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Asai H, Kato K, Miyasaka M, Hatsukawa K, Murakami N, Takeda N, Abe J, Aoyagi Y, Kohda Y, Gui MY, Jin YR, Li XW, Hitotsuyanagi Y, Takeya K, Andoh T, Kurosaki H, Fukuishi N. Kamebakaurin Suppresses Antigen-Induced Mast Cell Activation by Inhibition of FcεRI Signaling Pathway. Int Arch Allergy Immunol 2024:1-12. [PMID: 38797160 DOI: 10.1159/000536334] [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: 11/01/2023] [Accepted: 01/09/2024] [Indexed: 05/29/2024] Open
Abstract
INTRODUCTION Kamebakaurin is an active constituent of both Rabdosia japonica and Rabdosia excisa, which are utilized in Chinese traditional medicine for improving symptoms in patients with allergies. We investigated the molecular mechanisms of the anti-allergic effects of kamebakaurin using BMMCs. METHODS The degranulation ratio, histamine release, and the interleukin (IL)-4, leukotriene B4 (LTB4), and cysteinyl leukotriene productions on antigen-triggered BMMC were investigated. Additionally, the effects of kamebakaurin on signal transduction proteins were examined by Western blot and binding to the Syk and Lyn kinase domain was calculated. The effects of kamebakaurin on antigen-induced hyperpermeability were investigated using mouse model. RESULTS At 10 μm, kamebakaurin partially inhibited degranulation, histamine release, and IL-4 production. At 30 μm, kamebakaurin partially reduced LTB4 and cysteinyl leukotriene productions and suppressed degranulation, histamine release, and IL-4 production. Phosphorylation of both Syk Y519/520 and its downstream protein, Gab2, was reduced by kamebakaurin, and complete inhibition was observed with 30 μm kamebakaurin. In contrast, phosphorylation of Erk was only partially inhibited, even in the presence of 30 μm kamebakaurin. Syk Y519/520 is known to be auto-phosphorylated via intramolecular ATP present in its own ATP-binding site, and this auto-phosphorylation triggers degranulation, histamine release, and IL-4 production. Docking simulation study indicated kamebakaurin blocked ATP binding to the ATP-binding site in Syk. Therefore, inhibition of Syk auto-phosphorylation by kamebakaurin binding to the Syk ATP-binding site appeared to cause a reduction of histamine release and IL-4 production. Kamebakaurin inhibited antigen-induced vascular hyperpermeability in a dose-dependent fashion but did not reduce histamine-induced vascular hyperpermeability. CONCLUSION Kamebakaurin ameliorates allergic symptoms via inhibition of Syk phosphorylation; thus, kamebakaurin could be a lead compound for the new anti-allergic drug.
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Affiliation(s)
- Haruka Asai
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan,
| | - Koichi Kato
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Shonan University of Medical Sciences, Yokohama, Japan
| | - Mayu Miyasaka
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
| | - Kaho Hatsukawa
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
| | - Nanami Murakami
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
| | - Naoko Takeda
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
| | - Junna Abe
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
| | - Yutaka Aoyagi
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kinjo Gakuin University, Nagoya, Japan
| | - Yuka Kohda
- Department of Pharmacotherapeutics, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Ming-Yu Gui
- Department of Chemistry, Jilin University, Jilin, China
| | - Yong-Ri Jin
- Department of Chemistry, Jilin University, Jilin, China
| | - Xu-Wen Li
- Department of Chemistry, Jilin University, Jilin, China
| | - Yukio Hitotsuyanagi
- School of Pharmacy, Tokyo University of Pharmacy and Life Science, Tokyo, Japan
| | - Koichi Takeya
- School of Pharmacy, Tokyo University of Pharmacy and Life Science, Tokyo, Japan
| | - Tsugunobu Andoh
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
- Department of Pharmacology and Pathophysiology, Graduate School of Pharmaceutical Sciences, Kinjo Gakuin University, Nagoya, Japan
| | - Hiromasa Kurosaki
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
- Department of Analytical Chemistry, Graduate School of Pharmaceutical Sciences, Kinjo Gakuin University, Nagoya, Japan
| | - Nobuyuki Fukuishi
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Kinjo Gakuin University, Nagoya, Japan
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Jo S, Fischer BR, Cronin NM, Nurmalasari NPD, Loyd YM, Kerkvliet JG, Bailey EM, Anderson RB, Scott BL, Hoppe AD. Antibody surface mobility amplifies FcγR signaling via Arp2/3 during phagocytosis. Biophys J 2024:S0006-3495(24)00094-8. [PMID: 38321740 DOI: 10.1016/j.bpj.2024.01.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/07/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
We report herein that the anti-CD20 therapeutic antibody, rituximab, is rearranged into microclusters within the phagocytic synapse by macrophage Fcγ receptors (FcγR) during antibody-dependent cellular phagocytosis. These microclusters were observed to potently recruit Syk and to undergo rearrangements that were limited by the cytoskeleton of the target cell, with depolymerization of target-cell actin filaments leading to modest increases in phagocytic efficiency. Total internal reflection fluorescence analysis revealed that FcγR total phosphorylation, Syk phosphorylation, and Syk recruitment were enhanced when IgG-FcγR microclustering was enabled on fluid bilayers relative to immobile bilayers in a process that required Arp2/3. We conclude that on fluid surfaces, IgG-FcγR microclustering promotes signaling through Syk that is amplified by Arp2/3-driven actin rearrangements. Thus, the surface mobility of antigens bound by IgG shapes the signaling of FcγR with an unrecognized complexity beyond the zipper and trigger models of phagocytosis.
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Affiliation(s)
- Seongwan Jo
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota; BioSNTRii, South Dakota State University, Brookings, South Dakota
| | - Brady R Fischer
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota; BioSNTRii, South Dakota State University, Brookings, South Dakota
| | - Nicholas M Cronin
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota; BioSNTRii, South Dakota State University, Brookings, South Dakota
| | - Ni Putu Dewi Nurmalasari
- Department of Nanoscience & Biomedical Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota; BioSNTRii, South Dakota School of Mines and Technology, Rapid City, South Dakota
| | - Yoseph M Loyd
- Department of Nanoscience & Biomedical Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota; BioSNTRii, South Dakota School of Mines and Technology, Rapid City, South Dakota
| | - Jason G Kerkvliet
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota; BioSNTRii, South Dakota State University, Brookings, South Dakota
| | - Elizabeth M Bailey
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota; BioSNTRii, South Dakota State University, Brookings, South Dakota
| | - Robert B Anderson
- Department of Nanoscience & Biomedical Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota; BioSNTRii, South Dakota School of Mines and Technology, Rapid City, South Dakota
| | - Brandon L Scott
- Department of Nanoscience & Biomedical Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota; BioSNTRii, South Dakota School of Mines and Technology, Rapid City, South Dakota
| | - Adam D Hoppe
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota; BioSNTRii, South Dakota State University, Brookings, South Dakota.
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Lu W, Huang J, Flores J, Li P, Wang W, Liu S, Zhang JH, Tang J. GW0742 reduces mast cells degranulation and attenuates neurological impairments via PPAR β/δ/CD300a/SHP1 pathway after GMH in neonatal rats. Exp Neurol 2024; 372:114615. [PMID: 37995951 PMCID: PMC10842885 DOI: 10.1016/j.expneurol.2023.114615] [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: 08/01/2023] [Revised: 11/03/2023] [Accepted: 11/19/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Activation of mast cells plays an important role in brain inflammation. CD300a, an inhibitory receptor located on mast cell surfaces, has been reported to reduce the production of pro-inflammatory cytokines and exert protective effects in inflammation-related diseases. Peroxisome proliferator-activated receptor β/δ (PPARβ/δ), a ligand-activated nuclear receptor, activation upregulates the transcription of CD300a. In this study, we aim to investigate the role of PPARβ/δ in the attenuation of germinal matrix hemorrhage (GMH)-induced mast cell activation via CD300a/SHP1 pathway. METHODS GMH model was induced by intraparenchymal injection of bacterial collagenase into the right hemispheric ganglionic eminence in P7 Sprague Dawley rats. GW0742, a PPARβ/δ agonist, was administered intranasally at 1 h post-ictus. CD300a small interfering RNA (siRNA) and PPARβ/δ siRNA were injected intracerebroventricularly 5 days and 2 days before GMH induction. Behavioral tests, Western blot, immunofluorescence, Toluidine Blue staining, and Nissl staining were applied to assess post-GMH evaluation. RESULTS Results demonstrated that endogenous protein levels of PPARβ/δ and CD300a were decreased, whereas chymase, tryptase, IL-17A and transforming growth factor β1 (TGF-β1) were elevated after GMH. GMH induced significant short- and long-term neurobehavioral deficits in rat pups. GW0742 decreased mast cell degranulation, improved neurological outcomes, and attenuated ventriculomegaly after GMH. Additionally, GW0742 increased expression of PPARβ/δ, CD300a and phosphorylation of SHP1, decreased phosphorylation of Syk, chymase, tryptase, IL-17A and TGF-β1 levels. PPARβ/δ siRNA and CD300a siRNA abolished the beneficial effects of GW0742. CONCLUSIONS GW0742 inhibited mast cell-induced inflammation and improved neurobehavior after GMH, which is mediated by PPARβ/δ/CD300a/SHP1 pathway. GW0742 may serve as a potential treatment to reduce brain injury for GMH patients.
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Affiliation(s)
- Weitian Lu
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing 400016, China; Department of Physiology and Pharmacology, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Juan Huang
- Institute of Neuroscience, Basic Medical College, Chongqing Medical University, Chongqing 400016, China; Department of Physiology and Pharmacology, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Jerry Flores
- Department of Physiology and Pharmacology, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Peng Li
- Department of Physiology and Pharmacology, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Wenna Wang
- Department of Physiology and Pharmacology, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Shengpeng Liu
- Department of Physiology and Pharmacology, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - John H Zhang
- Department of Physiology and Pharmacology, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA; Department of Neurosurgery, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA; Department of Anesthesiology, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Jiping Tang
- Department of Physiology and Pharmacology, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA.
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Yang GS, Wagenknecht-Wiesner A, Yin B, Suresh P, London E, Baird BA, Bag N. Lipid-driven interleaflet coupling of plasma membrane order regulates FcεRI signaling in mast cells. Biophys J 2023:S0006-3495(23)00478-2. [PMID: 37533258 DOI: 10.1016/j.bpj.2023.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/04/2023] Open
Abstract
Interleaflet coupling-the influence of one leaflet on the properties of the opposing leaflet-is a fundamental plasma membrane organizational principle. This coupling is proposed to participate in maintaining steady-state biophysical properties of the plasma membrane, which in turn regulates some transmembrane signaling processes. A prominent example is antigen (Ag) stimulation of signaling by clustering transmembrane receptors for immunoglobulin E (IgE), FcεRI. This transmembrane signaling depends on the stabilization of ordered regions in the inner leaflet for sorting of intracellular signaling components. The resting inner leaflet has a lipid composition that is generally less ordered than the outer leaflet and that does not spontaneously phase separate in model membranes. We propose that interleaflet coupling can mediate ordering and disordering of the inner leaflet, which is poised in resting cells to reorganize upon stimulation. To test this in live cells, we first established a straightforward approach to evaluate induced changes in membrane order by measuring inner leaflet diffusion of lipid probes by imaging fluorescence correlation spectroscopy, by imaging fluorescence correlation spectroscopy (ImFCS), before and after methyl-α-cyclodexrin (mαCD)-catalyzed exchange of outer leaflet lipids (LEX) with exogenous order- or disorder-promoting phospholipids. We examined the functional impact of LEX by monitoring two Ag-stimulated responses: recruitment of cytoplasmic Syk kinase to the inner leaflet and exocytosis of secretory granules (degranulation). Based on the ImFCS data in resting cells, we observed global increase or decrease of inner leaflet order when outer leaflet is exchanged with order- or disorder-promoting lipids, respectively. We find that the degree of both stimulated Syk recruitment and degranulation correlates positively with LEX-mediated changes of inner leaflet order in resting cells. Overall, our results show that resting-state lipid ordering of the outer leaflet influences the ordering of the inner leaflet, likely via interleaflet coupling. This imposed lipid reorganization modulates transmembrane signaling stimulated by Ag clustering of IgE-FcεRI.
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Affiliation(s)
- Gil-Suk Yang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | | | - Boyu Yin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | - Pavana Suresh
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York
| | - Barbara A Baird
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York
| | - Nirmalya Bag
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York; Department of Chemistry, Indian Institute of Technology, Kharagpur, India.
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Xu W, Song X, Qu Q, Gong Z, Xiao W. Synergistic effects of L-theanine and epigallocatechin gallate in alleviating ovalbumin allergy by regulating intestinal immunity through inhibition of mast cell degranulation. Food Funct 2023; 14:2059-2073. [PMID: 36727615 DOI: 10.1039/d2fo03404b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Ovalbumin (OVA), a commonly consumed food protein, can cause severe allergies and intestinal immune disorders. L-Theanine (LTA) and epigallocatechin gallate (EGCG) regulate intestinal immunity. However, it is unclear whether an LTA and EGCG combined intervention can alleviate OVA allergy (OVA-A) by modulating intestinal-specific immunity, and it is unknown whether there is a synergistic effect between LTA and EGCG. Therefore, we treated BALB/c OVA-sensitized mice with LTA, EGCG, or a combination of both (LTA + EGCG) to investigate the effects of LTA and EGCG on intestinal-specific immunity regulation and underlying mechanisms. Female mice were intraperitoneally injected with OVA to establish OVA-sensitive mouse models. MLEO LTA + EGCG (20 mg kg-1 d-1 LTA + 80 mg kg-1 d-1 EGCG) and HLEO (30 mg kg-1 d-1 LTA + 120 mg kg-1 d-1 EGCG) exerted more beneficial effects on alleviating OVA-A (weight gain, allergy score, jejunum structure, mast cell [MC] degranulation, thymus and spleen indices) than LTA or EGCG alone (p < 0.01). Based on the alleviation of OVA-A by LTA + EGCG, we selected MLEO mice for 16S rDNA, flow cytometry, and western blot analyses. The 16S rDNA results showed that MLEO increased the abundance of Lactobacillaceae, Lachnospiraceae, and Ruminococcaceae, and decreased that of Helicobacteraceae (p < 0.01). The flow cytometry and western blotting results indicated that MLEO reduced the number of dendritic cells available to capture OVA, thereby lowering the Th2 immune response and decreasing the IL-4 and IL-13 levels. Meanwhile, the attenuation of the Th2 immune response inhibits the cross-linking of OVA and FcεRI, thus reducing MC degranulation and decreasing the serum HIS and mMCPT-1 levels through the FcεRI/Btk/PLCγ signaling pathway. LTA + EGCG also inhibits the Th2 immune response through the FcεRI/Lyn/Syk/PI3K/AKT signaling pathway and decreases the serum IL-4 and IL-13 levels. Notably, LTA + EGCG promotes the Treg and Th1 immune responses and inhibits the Th17 immune response, altering the levels of the corresponding cytokines. Therefore, LTA + EGCG can synergistically alleviate OVA-A by regulating intestinal immunity through MC degranulation inhibition.
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Affiliation(s)
- Wei Xu
- Key Lab of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China. .,National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan 410128, China.,Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, China.,Hunan Agricultural University, Hunan Collaborative Innovation Center for Utilization of Botanical Functional Ingredients, Changsha, Hunan 410128, China
| | - Xianying Song
- Key Lab of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China. .,National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan 410128, China.,Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, China.,Hunan Agricultural University, Hunan Collaborative Innovation Center for Utilization of Botanical Functional Ingredients, Changsha, Hunan 410128, China
| | - Qingyun Qu
- Key Lab of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China. .,National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan 410128, China.,Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, China.,Hunan Agricultural University, Hunan Collaborative Innovation Center for Utilization of Botanical Functional Ingredients, Changsha, Hunan 410128, China
| | - Zhihua Gong
- Key Lab of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China. .,National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan 410128, China.,Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, China.,Hunan Agricultural University, Hunan Collaborative Innovation Center for Utilization of Botanical Functional Ingredients, Changsha, Hunan 410128, China
| | - Wenjun Xiao
- Key Lab of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, China. .,National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan 410128, China.,Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, China.,Hunan Agricultural University, Hunan Collaborative Innovation Center for Utilization of Botanical Functional Ingredients, Changsha, Hunan 410128, China
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Sarkar S, Goswami D. Lifetime of actin-dependent protein nanoclusters. Biophys J 2023; 122:290-300. [PMID: 36518075 PMCID: PMC9892618 DOI: 10.1016/j.bpj.2022.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/23/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Protein nanoclusters (PNCs) are dynamic collections of a few proteins that spatially organize in nanometer-length clusters. PNCs are one of the principal forms of spatial organization of membrane proteins, and they have been shown or hypothesized to be important in various cellular processes, including cell signaling. PNCs show remarkable diversity in size, shape, and lifetime. In particular, the lifetime of PNCs can vary over a wide range of timescales. The diversity in size and shape can be explained by the interaction of the clustering proteins with the actin cytoskeleton or the lipid membrane, but very little is known about the processes that determine the lifetime of the nanoclusters. In this paper, using mathematical modeling of the cluster dynamics, we model the biophysical processes that determine the lifetime of actin-dependent PNCs. In particular, we investigated the role of actin aster fragmentation, which had been suggested to be a key determinant of the PNC lifetime, and we found that it is important only for a small class of PNCs. A simple extension of our model allowed us to investigate the kinetics of protein-ligand interaction near PNCs. We found an anomalous increase in the lifetime of ligands near PNCs, which agrees remarkably well with experimental data on RAS-RAF kinetics. In particular, analysis of the RAS-RAF data through our model provides falsifiable predictions and novel hypotheses that will not only shed light on the role of RAS-RAF kinetics in various cancers, but also will be useful in studying membrane protein clustering in general.
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Affiliation(s)
- Sumantra Sarkar
- The Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico; Theoretical Biophysics (T-6) Group, Los Alamos National Laboratory, Los Alamos, New Mexico; Department of Physics, Indian Institute of Science, Bengaluru, Karnataka 560012, India.
| | - Debanjan Goswami
- NCI RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, Maryland.
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Kerketta R, Erasmus MF, Wilson BS, Halasz AM, Edwards JS. Spatial Stochastic Model of the Pre-B Cell Receptor. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:683-693. [PMID: 35482702 PMCID: PMC10123485 DOI: 10.1109/tcbb.2022.3166149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Survival and proliferation of immature B lymphocytes requires expression and tonic signaling of the pre-B cell receptor (pre-BCR). This low level, ligand-independent signaling is likely achieved through frequent, but short-lived, homo interactions. Tonic signaling is also central in the pathology of precursor B acute lymphoblastic leukemia (B-ALL). In order to understand how repeated, transient events can lead to sustained signaling and to assess the impact of receptor accumulation induced by the membrane landscape, we developed a spatial stochastic model of receptor aggregation and downstream signaling events. Our rule- and agent-based model builds on previous mature BCR signaling models and incorporates novel parameters derived from single particle tracking of pre-BCR on surfaces of two different B-ALL cell lines, 697 and Nalm6. Live cell tracking of receptors on the two cell lines revealed characteristic differences in their dimer dissociation rates and diffusion coefficients. We report here that these differences affect pre-BCR aggregation and consequent signal initiation events. Receptors on Nalm6 cells, which have a lower off-rate and lower diffusion coefficient, more frequently form higher order oligomers than pre-BCR on 697 cells, resulting in higher levels of downstream phosphorylation in the Nalm6 cell line.
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Shelby SA, Shaw TR, Veatch SL. Measuring the Co-Localization and Dynamics of Mobile Proteins in Live Cells Undergoing Signaling Responses. Methods Mol Biol 2023; 2654:1-23. [PMID: 37106172 PMCID: PMC10758997 DOI: 10.1007/978-1-0716-3135-5_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] [Indexed: 04/29/2023]
Abstract
Single molecule imaging in live cells enables the study of protein interactions and dynamics as they participate in signaling processes. When combined with fluorophores that stochastically transition between fluorescent and reversible dark states, as in super-resolution localization imaging, labeled molecules can be visualized in single cells over time. This improvement in sampling enables the study of extended cellular responses at the resolution of single molecule localization. This chapter provides optimized experimental and analytical methods used to quantify protein interactions and dynamics within the membranes of adhered live cells. Importantly, the use of pair-correlation functions resolved in both space and time allows researchers to probe interactions between proteins on biologically relevant distance and timescales, even though fluorescence localization methods typically require long times to assemble well-sampled reconstructed images. We describe an application of this approach to measure protein interactions in B cell receptor signaling and include sample analysis code for post-processing of imaging data. These methods are quantitative, sensitive, and broadly applicable to a range of signaling systems.
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Affiliation(s)
- Sarah A Shelby
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Thomas R Shaw
- Program in Applied Physics, University of Michigan, Ann Arbor, MI, USA
| | - Sarah L Veatch
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA.
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Abstract
Mast cells originate from the CD34+/CD117+ hematopoietic progenitors in the bone marrow, migrate into circulation, and ultimately mature and reside in peripheral tissues. Microbiota/metabolites and certain immune cells (e.g., Treg cells) play a key role in maintaining immune tolerance. Cross-linking of allergen-specific IgE on mast cells activates the high-affinity membrane-bound receptor FcεRI, thereby initiating an intracellular signal cascade, leading to degranulation and release of pro-inflammatory mediators. The intracellular signal transduction is intricately regulated by various kinases, transcription factors, and cytokines. Importantly, multiple signal components in the FcεRI-mast cell–mediated allergic cascade can be targeted for therapeutic purposes. Pharmacological interventions that include therapeutic antibodies against IgE, FcεRI, and cytokines as well as inhibitors/activators of several key intracellular signaling molecues have been used to inhibit allergic reactions. Other factors that are not part of the signal pathway but can enhance an individual’s susceptibility to allergen stimulation are referred to as cofactors. Herein, we provide a mechanistic overview of the FcεRI-mast cell–mediated allergic signaling. This will broaden our scope and visions on specific preventive and therapeutic strategies for the clinical management of mast cell–associated hypersensitivity reactions.
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Chen X, Crosby KC, Feng A, Purkey AM, Aronova MA, Winters CA, Crocker VT, Leapman RD, Reese TS, Dell’Acqua ML. Palmitoylation of A-kinase anchoring protein 79/150 modulates its nanoscale organization, trafficking, and mobility in postsynaptic spines. Front Synaptic Neurosci 2022; 14:1004154. [PMID: 36186623 PMCID: PMC9521714 DOI: 10.3389/fnsyn.2022.1004154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
A-kinase anchoring protein 79-human/150-rodent (AKAP79/150) organizes signaling proteins to control synaptic plasticity. AKAP79/150 associates with the plasma membrane and endosomes through its N-terminal domain that contains three polybasic regions and two Cys residues that are reversibly palmitoylated. Mutations abolishing palmitoylation (AKAP79/150 CS) reduce its endosomal localization and association with the postsynaptic density (PSD). Here we combined advanced light and electron microscopy (EM) to characterize the effects of AKAP79/150 palmitoylation on its postsynaptic nanoscale organization, trafficking, and mobility in hippocampal neurons. Immunogold EM revealed prominent extrasynaptic membrane AKAP150 labeling with less labeling at the PSD. The label was at greater distances from the spine membrane for AKAP150 CS than WT in the PSD but not in extra-synaptic locations. Immunogold EM of GFP-tagged AKAP79 WT showed that AKAP79 adopts a vertical, extended conformation at the PSD with its N-terminus at the membrane, in contrast to extrasynaptic locations where it adopts a compact or open configurations of its N- and C-termini with parallel orientation to the membrane. In contrast, GFP-tagged AKAP79 CS was displaced from the PSD coincident with disruption of its vertical orientation, while proximity and orientation with respect to the extra-synaptic membrane was less impacted. Single-molecule localization microscopy (SMLM) revealed a heterogeneous distribution of AKAP150 with distinct high-density, nano-scale regions (HDRs) overlapping the PSD but more prominently located in the extrasynaptic membrane for WT and the CS mutant. Thick section scanning transmission electron microscopy (STEM) tomography revealed AKAP150 immunogold clusters similar in size to HDRs seen by SMLM and more AKAP150 labeled endosomes in spines for WT than for CS, consistent with the requirement for AKAP palmitoylation in endosomal trafficking. Hidden Markov modeling of single molecule tracking data revealed a bound/immobile fraction and two mobile fractions for AKAP79 in spines, with the CS mutant having shorter dwell times and faster transition rates between states than WT, suggesting that palmitoylation stabilizes individual AKAP molecules in various spine subpopulations. These data demonstrate that palmitoylation fine tunes the nanoscale localization, mobility, and trafficking of AKAP79/150 in dendritic spines, which might have profound effects on its regulation of synaptic plasticity.
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Affiliation(s)
- Xiaobing Chen
- Laboratory of Neurobiology, National Institute of Neurological Diseases and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, United States
- *Correspondence: Xiaobing Chen,
| | - Kevin C. Crosby
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, United States
| | - Austin Feng
- Laboratory of Neurobiology, National Institute of Neurological Diseases and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Alicia M. Purkey
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, United States
| | - Maria A. Aronova
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Christine A. Winters
- Laboratory of Neurobiology, National Institute of Neurological Diseases and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Virginia T. Crocker
- Laboratory of Neurobiology, National Institute of Neurological Diseases and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Richard D. Leapman
- Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Thomas S. Reese
- Laboratory of Neurobiology, National Institute of Neurological Diseases and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Mark L. Dell’Acqua
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, United States
- Mark L. Dell’Acqua,
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11
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Kanagy WK, Cleyrat C, Fazel M, Lucero SR, Bruchez MP, Lidke KA, Wilson BS, Lidke DS. Docking of Syk to FcεRI is enhanced by Lyn but limited in duration by SHIP1. Mol Biol Cell 2022; 33:ar89. [PMID: 35793126 PMCID: PMC9582627 DOI: 10.1091/mbc.e21-12-0603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The high-affinity immunoglobulin E (IgE) receptor, FcεRI, is the primary immune receptor found on mast cells and basophils. Signal initiation is classically attributed to phosphorylation of FcεRI β− and γ-subunits by the Src family kinase (SFK) Lyn, followed by the recruitment and activation of the tyrosine kinase Syk. FcεRI signaling is tuned by the balance between Syk-driven positive signaling and the engagement of inhibitory molecules, including SHIP1. Here, we investigate the mechanistic contributions of Lyn, Syk, and SHIP1 to the formation of the FcεRI signalosome. Using Lyn-deficient RBL-2H3 mast cells, we found that another SFK can weakly monophosphorylate the γ-subunit, yet Syk still binds the incompletely phosphorylated immunoreceptor tyrosine-based activation motifs (ITAMs). Once recruited, Syk further enhances γ-phosphorylation to propagate signaling. In contrast, the loss of SHIP1 recruitment indicates that Lyn is required for phosphorylation of the β-subunit. We demonstrate two noncanonical Syk binding modes, trans γ-bridging and direct β-binding, that can support signaling when SHIP1 is absent. Using single particle tracking, we reveal a novel role of SHIP1 in regulating Syk activity, where the presence of SHIP1 in the signaling complex acts to increase the Syk:receptor off-rate. These data suggest that the composition and dynamics of the signalosome modulate immunoreceptor signaling activities.
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Affiliation(s)
- William K Kanagy
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - Cédric Cleyrat
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131.,Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Mohamadreza Fazel
- Department of Physics, University of New Mexico, Albuquerque, NM 87131
| | - Shayna R Lucero
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - Marcel P Bruchez
- Department of Biological Sciences and Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Keith A Lidke
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131.,Department of Physics, University of New Mexico, Albuquerque, NM 87131
| | - Bridget S Wilson
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131.,Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Diane S Lidke
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131.,Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
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12
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Dok-1 regulates mast cell degranulation negatively through inhibiting calcium-dependent F-actin disassembly. Clin Immunol 2022; 238:109008. [PMID: 35421591 DOI: 10.1016/j.clim.2022.109008] [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: 11/26/2021] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/24/2022]
Abstract
In food allergies, antigen-induced aggregation of FcεRI on mast cells initiates highly ordered and sequential signaling events. Dok-1(downstream of tyrosine kinase 1), undergoes intense tyrosine phosphorylation upon FcεRI stimulation, which negatively regulates Ras/Erk signaling and the subsequent cytokine release, but it remains unclear whether Dok-1 regulates Fc-mediated degranulation. In this study, we investigated the role of Dok-1 in FcεRI-mediated degranulation. Dok-1 overexpressing RBL-2H3 cells were established. Degranulation, immunoprecipitation, co-immunoprecipitation, immunoblotting and flow cytometry assay were performed to explore the effects of Dok-1 and its underlying mechanisms. We found that, following FcεRI activation, Dok-1 was recruited to the plasma membrane, leading to tyrosine phosphorylation. Phosphorylated Dok-1 inhibits FcεRI-operated calcium influx, and negatively regulated degranulation by inhibiting calcium-dependent disassembly of actin filaments. Our data revealed that Dok-1 is a negative regulator of FcεRI-mediated mast cell degranulation. These findings contribute to the identification of therapeutic targets for food allergies.
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13
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Dephosphorylation accelerates the dissociation of ZAP70 from the T cell receptor. Proc Natl Acad Sci U S A 2022; 119:2116815119. [PMID: 35197288 PMCID: PMC8892339 DOI: 10.1073/pnas.2116815119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2021] [Indexed: 11/20/2022] Open
Abstract
Src homology 2 (SH2) domains are phosphotyrosine binding motifs that play key roles in cellular signaling. There are 110 proteins in the human genome containing SH2 binding domains, of which 10 contain tandem SH2 domains. Tandem domains have been shown to improve avidity and specificity and contribute to allostery. Here, we show that tandem SH2 domains can also exhibit binding lifetimes that are accelerated by the activity of phosphatases. This accelerated unbinding requires tandem SH2 domains to engage their substrates in dynamic binding modes that cycle between single SH2-bound states. We experimentally confirm that this is the case for the well-studied kinase ZAP70 binding the T cell receptor. We suggest that accelerated unbinding is a general feature of signaling networks. Protein–protein binding domains are critical in signaling networks. Src homology 2 (SH2) domains are binding domains that interact with sequences containing phosphorylated tyrosines. A subset of SH2 domain–containing proteins has tandem domains, which are thought to enhance binding affinity and specificity. However, a trade-off exists between long-lived binding and the ability to rapidly reverse signaling, which is a critical requirement of noise-filtering mechanisms such as kinetic proofreading. Here, we use modeling to show that the unbinding rate of tandem, but not single, SH2 domains can be accelerated by phosphatases. Using surface plasmon resonance, we show that the phosphatase CD45 can accelerate the unbinding rate of zeta chain–associated protein kinase 70 (ZAP70), a tandem SH2 domain–containing kinase, from biphosphorylated peptides from the T cell receptor (TCR). An important functional prediction of accelerated unbinding is that the intracellular ZAP70–TCR half-life in T cells will not be fixed but rather, dependent on the extracellular TCR–antigen half-life, and we show that this is the case in both cell lines and primary T cells. The work highlights that tandem SH2 domains can break the trade-off between signal fidelity (requiring long half-life) and signal reversibility (requiring short half-life), which is a key requirement for T cell antigen discrimination mediated by kinetic proofreading.
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14
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Arthur GK, Cruse G. Regulation of Trafficking and Signaling of the High Affinity IgE Receptor by FcεRIβ and the Potential Impact of FcεRIβ Splicing in Allergic Inflammation. Int J Mol Sci 2022; 23:ijms23020788. [PMID: 35054974 PMCID: PMC8776166 DOI: 10.3390/ijms23020788] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 12/23/2022] Open
Abstract
Mast cells are tissue-resident immune cells that function in both innate and adaptive immunity through the release of both preformed granule-stored mediators, and newly generated proinflammatory mediators that contribute to the generation of both the early and late phases of the allergic inflammatory response. Although mast cells can be activated by a vast array of mediators to contribute to homeostasis and pathophysiology in diverse settings and contexts, in this review, we will focus on the canonical setting of IgE-mediated activation and allergic inflammation. IgE-dependent activation of mast cells occurs through the high affinity IgE receptor, FcεRI, which is a multimeric receptor complex that, once crosslinked by antigen, triggers a cascade of signaling to generate a robust response in mast cells. Here, we discuss FcεRI structure and function, and describe established and emerging roles of the β subunit of FcεRI (FcεRIβ) in regulating mast cell function and FcεRI trafficking and signaling. We discuss current approaches to target IgE and FcεRI signaling and emerging approaches that could target FcεRIβ specifically. We examine how alternative splicing of FcεRIβ alters protein function and how manipulation of splicing could be employed as a therapeutic approach. Targeting FcεRI directly and/or IgE binding to FcεRI are promising approaches to therapeutics for allergic inflammation. The characteristic role of FcεRIβ in both trafficking and signaling of the FcεRI receptor complex, the specificity to IgE-mediated activation pathways, and the preferential expression in mast cells and basophils, makes FcεRIβ an excellent, but challenging, candidate for therapeutic strategies in allergy and asthma, if targeting can be realized.
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Affiliation(s)
- Greer K. Arthur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, NC State University, Raleigh, NC 27607, USA;
| | - Glenn Cruse
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC 27607, USA
- Correspondence: ; Tel.: +1-919-515-8865
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15
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Masucci EM, Relich PK, Lakadamyali M, Ostap EM, Holzbaur ELF. Microtubule dynamics influence the retrograde biased motility of kinesin-4 motor teams in neuronal dendrites. Mol Biol Cell 2021; 33:ar52. [PMID: 34705476 PMCID: PMC9265162 DOI: 10.1091/mbc.e21-10-0480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Microtubules establish the directionality of intracellular transport by kinesins and dynein through polarized assembly, but it remains unclear how directed transport occurs along microtubules organized with mixed polarity. We investigated the ability of the plus end–directed kinesin-4 motor KIF21B to navigate mixed polarity microtubules in mammalian dendrites. Reconstitution assays with recombinant KIF21B and engineered microtubule bundles or extracted neuronal cytoskeletons indicate that nucleotide-independent microtubule-binding regions of KIF21B modulate microtubule dynamics and promote directional switching on antiparallel microtubules. Optogenetic recruitment of KIF21B to organelles in live neurons induces unidirectional transport in axons but bidirectional transport with a net retrograde bias in dendrites. Removal of the secondary microtubule-binding regions of KIF21B or dampening of microtubule dynamics with low concentrations of nocodazole eliminates retrograde bias in live dendrites. Further exploration of the contribution of microtubule dynamics in dendrites to directionality revealed plus end–out microtubules to be more dynamic than plus end–in microtubules, with nocodazole preferentially stabilizing the plus end–out population. We propose a model in which both nucleotide-sensitive and -insensitive microtubule-binding sites of KIF21B motors contribute to the search and selection of stable plus end–in microtubules within the mixed polarity microtubule arrays characteristic of mammalian dendrites to achieve net retrograde movement of KIF21B-bound cargoes.
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Affiliation(s)
- Erin M Masucci
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Peter K Relich
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Melike Lakadamyali
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - E Michael Ostap
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Erika L F Holzbaur
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
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16
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Masucci EM, Relich PK, Ostap EM, Holzbaur ELF, Lakadamyali M. Cega: a single particle segmentation algorithm to identify moving particles in a noisy system. Mol Biol Cell 2021; 32:931-941. [PMID: 33788586 PMCID: PMC8108521 DOI: 10.1091/mbc.e20-11-0744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Improvements to particle tracking algorithms are required to effectively analyze the motility of biological molecules in complex or noisy systems. A typical single particle tracking (SPT) algorithm detects particle coordinates for trajectory assembly. However, particle detection filters fail for data sets with low signal-to-noise levels. When tracking molecular motors in complex systems, standard techniques often fail to separate the fluorescent signatures of moving particles from background signal. We developed an approach to analyze the motility of kinesin motor proteins moving along the microtubule cytoskeleton of extracted neurons using the Kullback-Leibler divergence to identify regions where there are significant differences between models of moving particles and background signal. We tested our software on both simulated and experimental data and found a noticeable improvement in SPT capability and a higher identification rate of motors as compared with current methods. This algorithm, called Cega, for “find the object,” produces data amenable to conventional blob detection techniques that can then be used to obtain coordinates for downstream SPT processing. We anticipate that this algorithm will be useful for those interested in tracking moving particles in complex in vitro or in vivo environments.
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Affiliation(s)
- Erin M Masucci
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104.,Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104.,The Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Peter K Relich
- Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104.,The Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - E Michael Ostap
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104.,Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104.,The Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Erika L F Holzbaur
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104.,Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104.,The Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Melike Lakadamyali
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104.,Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104.,The Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
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17
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Han L, Wei XX, Zheng YJ, Zhang LL, Wang XM, Yang HY, Ma X, Zhao LH, Tong XL. Potential mechanism prediction of Cold-Damp Plague Formula against COVID-19 via network pharmacology analysis and molecular docking. Chin Med 2020; 15:78. [PMID: 32754224 PMCID: PMC7391051 DOI: 10.1186/s13020-020-00360-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/24/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is a new global public health emergency. The therapeutic benefits of Cold‒Damp Plague Formula (CDPF) against COVID-19, which was used to treat "cold‒dampness stagnation in the lung" in Trial Versions 6 and 7 of the "Diagnosis and Treatment Protocol for COVID-19", have been demonstrated, but the effective components and their mechanism of action remain unclear. METHODS In this study, a network pharmacology approach was employed, including drug-likeness evaluation, oral bioavailability prediction, protein‒protein interaction (PPI) network construction and analysis, Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, and virtual docking, to predict the bioactive components, potential targets, and molecular mechanism of CDPF for COVID-19 treatment. RESULTS The active compound of herbs in CDPF and their candidate targets were obtained through database mining, and an herbs-ingredients-targets network was constructed. Subsequently, the candidate targets of the active compounds were compared to those relevant to COVID-19, to identify the potential targets of CDPF for COVID-19 treatment. Subsequently, the PPI network was constructed, which provided a basis for cluster analysis and hub gene screening. The seed targets in the most significant module were selected for further functional annotation. GO enrichment analysis identified four main areas: (1) cellular responses to external stimuli, (2) regulation of blood production and circulation, (3) free radical regulation, (4) immune regulation and anti-inflammatory effects. KEGG pathway analysis also revealed that CDPF could play pharmacological roles against COVID-19 through "multi components‒multi targets‒multi pathways" at the molecular level, mainly involving anti-viral, immune-regulatory, and anti-inflammatory pathways; consequently, a "CDPF-herbs-ingredients-targets-pathways-COVID-19" network was constructed. In hub target analysis, the top hub target IL6, and ACE2, the receptor via which SARS-CoV-2 typically enters host cells, were selected for molecular docking analyses, and revealed good binding activities. CONCLUSIONS This study revealed the active ingredients and potential molecular mechanism by which CDPF treatment is effective against COVID-19, and provides a reference basis for the wider application and further mechanistic investigations of CDPF in the fight against COVID-19.
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Affiliation(s)
- Lin Han
- Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053 China
| | - Xiu-Xiu Wei
- Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Yu-Jiao Zheng
- Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Li-Li Zhang
- Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053 China
| | - Xin-Miao Wang
- Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053 China
| | - Hao-Yu Yang
- Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Xu Ma
- Gansu University of Chinese Medicine, Lanzhou, 730000 China
| | - Lin-Hua Zhao
- Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053 China
| | - Xiao-Lin Tong
- Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053 China
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18
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High-speed single molecule imaging datasets of membrane proteins in rat basophilic leukemia cells. Data Brief 2020; 30:105424. [PMID: 32322610 PMCID: PMC7168344 DOI: 10.1016/j.dib.2020.105424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 11/23/2022] Open
Abstract
A high-speed fluorescence microscope operating at a 490 Hz frame rate was used to image two different membrane proteins- the high-affinity IgE receptor FcɛRI, a transmembrane protein, and an outer-leaflet GPI-anchored protein. The IgE receptor was imaged via IgE labeled with Janelia Fluor 646 and the GPI-anchored protein was imaged using a GPI-GFP fusion protein and an ATTO 647 N labeled anti-GFP nanobody. Data was collected for both proteins in untreated cells and cells that had actin stabilized by phalloidin. This dataset can be used for development and testing of single-particle tracking methods on experimental data and to explore the hypothesis that the actin cytoskeleton may affect the movement of membrane proteins.
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19
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Gowthaman U, Chen JS, Eisenbarth SC. Regulation of IgE by T follicular helper cells. J Leukoc Biol 2020; 107:409-418. [PMID: 31965637 DOI: 10.1002/jlb.3ri1219-425r] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/02/2019] [Accepted: 12/09/2019] [Indexed: 12/24/2022] Open
Abstract
Allergies to food and environmental antigens have steeply grown to epidemic proportions. IgE antibodies are key mediators of allergic disease, including life-threatening anaphylaxis. There is now compelling evidence that one of the hallmarks of anaphylaxis-inducing IgE molecules is their high affinity for allergen, and the cellular pathway to high-affinity IgE is typically through sequential switching of IgG B cells. Further, in contrast to the previously held paradigm that a subset of CD4+ T cells called Th2 cells promotes IgE responses, recent studies suggest that T follicular helper cells are crucial for inducing anaphylactic IgE. Here we discuss recent studies that have enabled us to understand the nature, induction, and regulation of this enigmatic antibody isotype in allergic sensitization.
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Affiliation(s)
- Uthaman Gowthaman
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jennifer S Chen
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Stephanie C Eisenbarth
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
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20
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Salazar-Cavazos E, Nitta CF, Mitra ED, Wilson BS, Lidke KA, Hlavacek WS, Lidke DS. Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes. Mol Biol Cell 2020; 31:695-708. [PMID: 31913761 PMCID: PMC7202077 DOI: 10.1091/mbc.e19-09-0548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Differential epidermal growth factor receptor (EGFR) phosphorylation is thought to couple receptor activation to distinct signaling pathways. However, the molecular mechanisms responsible for biased signaling are unresolved due to a lack of insight into the phosphorylation patterns of full-length EGFR. We extended a single-molecule pull-down technique previously used to study protein-protein interactions to allow for robust measurement of receptor phosphorylation. We found that EGFR is predominantly phosphorylated at multiple sites, yet phosphorylation at specific tyrosines is variable and only a subset of receptors share phosphorylation at the same site, even with saturating ligand concentrations. We found distinct populations of receptors as soon as 1 min after ligand stimulation, indicating early diversification of function. To understand this heterogeneity, we developed a mathematical model. The model predicted that variations in phosphorylation are dependent on the abundances of signaling partners, while phosphorylation levels are dependent on dimer lifetimes. The predictions were confirmed in studies of cell lines with different expression levels of signaling partners, and in experiments comparing low- and high-affinity ligands and oncogenic EGFR mutants. These results reveal how ligand-regulated receptor dimerization dynamics and adaptor protein concentrations play critical roles in EGFR signaling.
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Affiliation(s)
| | | | - Eshan D Mitra
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | | | - Keith A Lidke
- Comprehensive Cancer Center, and.,Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - William S Hlavacek
- Comprehensive Cancer Center, and.,Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Diane S Lidke
- Department of Pathology.,Comprehensive Cancer Center, and
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21
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Travers T, Kanagy WK, Mansbach RA, Jhamba E, Cleyrat C, Goldstein B, Lidke DS, Wilson BS, Gnanakaran S. Combinatorial diversity of Syk recruitment driven by its multivalent engagement with FcεRIγ. Mol Biol Cell 2019; 30:2331-2347. [PMID: 31216232 PMCID: PMC6743456 DOI: 10.1091/mbc.e18-11-0722] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/17/2019] [Accepted: 06/10/2019] [Indexed: 12/14/2022] Open
Abstract
Syk/Zap70 family kinases are essential for signaling via multichain immune-recognition receptors such as tetrameric (αβγ2) FcεRI. Syk activation is generally attributed to cis binding of its tandem SH2 domains to dual phosphotyrosines within FcεRIγ-ITAMs (immunoreceptor tyrosine-based activation motifs). However, the mechanistic details of Syk docking on γ homodimers are unresolved. Here, we estimate that multivalent interactions for WT Syk improve cis-oriented binding by three orders of magnitude. We applied molecular dynamics (MD), hybrid MD/worm-like chain polymer modeling, and live cell imaging to evaluate relative binding and signaling output for all possible cis and trans Syk-FcεRIγ configurations. Syk binding is likely modulated during signaling by autophosphorylation on Y130 in interdomain A, since a Y130E phosphomimetic form of Syk is predicted to lead to reduced helicity of interdomain A and alter Syk's bias for cis binding. Experiments in reconstituted γ-KO cells, whose γ subunits are linked by disulfide bonds, as well as in cells expressing monomeric ITAM or hemITAM γ-chimeras, support model predictions that short distances between γ ITAM pairs are required for trans docking. We propose that the full range of docking configurations improves signaling efficiency by expanding the combinatorial possibilities for Syk recruitment, particularly under conditions of incomplete ITAM phosphorylation.
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Affiliation(s)
- Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - William K. Kanagy
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Rachael A. Mansbach
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Elton Jhamba
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Cedric Cleyrat
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Byron Goldstein
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Diane S. Lidke
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Bridget S. Wilson
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
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22
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Brian BF, Jolicoeur AS, Guerrero CR, Nunez MG, Sychev ZE, Hegre SA, Sætrom P, Habib N, Drake JM, Schwertfeger KL, Freedman TS. Unique-region phosphorylation targets LynA for rapid degradation, tuning its expression and signaling in myeloid cells. eLife 2019; 8:e46043. [PMID: 31282857 PMCID: PMC6660195 DOI: 10.7554/elife.46043] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/06/2019] [Indexed: 12/23/2022] Open
Abstract
The activity of Src-family kinases (SFKs), which phosphorylate immunoreceptor tyrosine-based activation motifs (ITAMs), is a critical factor regulating myeloid-cell activation. We reported previously that the SFK LynA is uniquely susceptible to rapid ubiquitin-mediated degradation in macrophages, functioning as a rheostat regulating signaling (Freedman et al., 2015). We now report the mechanism by which LynA is preferentially targeted for degradation and how cell specificity is built into the LynA rheostat. Using genetic, biochemical, and quantitative phosphopeptide analyses, we found that the E3 ubiquitin ligase c-Cbl preferentially targets LynA via a phosphorylated tyrosine (Y32) in its unique region. This distinct mode of c-Cbl recognition depresses steady-state expression of LynA in macrophages derived from mice. Mast cells, however, express little c-Cbl and have correspondingly high LynA. Upon activation, mast-cell LynA is not rapidly degraded, and SFK-mediated signaling is amplified relative to macrophages. Cell-specific c-Cbl expression thus builds cell specificity into the LynA checkpoint.
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Affiliation(s)
- Ben F Brian
- Department of PharmacologyUniversity of MinnesotaMinneapolisUnited States
| | | | - Candace R Guerrero
- College of Biological Sciences Center for Mass Spectrometry and ProteomicsUniversity of MinnesotaMinneapolisUnited States
| | - Myra G Nunez
- Department of PharmacologyUniversity of MinnesotaMinneapolisUnited States
| | - Zoi E Sychev
- Department of PharmacologyUniversity of MinnesotaMinneapolisUnited States
| | - Siv A Hegre
- Department of Clinical and Molecular MedicineNorwegian University of Science and TechnologyTrondheimNorway
| | - Pål Sætrom
- Department of Clinical and Molecular MedicineNorwegian University of Science and TechnologyTrondheimNorway
- Department of Computer ScienceNorwegian University of Science and TechnologyTrondheimNorway
| | - Nagy Habib
- Department of Surgery and CancerHammersmith Hospital, Imperial College LondonLondonUnited Kingdom
| | - Justin M Drake
- Department of PharmacologyUniversity of MinnesotaMinneapolisUnited States
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisUnited States
- Department of UrologyUniversity of MinnesotaMinneapolisUnited States
| | - Kathryn L Schwertfeger
- Department of PharmacologyUniversity of MinnesotaMinneapolisUnited States
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisUnited States
- Center for ImmunologyUniversity of MinnesotaMinneapolisUnited States
- Department of Laboratory Medicine and PathologyUniversity of MinnesotaMinneapolisUnited States
| | - Tanya S Freedman
- Department of PharmacologyUniversity of MinnesotaMinneapolisUnited States
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisUnited States
- Center for ImmunologyUniversity of MinnesotaMinneapolisUnited States
- Center for Autoimmune Diseases ResearchUniversity of MinnesotaMinneapolisUnited States
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23
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Abstract
Higher organisms are all born with general immunity as well as with, increasingly, more specific immune systems. All immune mechanisms function with the intent of aiding the body in defense against infection. Internal and external factors alike have varying effects on the immune system, and the immune response is tailored specifically to each one. Accompanying the components of the human innate and adaptive immune systems are the other intermingling systems of the human body. Increasing understanding of the body's immune interactions with other systems has opened new avenues of study, including that of the microbiome. The microbiome has become a highly active area of research over the last 10 to 20 years since the NIH began funding the Human Microbiome Project (HMP), which was established in 2007. Several publications have focused on the characterization, functions, and complex interplay of the microbiome as it relates to the rest of the body. A dysfunction between the microbiome and the host has been linked to various diseases including cancers, metabolic deficiencies, autoimmune disorders, and infectious diseases. Further understanding of the microbiome and its interaction with the host in relation to diseases is needed in order to understand the implications of microbiome dysfunction and the possible use of microbiota in the prevention of disease. In this review, we have summarized information on the immune system, the microbiome, the microbiome's interplay with other systems, and the association of the immune system and the microbiome in diseases such as diabetes and colorectal cancer.
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Affiliation(s)
| | - Sohail Siraj
- Texas College of Osteopathic Medicine, UNT Health Science Center, Fort Worth, TX
| | - Krishna Patel
- Texas College of Osteopathic Medicine, UNT Health Science Center, Fort Worth, TX
| | - Umesh T. Sankpal
- Texas College of Osteopathic Medicine, UNT Health Science Center, Fort Worth, TX
| | - Stephen Mathew
- Graduate School of Biomedical Sciences, UNT Health Science Center, Fort Worth, TX
| | - Riyaz Basha
- Graduate School of Biomedical Sciences, UNT Health Science Center, Fort Worth, TX
- Texas College of Osteopathic Medicine, UNT Health Science Center, Fort Worth, TX
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24
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Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation. Sci Rep 2017; 7:15586. [PMID: 29138425 PMCID: PMC5686181 DOI: 10.1038/s41598-017-15568-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 10/26/2017] [Indexed: 02/02/2023] Open
Abstract
The high-affinity receptor for IgE expressed on the surface of mast cells and basophils interacts with antigens, via bound IgE antibody, and triggers secretion of inflammatory mediators that contribute to allergic reactions. To understand how past inputs (memory) influence future inflammatory responses in mast cells, a microfluidic device was used to precisely control exposure of cells to alternating stimulatory and non-stimulatory inputs. We determined that the response to subsequent stimulation depends on the interval of signaling quiescence. For shorter intervals of signaling quiescence, the second response is blunted relative to the first response, whereas longer intervals of quiescence induce an enhanced second response. Through an iterative process of computational modeling and experimental tests, we found that these memory-like phenomena arise from a confluence of rapid, short-lived positive signals driven by the protein tyrosine kinase Syk; slow, long-lived negative signals driven by the lipid phosphatase Ship1; and slower degradation of Ship1 co-factors. This work advances our understanding of mast cell signaling and represents a generalizable approach for investigating the dynamics of signaling systems.
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