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Abstract
Effective regulation of immune-cell activation is critical for ensuring that the immune response, and inflammation generated for the purpose of pathogen elimination, are limited in space and time to minimize tissue damage. Autoimmune disease can occur when immunoreceptor signaling is dysregulated, leading to unrestrained inflammation and organ damage. Conversely, tumors can coopt the tissue healing and immunosuppressive functions of hematopoietic cells to promote metastasis and evade therapy. The Src-family kinase Lyn is an essential regulator of immunoreceptor signaling, initiating both proinflammatory and suppressive signaling pathways in myeloid immune cells (eg, neutrophils, dendritic cells, monocytes, macrophages) and in B lymphocytes. Defects in Lyn signaling are implicated in autoimmune disease, but mechanisms by which Lyn, expressed along with a battery of other Src-family kinases, may uniquely direct both positive and negative signaling remain incompletely defined. This review describes our current understanding of the activating and inhibitory contributions of Lyn to immunoreceptor signaling and how these processes contribute to myeloid and B-cell function. We also highlight recent work suggesting that the 2 proteins generated by alternative splicing of lyn, LynA and LynB, differentially regulate both immune and cancer-cell signaling. These principles may also extend to other Lyn-expressing cells, such as neuronal and endocrine cells. Unraveling the common and cell-specific aspects of Lyn function could lead to new approaches to therapeutically target dysregulated pathways in pathologies ranging from autoimmune and neurogenerative disease to cancer.
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Affiliation(s)
- Ben F Brian
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Current Affiliation: Current affiliation for B.F.B.: Division of Immunology & Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Tanya S Freedman
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Autoimmune Diseases Research, University of Minnesota, Minneapolis, MN, USA
- Correspondence: Tanya S. Freedman, PhD, University of Minnesota Twin Cities Campus: University of Minnesota, 6-120 Jackson Hall, 321 Church St. S.E., Minneapolis, MN 55455, USA. E-mail:
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2
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Wittmann J. Modeling Lymphocytes. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11608-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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3
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Bobrowski A, Rudnicki R. On convergence and asymptotic behaviour of semigroups of operators. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190613. [PMID: 33070749 PMCID: PMC7658744 DOI: 10.1098/rsta.2019.0613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/16/2020] [Indexed: 06/11/2023]
Abstract
The classical and modern theorems on convergence, approximation and asymptotic stability of semigroups of operators are presented, and their applications to recent biological models are discussed. This article is part of the theme issue 'Semigroup applications everywhere'.
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Affiliation(s)
- Adam Bobrowski
- Lublin University of Technology, Nadbystrzycka 38A, 20-618 Lublin, Poland
| | - Ryszard Rudnicki
- Institute of Mathematics, Polish Academy of Sciences, Bankowa 14, 40-007 Katowice, Poland
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4
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Ma J, Do M, Le Gros MA, Peskin CS, Larabell CA, Mori Y, Isaacson SA. Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus. PLoS Comput Biol 2020; 16:e1008356. [PMID: 33196636 PMCID: PMC7704053 DOI: 10.1371/journal.pcbi.1008356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 11/30/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
For a chemical signal to propagate across a cell, it must navigate a tortuous environment involving a variety of organelle barriers. In this work we study mathematical models for a basic chemical signal, the arrival times at the nuclear membrane of proteins that are activated at the cell membrane and diffuse throughout the cytosol. Organelle surfaces within human B cells are reconstructed from soft X-ray tomographic images, and modeled as reflecting barriers to the molecules’ diffusion. We show that signal inactivation sharpens signals, reducing variability in the arrival time at the nuclear membrane. Inactivation can also compensate for an observed slowdown in signal propagation induced by the presence of organelle barriers, leading to arrival times at the nuclear membrane that are comparable to models in which the cytosol is treated as an open, empty region. In the limit of strong signal inactivation this is achieved by filtering out molecules that traverse non-geodesic paths. The inside of cells is a complex spatial environment, filled with organelles, filaments and proteins. It is an open question how cell signaling pathways function robustly in the presence of such spatial heterogeneity. In this work we study how organelle barriers influence the most basic of chemical signals; the diffusive propagation of an activated protein from the cell membrane to nucleus. Three-dimensional B cell organelle and membrane geometries reconstructed from soft X-ray tomographic images are used in building mathematical models of the signal propagation process. Our models demonstrate that organelle barriers significantly increase the time required for a diffusing protein to traverse from the cell membrane to nucleus when compared to a cell with an empty cytosolic space. We also show that signal inactivation, a fundamental component of all signaling pathways, can provide robustness in the signal arrival time in two ways. Increasing rates of signal inactivation reduce variability in the arrival time, while also dramatically reducing the degree to which organelle barriers increase the arrival time (in comparison to a cell with an empty cytosol).
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Affiliation(s)
- Jingwei Ma
- Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, United States of America
| | - Myan Do
- Department of Cellular and Molecular Medicine, University of California, San Diego Medical School, San Diego, California, United States of America
| | - Mark A. Le Gros
- Department of Anatomy, University of California, San Francisco, San Francisco, California, United States of America
- National Center for X-ray Tomography, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Charles S. Peskin
- Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
| | - Carolyn A. Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, California, United States of America
- National Center for X-ray Tomography, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Yoichiro Mori
- Department of Mathematics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Samuel A. Isaacson
- Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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5
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Gonelli CA, Khoury G, Center RJ, Purcell DFJ. HIV-1-based Virus-like Particles that Morphologically Resemble Mature, Infectious HIV-1 Virions. Viruses 2019; 11:v11060507. [PMID: 31159488 PMCID: PMC6630479 DOI: 10.3390/v11060507] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 01/04/2023] Open
Abstract
A prophylactic vaccine eliciting both broad neutralizing antibodies (bNAbs) to the HIV-1 envelope glycoprotein (Env) and strong T cell responses would be optimal for preventing HIV-1 transmissions. Replication incompetent HIV-1 virus-like particles (VLPs) offer the opportunity to present authentic-structured, virion-associated Env to elicit bNAbs, and also stimulate T cell responses. Here, we optimize our DNA vaccine plasmids as VLP expression vectors for efficient Env incorporation and budding. The original vector that was used in human trials inefficiently produced VLPs, but maximized safety by inactivating RNA genome packaging, enzyme functions that are required for integration into the host genome, and deleting accessory proteins Vif, Vpr, and Nef. These original DNA vaccine vectors generated VLPs with incomplete protease-mediated cleavage of Gag and were irregularly sized. Mutations to restore function within the defective genes revealed that several of the reverse transcriptase (RT) deletions mediated this immature phenotype. Here, we made efficient budding, protease-processed, and mature-form VLPs that resembled infectious virions by introducing alternative mutations that completely removed the RT domain, but preserved most other safety mutations. These VLPs, either expressed from DNA vectors in vivo or purified after expression in vitro, are potentially useful immunogens that can be used to elicit antibody responses that target Env on fully infectious HIV-1 virions.
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Affiliation(s)
- Christopher A Gonelli
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
| | - Georges Khoury
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
| | - Rob J Center
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
- Viral Entry and Vaccines Laboratory, Disease Elimination, Burnet Institute, Melbourne, Victoria 3004, Australia.
| | - Damian F J Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
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6
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Bialecki S, Kazmierczak B, Lipniacki T. Polarization of concave domains by traveling wave pinning. PLoS One 2017; 12:e0190372. [PMID: 29284045 PMCID: PMC5746273 DOI: 10.1371/journal.pone.0190372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 12/13/2017] [Indexed: 01/28/2023] Open
Abstract
Pattern formation is one of the most fundamental yet puzzling phenomena in physics and biology. We propose that traveling front pinning into concave portions of the boundary of 3-dimensional domains can serve as a generic gradient-maintaining mechanism. Such a mechanism of domain polarization arises even for scalar bistable reaction-diffusion equations, and, depending on geometry, a number of stationary fronts may be formed leading to complex spatial patterns. The main advantage of the pinning mechanism, with respect to the Turing bifurcation, is that it allows for maintaining gradients in the specific regions of the domain. By linking the instant domain shape with the spatial pattern, the mechanism can be responsible for cellular polarization and differentiation.
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Affiliation(s)
- Slawomir Bialecki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Bogdan Kazmierczak
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Lipniacki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
- Department of Statistics, Rice University, Houston, Texas, United States of America
- * E-mail:
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7
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Relaxation oscillations and hierarchy of feedbacks in MAPK signaling. Sci Rep 2017; 7:38244. [PMID: 28045041 PMCID: PMC5206726 DOI: 10.1038/srep38244] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/07/2016] [Indexed: 12/21/2022] Open
Abstract
We formulated a computational model for a MAPK signaling cascade downstream of the EGF receptor to investigate how interlinked positive and negative feedback loops process EGF signals into ERK pulses of constant amplitude but dose-dependent duration and frequency. A positive feedback loop involving RAS and SOS, which leads to bistability and allows for switch-like responses to inputs, is nested within a negative feedback loop that encompasses RAS and RAF, MEK, and ERK that inhibits SOS via phosphorylation. This negative feedback, operating on a longer time scale, changes switch-like behavior into oscillations having a period of 1 hour or longer. Two auxiliary negative feedback loops, from ERK to MEK and RAF, placed downstream of the positive feedback, shape the temporal ERK activity profile but are dispensable for oscillations. Thus, the positive feedback introduces a hierarchy among negative feedback loops, such that the effect of a negative feedback depends on its position with respect to the positive feedback loop. Furthermore, a combination of the fast positive feedback involving slow-diffusing membrane components with slower negative feedbacks involving faster diffusing cytoplasmic components leads to local excitation/global inhibition dynamics, which allows the MAPK cascade to transmit paracrine EGF signals into spatially non-uniform ERK activity pulses.
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8
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Sharma R, Roberts E. Gradient sensing by a bistable regulatory motif enhances signal amplification but decreases accuracy in individual cells. Phys Biol 2016; 13:036003. [DOI: 10.1088/1478-3975/13/3/036003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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9
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Miller H, Castro-Gomes T, Corrotte M, Tam C, Maugel TK, Andrews NW, Song W. Lipid raft-dependent plasma membrane repair interferes with the activation of B lymphocytes. J Cell Biol 2016; 211:1193-205. [PMID: 26694840 PMCID: PMC4687878 DOI: 10.1083/jcb.201505030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Repair of plasma membrane wounds in B lymphocytes that lack caveolin requires lysosome exocytosis and lipid raft–mediated endocytosis and inhibits activation of the B cell receptor by sequestering lipid rafts. Cells rapidly repair plasma membrane (PM) damage by a process requiring Ca2+-dependent lysosome exocytosis. Acid sphingomyelinase (ASM) released from lysosomes induces endocytosis of injured membrane through caveolae, membrane invaginations from lipid rafts. How B lymphocytes, lacking any known form of caveolin, repair membrane injury is unknown. Here we show that B lymphocytes repair PM wounds in a Ca2+-dependent manner. Wounding induces lysosome exocytosis and endocytosis of dextran and the raft-binding cholera toxin subunit B (CTB). Resealing is reduced by ASM inhibitors and ASM deficiency and enhanced or restored by extracellular exposure to sphingomyelinase. B cell activation via B cell receptors (BCRs), a process requiring lipid rafts, interferes with PM repair. Conversely, wounding inhibits BCR signaling and internalization by disrupting BCR–lipid raft coclustering and by inducing the endocytosis of raft-bound CTB separately from BCR into tubular invaginations. Thus, PM repair and B cell activation interfere with one another because of competition for lipid rafts, revealing how frequent membrane injury and repair can impair B lymphocyte–mediated immune responses.
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Affiliation(s)
- Heather Miller
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Thiago Castro-Gomes
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Matthias Corrotte
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Christina Tam
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Timothy K Maugel
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Norma W Andrews
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Wenxia Song
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
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10
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Mlynarczyk PJ, Pullen RH, Abel SM. Confinement and diffusion modulate bistability and stochastic switching in a reaction network with positive feedback. J Chem Phys 2016; 144:015102. [DOI: 10.1063/1.4939219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Paul J. Mlynarczyk
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Robert H. Pullen
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Steven M. Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
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11
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Hartwell BL, Antunez L, Sullivan BP, Thati S, Sestak JO, Berkland C. Multivalent Nanomaterials: Learning from Vaccines and Progressing to Antigen-Specific Immunotherapies. J Pharm Sci 2015; 104:346-61. [DOI: 10.1002/jps.24273] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 10/26/2014] [Accepted: 10/28/2014] [Indexed: 12/28/2022]
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12
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Szymańska P, Kochańczyk M, Miękisz J, Lipniacki T. Effective reaction rates in diffusion-limited phosphorylation-dephosphorylation cycles. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:022702. [PMID: 25768526 DOI: 10.1103/physreve.91.022702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Indexed: 06/04/2023]
Abstract
We investigate the kinetics of the ubiquitous phosphorylation-dephosphorylation cycle on biological membranes by means of kinetic Monte Carlo simulations on the triangular lattice. We establish the dependence of effective macroscopic reaction rate coefficients as well as the steady-state phosphorylated substrate fraction on the diffusion coefficient and concentrations of opposing enzymes: kinases and phosphatases. In the limits of zero and infinite diffusion, the numerical results agree with analytical predictions; these two limits give the lower and the upper bound for the macroscopic rate coefficients, respectively. In the zero-diffusion limit, which is important in the analysis of dense systems, phosphorylation and dephosphorylation reactions can convert only these substrates which remain in contact with opposing enzymes. In the most studied regime of nonzero but small diffusion, a contribution linearly proportional to the diffusion coefficient appears in the reaction rate. In this regime, the presence of opposing enzymes creates inhomogeneities in the (de)phosphorylated substrate distributions: The spatial correlation function shows that enzymes are surrounded by clouds of converted substrates. This effect becomes important at low enzyme concentrations, substantially lowering effective reaction rates. Effective reaction rates decrease with decreasing diffusion and this dependence is more pronounced for the less-abundant enzyme. Consequently, the steady-state fraction of phosphorylated substrates can increase or decrease with diffusion, depending on relative concentrations of both enzymes. Additionally, steady states are controlled by molecular crowders which, mostly by lowering the effective diffusion of reactants, favor the more abundant enzyme.
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Affiliation(s)
- Paulina Szymańska
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland
| | - Marek Kochańczyk
- Institute of Fundamental Technological Research, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Jacek Miękisz
- Institute of Applied Mathematics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland
| | - Tomasz Lipniacki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, 02-106 Warsaw, Poland and Department of Statistics, Rice University, Houston, Texas 77005, USA
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13
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A review of quantitative modeling of B cell responses to antigenic challenge. J Pharmacokinet Pharmacodyn 2014; 41:445-59. [DOI: 10.1007/s10928-014-9388-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/17/2014] [Indexed: 01/15/2023]
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14
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Goodwin D, Simerska P, Chang CH, Mansfeld FM, Varamini P, D’Occhio MJ, Toth I. Active immunisation of mice with GnRH lipopeptide vaccine candidates: Importance of T helper or multi-dimer GnRH epitope. Bioorg Med Chem 2014; 22:4848-54. [DOI: 10.1016/j.bmc.2014.06.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/13/2014] [Accepted: 06/23/2014] [Indexed: 10/25/2022]
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15
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Yuseff MI, Pierobon P, Reversat A, Lennon-Duménil AM. How B cells capture, process and present antigens: a crucial role for cell polarity. Nat Rev Immunol 2013; 13:475-86. [PMID: 23797063 DOI: 10.1038/nri3469] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
B cells are key components of the adaptive immune response. Their differentiation into either specific memory B cells or antibody-secreting plasma cells is a consequence of activation steps that involve the processing and presentation of antigens. The engagement of B cell receptors by surface-tethered antigens leads to the formation of an immunological synapse that coordinates cell signalling events and that promotes antigen uptake for presentation on MHC class II molecules. In this Review, we discuss membrane trafficking and the associated molecular mechanisms that are involved in antigen extraction and processing at the B cell synapse, and we highlight how B cells use cell polarity to coordinate the complex events that ultimately lead to efficient humoral responses.
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Super-resolution microscopy of the immunological synapse. Curr Opin Immunol 2013; 25:307-12. [PMID: 23746999 DOI: 10.1016/j.coi.2013.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 04/12/2013] [Accepted: 04/15/2013] [Indexed: 12/18/2022]
Abstract
Deciphering the spatial organisation of signalling proteins is the key to understanding the mechanisms underlying immune cell activation. Every advance in imaging technology has led to major breakthroughs in unravelling how receptor and signalling proteins are distributed within the plasma membrane and how membrane signalling is integrated with endosomes and vesicular trafficking. Recently, super-resolution fluorescence microscopy has been applied to immunological synapses, gaining new insights into the nanoscale organisation of signalling processes. Here, we review the advantages and potential of super-resolution microscopy for elucidating the regulation of many aspects of immune signalling.
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Kochanczyk M, Jaruszewicz J, Lipniacki T. Stochastic transitions in a bistable reaction system on the membrane. J R Soc Interface 2013; 10:20130151. [PMID: 23635492 DOI: 10.1098/rsif.2013.0151] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Transitions between steady states of a multi-stable stochastic system in the perfectly mixed chemical reactor are possible only because of stochastic switching. In realistic cellular conditions, where diffusion is limited, transitions between steady states can also follow from the propagation of travelling waves. Here, we study the interplay between the two modes of transition for a prototype bistable system of kinase-phosphatase interactions on the plasma membrane. Within microscopic kinetic Monte Carlo simulations on the hexagonal lattice, we observed that for finite diffusion the behaviour of the spatially extended system differs qualitatively from the behaviour of the same system in the well-mixed regime. Even when a small isolated subcompartment remains mostly inactive, the chemical travelling wave may propagate, leading to the activation of a larger compartment. The activating wave can be induced after a small subdomain is activated as a result of a stochastic fluctuation. Such a spontaneous onset of activity is radically more probable in subdomains characterized by slower diffusion. Our results show that a local immobilization of substrates can lead to the global activation of membrane proteins by the mechanism that involves stochastic fluctuations followed by the propagation of a semi-deterministic travelling wave.
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Affiliation(s)
- Marek Kochanczyk
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
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18
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Ravichandran S, Rao KVS, Jain S. Bistability in a model of early B cell receptor activation and its role in tonic signaling and system tunability. MOLECULAR BIOSYSTEMS 2013; 9:2498-511. [DOI: 10.1039/c3mb70099b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Zuk PJ, Kochańczyk M, Jaruszewicz J, Bednorz W, Lipniacki T. Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth–death process. Phys Biol 2012; 9:055002. [DOI: 10.1088/1478-3975/9/5/055002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Barua D, Hlavacek WS, Lipniacki T. A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. THE JOURNAL OF IMMUNOLOGY 2012; 189:646-58. [PMID: 22711887 DOI: 10.4049/jimmunol.1102003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BCR signaling regulates the activities and fates of B cells. BCR signaling encompasses two feedback loops emanating from Lyn and Fyn, which are Src family protein tyrosine kinases (SFKs). Positive feedback arises from SFK-mediated trans phosphorylation of BCR and receptor-bound Lyn and Fyn, which increases the kinase activities of Lyn and Fyn. Negative feedback arises from SFK-mediated cis phosphorylation of the transmembrane adapter protein PAG1, which recruits the cytosolic protein tyrosine kinase Csk to the plasma membrane, where it acts to decrease the kinase activities of Lyn and Fyn. To study the effects of the positive and negative feedback loops on the dynamical stability of BCR signaling and the relative contributions of Lyn and Fyn to BCR signaling, we consider in this study a rule-based model for early events in BCR signaling that encompasses membrane-proximal interactions of six proteins, as follows: BCR, Lyn, Fyn, Csk, PAG1, and Syk, a cytosolic protein tyrosine kinase that is activated as a result of SFK-mediated phosphorylation of BCR. The model is consistent with known effects of Lyn and Fyn deletions. We find that BCR signaling can generate a single pulse or oscillations of Syk activation depending on the strength of Ag signal and the relative levels of Lyn and Fyn. We also show that bistability can arise in Lyn- or Csk-deficient cells.
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Affiliation(s)
- Dipak Barua
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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