and timing of inflammatory signalling and cell proliferation. eLife 2016; 5. [PMID: 27185527 PMCID: PMC4869934 DOI: 10.7554/elife.10473] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 04/13/2016] [Indexed: 01/07/2023] Open
Abstract
Dynamic cellular systems reprogram gene expression to ensure appropriate cellular fate responses to specific extracellular cues. Here we demonstrate that the dynamics of Nuclear Factor kappa B (NF-κB) signalling and the cell cycle are prioritised differently depending on the timing of an inflammatory signal. Using iterative experimental and computational analyses, we show physical and functional interactions between NF-κB and the E2 Factor 1 (E2F-1) and E2 Factor 4 (E2F-4) cell cycle regulators. These interactions modulate the NF-κB response. In S-phase, the NF-κB response was delayed or repressed, while cell cycle progression was unimpeded. By contrast, activation of NF-κB at the G1/S boundary resulted in a longer cell cycle and more synchronous initial NF-κB responses between cells. These data identify new mechanisms by which the cellular response to stress is differentially controlled at different stages of the cell cycle. DOI:http://dx.doi.org/10.7554/eLife.10473.001 Investigating how cells adapt to the constantly changing environment inside the body is vitally important for understanding how the body responds to an injury or infection. One of the ways in which human cells adapt is by dividing to produce new cells. This takes place in a repeating pattern of events, known as the cell cycle, through which a cell copies its DNA (in a stage known as S-phase) and then divides to make two daughter cells. Each stage of the cell cycle is tightly controlled; for example, a family of proteins called E2 factors control the entry of the cell into S phase. “Inflammatory” signals produced by a wound or during an infection can activate a protein called Nuclear Factor-kappaB (NF-κB), which controls the activity of genes that allow cells to adapt to the situation. Research shows that the activity of NF-κB is also regulated by the cell cycle, but it has not been clear how this works. Here, Ankers et al. investigated whether the stage of the cell cycle might affect how NF-κB responds to inflammatory signals. The experiments show that the NF-κB response was stronger in cells that were just about to enter S-phase than in cells that were already copying their DNA. An E2 factor called E2F-1 –which accumulates in the run up to S-phase – interacts with NF-κB and can alter the activity of certain genes. However, during S-phase, another E2 factor family member called E2F-4 binds to NF-κB and represses its activation. Next, Ankers et al. used a mathematical model to understand how these protein interactions can affect the response of cells to inflammatory signals. These findings suggest that direct interactions between E2 factor proteins and NF-κB enable cells to decide whether to divide or react in different ways to inflammatory signals. The research tools developed in this study, combined with other new experimental techniques, will allow researchers to accurately predict how cells will respond to inflammatory signals at different points in the cell cycle. DOI:http://dx.doi.org/10.7554/eLife.10473.002
Collapse
Affiliation(s)
- John M Ankers
- Centre for Cell Imaging, Institute of Integrative Biology, Liverpool, United Kingdom
| | - Raheela Awais
- Centre for Cell Imaging, Institute of Integrative Biology, Liverpool, United Kingdom.,Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Nicholas A Jones
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - James Boyd
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Sheila Ryan
- Centre for Cell Imaging, Institute of Integrative Biology, Liverpool, United Kingdom.,Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Antony D Adamson
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Claire V Harper
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Lloyd Bridge
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom.,Department of Mathematics, University of Swansea, Swansea, United Kingdom
| | - David G Spiller
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Dean A Jackson
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Pawel Paszek
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Violaine Sée
- Centre for Cell Imaging, Institute of Integrative Biology, Liverpool, United Kingdom
| | - Michael Rh White
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| |
Collapse
|
43
|
Sero JE, Sailem HZ, Ardy RC, Almuttaqi H, Zhang T, Bakal C. Cell shape and the microenvironment regulate nuclear translocation of NF-κB in breast epithelial and tumor cells. Mol Syst Biol 2016; 11:790. [PMID: 26148352 PMCID: PMC4380925 DOI: 10.15252/msb.20145644] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Although a great deal is known about the signaling events that promote nuclear translocation of NF-κB, how cellular biophysics and the microenvironment might regulate the dynamics of this pathway is poorly understood. In this study, we used high-content image analysis and Bayesian network modeling to ask whether cell shape and context features influence NF-κB activation using the inherent variability present in unperturbed populations of breast tumor and non-tumor cell lines. Cell–cell contact, cell and nuclear area, and protrusiveness all contributed to variability in NF-κB localization in the absence and presence of TNFα. Higher levels of nuclear NF-κB were associated with mesenchymal-like versus epithelial-like morphologies, and RhoA-ROCK-myosin II signaling was critical for mediating shape-based differences in NF-κB localization and oscillations. Thus, mechanical factors such as cell shape and the microenvironment can influence NF-κB signaling and may in part explain how different phenotypic outcomes can arise from the same chemical cues.
Collapse
Affiliation(s)
- Julia E Sero
- Chester Beatty Laboratories, Division of Cancer Biology, Institute of Cancer ResearchLondon, UK
- * Corresponding author. Tel: +44 207 153 5170; E-mail:
| | - Heba Zuhair Sailem
- Chester Beatty Laboratories, Division of Cancer Biology, Institute of Cancer ResearchLondon, UK
| | - Rico Chandra Ardy
- Chester Beatty Laboratories, Division of Cancer Biology, Institute of Cancer ResearchLondon, UK
| | - Hannah Almuttaqi
- Chester Beatty Laboratories, Division of Cancer Biology, Institute of Cancer ResearchLondon, UK
| | - Tongli Zhang
- Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of OxfordOxford, UK
| | - Chris Bakal
- Chester Beatty Laboratories, Division of Cancer Biology, Institute of Cancer ResearchLondon, UK
- ** Corresponding author. Tel: +44 207 153 5080; E-mail:
| |
Collapse
|
44
|
Redefining Signaling Pathways with an Expanding Single-Cell Toolbox. Trends Biotechnol 2016; 34:458-469. [PMID: 26968612 DOI: 10.1016/j.tibtech.2016.02.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 02/12/2016] [Accepted: 02/16/2016] [Indexed: 01/12/2023]
Abstract
Genetically identical cells respond heterogeneously to uniform environmental stimuli. Consequently, investigating the signaling networks that control these cell responses using 'average' bulk cell measurements can obscure underlying mechanisms and misses information emerging from cell-to-cell variability. Here we review recent technological advances including live-cell fluorescence imaging-based approaches and microfluidic devices that enable measurements of signaling networks, dynamics, and responses in single cells. We discuss how these single-cell tools have uncovered novel mechanistic insights for canonical signaling pathways that control cell proliferation (ERK), DNA-damage responses (p53), and innate immune and stress responses (NF-κB). Future improvements in throughput and multiplexing, analytical pipelines, and in vivo applicability will all significantly expand the biological information gained from single-cell measurements of signaling pathways.
Collapse
|
45
|
Ichikawa K, Ohshima D, Sagara H. Regulation of signal transduction by spatial parameters: a case in NF-κB oscillation. IET Syst Biol 2016; 9:41-51. [PMID: 26672147 DOI: 10.1049/iet-syb.2013.0020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
NF-κB is a transcription factor regulating expression of more than 500 genes, and its dysfunction leads to the autoimmune and inflammatory diseases. In malignant cancer cells, NF-κB is constitutively activated. Thus the elucidation of mechanisms for NF-κB regulation is important for the establishment of therapeutic treatment caused by incorrect NF-κB responses. Cytoplasmic NF-κB translocates to the nucleus by the application of extracellular stimuli such as cytokines. Nuclear NF-κB is known to oscillate with the cycle of 1.5-4.5 h, and it is thought that the oscillation pattern regulates the expression profiles of genes. In this review, first we briefly describe regulation mechanisms of NF-κB. Next, published computational simulations on the oscillation of NF-κB are summarised. There are at least 60 reports on the computational simulation and analysis of NF-κB oscillation. Third, the importance of a 'space' for the regulation of oscillation pattern of NF-κB is discussed, showing altered oscillation pattern by the change in spatial parameters such as diffusion coefficient, nuclear to cytoplasmic volume ratio (N/C ratio), and transport through nuclear membrane. Finally, simulations in a true intracellular space (TiCS), which is an intracellular 3D space reconstructed in a computer with organelles such as nucleus and mitochondria are discussed.
Collapse
|
46
|
Zambrano S, De Toma I, Piffer A, Bianchi ME, Agresti A. NF-κB oscillations translate into functionally related patterns of gene expression. eLife 2016; 5:e09100. [PMID: 26765569 PMCID: PMC4798970 DOI: 10.7554/elife.09100] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 01/13/2016] [Indexed: 12/18/2022] Open
Abstract
Several transcription factors (TFs) oscillate, periodically relocating between the cytoplasm and the nucleus. NF-κB, which plays key roles in inflammation and cancer, displays oscillations whose biological advantage remains unclear. Recent work indicated that NF-κB displays sustained oscillations that can be entrained, that is, reach a persistent synchronized state through small periodic perturbations. We show here that for our GFP-p65 knock-in cells NF-κB behaves as a damped oscillator able to synchronize to a variety of periodic external perturbations with no memory. We imposed synchronous dynamics to prove that transcription of NF-κB-controlled genes also oscillates, but mature transcript levels follow three distinct patterns. Two sets of transcripts accumulate fast or slowly, respectively. Another set, comprising chemokine and chemokine receptor mRNAs, oscillates and resets at each new stimulus, with no memory of the past. We propose that TF oscillatory dynamics is a means of segmenting time to provide renewing opportunity windows for decision.
Collapse
Affiliation(s)
- Samuel Zambrano
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
- San Raffaele University, Milan, Italy
| | | | | | - Marco E Bianchi
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
- San Raffaele University, Milan, Italy
| | - Alessandra Agresti
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| |
Collapse
|
47
|
West S, Bridge LJ, White MRH, Paszek P, Biktashev VN. A method of ‘speed coefficients’ for biochemical model reduction applied to the NF-κB system. J Math Biol 2015; 70:591-620. [PMID: 24658784 PMCID: PMC4311267 DOI: 10.1007/s00285-014-0775-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 02/26/2014] [Indexed: 11/30/2022]
Abstract
The relationship between components of biochemical network and the resulting dynamics of the overall system is a key focus of computational biology. However, as these networks and resulting mathematical models are inherently complex and non-linear, the understanding of this relationship becomes challenging. Among many approaches, model reduction methods provide an avenue to extract components responsible for the key dynamical features of the system. Unfortunately, these approaches often require intuition to apply. In this manuscript we propose a practical algorithm for the reduction of biochemical reaction systems using fast-slow asymptotics. This method allows the ranking of system variables according to how quickly they approach their momentary steady state, thus selecting the fastest for a steady state approximation. We applied this method to derive models of the Nuclear Factor kappa B network, a key regulator of the immune response that exhibits oscillatory dynamics. Analyses with respect to two specific solutions, which corresponded to different experimental conditions identified different components of the system that were responsible for the respective dynamics. This is an important demonstration of how reduction methods that provide approximations around a specific steady state, could be utilised in order to gain a better understanding of network topology in a broader context.
Collapse
Affiliation(s)
- Simon West
- Institute of Integrative Biology, University of Liverpool, Crown Street, L69 7ZB Liverpool, UK
| | - Lloyd J. Bridge
- Department of Mathematics, Swansea University, Singleton Park, Swansea, SA2 8PP UK
| | - Michael R. H. White
- Faculty of Life Science, University of Manchester, Oxford Road, Manchester , M13 9PT UK
| | - Pawel Paszek
- Faculty of Life Science, University of Manchester, Oxford Road, Manchester , M13 9PT UK
| | - Vadim N. Biktashev
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, North Park Road, Exeter, EX4 4QF UK
| |
Collapse
|
48
|
Seki T, Yamamoto M, Taguchi Y, Miyauchi M, Akiyama N, Yamaguchi N, Gohda J, Akiyama T, Inoue JI. Visualization of RelB expression and activation at the single-cell level during dendritic cell maturation in Relb-Venus knock-in mice. J Biochem 2015; 158:485-95. [PMID: 26115685 DOI: 10.1093/jb/mvv064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 05/25/2015] [Indexed: 12/19/2022] Open
Abstract
RelB is activated by the non-canonical NF-κB pathway, which is crucial for immunity by establishing lymphoid organogenesis and B-cell and dendritic cell (DC) maturation. To elucidate the mechanism of the RelB-mediated immune cell maturation, a precise understanding of the relationship between cell maturation and RelB expression and activation at the single-cell level is required. Therefore, we generated knock-in mice expressing a fusion protein between RelB and fluorescent protein (RelB-Venus) from the Relb locus. The Relb(Venus/Venus) mice developed without any abnormalities observed in the Relb(-/-) mice, allowing us to monitor RelB-Venus expression and nuclear localization as RelB expression and activation. Relb(Venus/Venus) DC analyses revealed that DCs consist of RelB(-), RelB(low) and RelB(high) populations. The RelB(high) population, which included mature DCs with projections, displayed RelB nuclear localization, whereas RelB in the RelB(low) population was in the cytoplasm. Although both the RelB(low) and RelB(-) populations barely showed projections, MHC II and co-stimulatory molecule expression were higher in the RelB(low) than in the RelB(-) splenic conventional DCs. Taken together, our results identify the RelB(low) population as a possible novel intermediate maturation stage of cDCs and the Relb(Venus/Venus) mice as a useful tool to analyse the dynamic regulation of the non-canonical NF-κB pathway.
Collapse
Affiliation(s)
- Takao Seki
- Division of Cellular and Molecular Biology, Department of Cancer Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Mami Yamamoto
- Division of Cellular and Molecular Biology, Department of Cancer Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yuu Taguchi
- Division of Cellular and Molecular Biology, Department of Cancer Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Maki Miyauchi
- Division of Cellular and Molecular Biology, Department of Cancer Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Nobuko Akiyama
- Division of Cellular and Molecular Biology, Department of Cancer Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Noritaka Yamaguchi
- Department of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan; and
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Taishin Akiyama
- Division of Cellular and Molecular Biology, Department of Cancer Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Jun-ichiro Inoue
- Division of Cellular and Molecular Biology, Department of Cancer Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan;
| |
Collapse
|
49
|
Regulation of NF-κB Oscillation by Nuclear Transport: Mechanisms Determining the Persistency and Frequency of Oscillation. PLoS One 2015; 10:e0127633. [PMID: 26042739 PMCID: PMC4456371 DOI: 10.1371/journal.pone.0127633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/16/2015] [Indexed: 11/19/2022] Open
Abstract
The activated transcription factor NF-κB shuttles between the cytoplasm and the nucleus resulting in the oscillation of nuclear NF-κB (NF-κBn). The oscillation pattern of NF-κBn is implicated in the regulation of gene expression profiles. Using computational models, we previously reported that spatial parameters, such as the diffusion coefficient, nuclear to cytoplasmic volume ratio, transport through the nuclear envelope, and the loci of translation of IκB protein, modified the oscillation pattern of NF-κBn. In a subsequent report, we elucidated the importance of the “reset” of NF-κBn (returning of NF-κB to the original level) and of a “reservoir” of IκB in the cytoplasm. When the diffusion coefficient of IκB was large, IκB stored at a distant location from the nucleus diffused back to the nucleus and “reset” NF-κBn. Herein, we report mechanisms that regulate the persistency and frequency of NF-κBn oscillation by nuclear transport. Among the four parameters of nuclear transport tested in our spatio-temporal computational model, the export of IκB mRNA from the nucleus regulated the persistency of oscillation. The import of IκB to the nucleus regulated the frequency of oscillation. The remaining two parameters, import and export of NF-κB to and from the nucleus, had virtually no effect on the persistency or frequency. Our analyses revealed that lesser export of IκB mRNA allowed NF-κBn to transcript greater amounts of IκB mRNA, which was retained in the nucleus, and was subsequently exported to the cytoplasm, where large amounts of IκB were synthesized to “reset” NF-κBn and drove the persistent oscillation. On the other hand, import of greater amounts of IκB led to an increase in the influx and the efflux of NF-κB to and from the nucleus, resulting in an increase in the oscillation frequency. Our study revealed the importance of nuclear transport in regulating the oscillation pattern of NF-κBn.
Collapse
|
50
|
Webb JT, Behar M. Topology, dynamics, and heterogeneity in immune signaling. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:285-300. [DOI: 10.1002/wsbm.1306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/14/2015] [Accepted: 04/21/2015] [Indexed: 12/28/2022]
Affiliation(s)
- J. Taylor Webb
- Department of Biomedical Engineering; The University of Texas at Austin; Austin TX USA
| | - Marcelo Behar
- Department of Biomedical Engineering; The University of Texas at Austin; Austin TX USA
| |
Collapse
|