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Wei J, Moon J, Yasumizu Y, Zhang L, Radassi K, Buitrago-Pocasangre N, Deerhake ME, Strauli N, Chan A, Herman A, Pedotte R, Raposo C, Tackenberg B, Yim I, Pappalardo J, Longbrake EE, Sumida TS, Axisa PP, Hafler DA. Systems Analysis of Immune Changes after B-cell Depletion in Autoimmune Multiple Sclerosis. bioRxiv 2024:2024.02.07.576204. [PMID: 38370778 PMCID: PMC10871268 DOI: 10.1101/2024.02.07.576204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Multiple sclerosis (MS) is a complex genetically mediated autoimmune disease of the central nervous system where anti-CD20-mediated B cell depletion is remarkably effective in the treatment of early disease. While previous studies investigated the effect of B cell depletion on select immune cell subsets using flow cytometry-based methods, the therapeutic impact on patient immune landscape is unknown. In this study, we explored how a therapy-driven " in vivo perturbation " modulates the diverse immune landscape by measuring transcriptomic granularity with single-cell RNA sequencing (scRNAseq). We demonstrate that B cell depletion leads to cell type-specific changes in the abundance and function of CSF macrophages and peripheral blood monocytes. Specifically, a CSF-specific macrophage population with an anti-inflammatory transcriptomic signature and peripheral CD16 + monocytes increased in frequency post-B cell depletion. In addition, we observed increases in TNFα messenger RNA and protein in monocytes post-B cell depletion, consistent with the finding that anti-TNFα treatment exacerbates autoimmune activity in MS. In parallel, B cell depletion also induced changes in peripheral CD4 + T cell populations, including increases in the frequency of TIGIT + regulatory T cells and marked decreases in the frequency of myelin peptide loaded-tetramer binding CD4 + T cells. Collectively, this study provides an exhaustive transcriptomic map of immunological changes, revealing different mechanisms of action contributing to the high efficacy in B cell depletion treatment of MS.
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2
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Deerhake ME, Cardakli ED, Shinohara ML. Dectin-1 signaling in neutrophils up-regulates PD-L1 and triggers ROS-mediated suppression of CD4 + T cells. J Leukoc Biol 2022; 112:1413-1425. [PMID: 36073780 PMCID: PMC9701158 DOI: 10.1002/jlb.3a0322-152rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/11/2022] [Indexed: 01/04/2023] Open
Abstract
Dectin-1 is known to drive proinflammatory cytokine production by macrophages and dendritic cells which promotes Th17 CD4+ T cell responses in the setting of fungal infection. However, the role of Dectin-1 signaling in neutrophils and its impact on CD4+ T cells is not well understood. In this study, we found that neutrophils stimulated with a Dectin-1 agonist diminish CD4+ T cell viability in a rapid and reactive oxygen species (ROS)-dependent manner. Furthermore, Dectin-1 promoted neutrophil PD-L1 expression via Syk and Card9 signaling, along with other immune-checkpoint factors in a neutrophil-biased manner. Although neutrophil PD-L1 did not significantly impact disease severity in experimental autoimmune encephalomyelitis (EAE), we found that CNS-infiltrated neutrophils potently up-regulate PD-L1 expression. Furthermore, a subset of PD-L1+ neutrophils was also found to express MHC-II during EAE. In summary, we found that Dectin-1 elicits a biphasic neutrophil response in which (1) T-cell suppressive ROS is followed by (2) up-regulation of PD-L1 expression. This response may serve to limit excess CD4+ T cell-driven inflammation in infection or autoimmunity while preserving host-defense functions of neutrophils. Summary sentence: Mechanisms by which Dectin-1 signaling in neutrophils promotes a cellular phenotype with T cell-suppressive properties.
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Affiliation(s)
| | - Emre D. Cardakli
- Department of Immunology, Duke University School of
Medicine, Durham, NC 27710, USA
- Tri-Institutional MD-PhD Program, Weill Cornell
Medical College, Rockefeller University and Memorial Sloan Kettering Cancer Center,
New York, NY 10021, USA
| | - Mari L. Shinohara
- Department of Immunology, Duke University School of
Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology,
Duke University School of Medicine, Durham, NC 27710, USA
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3
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Barclay WE, Aggarwal N, Deerhake ME, Inoue M, Nonaka T, Nozaki K, Luzum NA, Miao EA, Shinohara ML. The AIM2 inflammasome is activated in astrocytes during the late phase of EAE. JCI Insight 2022; 7:155563. [PMID: 35451371 PMCID: PMC9089781 DOI: 10.1172/jci.insight.155563] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Inflammasomes are a class of innate immune signaling platforms that activate in response to an array of cellular damage and pathogens. Inflammasomes promote inflammation under many circumstances to enhance immunity against pathogens and inflammatory responses through their effector cytokines, IL-1β and IL-18. Multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE), are autoimmune conditions influenced by inflammasomes. Despite work investigating inflammasomes during EAE, little remains known concerning the role of inflammasomes in the central nervous system (CNS) during the disease. Here, we used multiple genetically modified mouse models to monitor activated inflammasomes in situ based on oligomerization of apoptosis-associated speck-like protein containing a CARD (ASC) in the spinal cord. Using inflammasome reporter mice, we found heightened inflammasome activation in astrocytes after the disease peak. In contrast, microglia and CNS-infiltrated myeloid cells had few activated inflammasomes in the CNS during EAE. Astrocyte inflammasome activation during EAE was dependent on absent in melanoma 2 (AIM2), but low IL-1β release and no significant signs of cell death were found. Thus, the AIM2 inflammasome activation in astrocytes may have a distinct role from traditional inflammasome-mediated inflammation.
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Affiliation(s)
- William E. Barclay
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nupur Aggarwal
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - M. Elizabeth Deerhake
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Makoto Inoue
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Toshiaki Nonaka
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Kengo Nozaki
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nathan A. Luzum
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Edward A. Miao
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Mari L. Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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4
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Deerhake ME, Shinohara ML. Emerging roles of Dectin-1 in noninfectious settings and in the CNS. Trends Immunol 2021; 42:891-903. [PMID: 34489167 DOI: 10.1016/j.it.2021.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 12/15/2022]
Abstract
Dectin-1 is a C-type lectin receptor (CLR) expressed on the surface of various mammalian myeloid cells. Dectin-1 recognizes β-glucans and elicits antifungal proinflammatory immune responses. Recent studies have begun to examine the biology of Dectin-1 in previously less explored settings, such as homeostasis, sterile inflammation, and in the central nervous system. Indeed, in certain contexts, Dectin-1 is now known to promote tolerance, and anti-inflammatory and neuroprotective responses. In this review, we provide an overview of the current understanding of the roles of Dectin-1 in immunology beyond the context of fungal infections, mainly focusing on in vivo neuroimmunology studies, which could reveal new therapeutic approaches to modify innate immune responses in neurologic disorders.
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Affiliation(s)
- M Elizabeth Deerhake
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Mari L Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27705, USA.
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5
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Bernagros JT, Pankani D, Struck SD, Deerhake ME. Estimating Regionalized Planning Costs of Green Infrastructure and Low-Impact Development Stormwater Management Practices: Updates to the US Environmental Protection Agency's National Stormwater Calculator. J Sustain Water Built Environ 2021; 7:10.1061/jswbay.0000934. [PMID: 33628872 PMCID: PMC7898140 DOI: 10.1061/jswbay.0000934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/30/2020] [Indexed: 06/12/2023]
Abstract
Estimating regional costs of green infrastructure (GI) and low-impact development (LID) stormwater management controls is an important issue for many municipalities and water utilities in the United States. The National Stormwater Calculator (NSWC) is a site-scale, planning-level tool. A regional cost estimation methodology was recently added to the NSWC, enabling users to estimate region-specific capital and maintenance costs of commonly used GI controls. This paper discusses the approach used to estimate and regionalize costs in the NSWC.
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Affiliation(s)
- J T Bernagros
- Biologist, Center for Environmental Solutions and Emergency Response, Office of Research and Development, US Environmental Protection Agency, 1200 Pennsylvania Ave. NW, MC 8801R, Washington, DC 20460
| | - D Pankani
- Senior Engineer, Geosyntec Consultants, 920 SW 6th Ave., Suite 600, Portland, OR 97204
| | - S D Struck
- Principal Engineer, Geosyntec Consultants, 1376 Miners Dr., Suite 108, Lafayette, CO 80026
| | - M E Deerhake
- Senior Research Environmental Scientist, RTI International, 3040 East Cornwallis Rd., P.O. Box 12194, Research Triangle Park, NC 27709
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Deerhake ME, Danzaki K, Inoue M, Cardakli E, Nonaka T, Aggarwal N, Barclay W, Ji RR, Shinohara ML. Dectin-1 limits CNS autoimmunity through a non-canonical pathway. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.96.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
Innate immunity mediates both damage and repair of the central nervous system (CNS) in neurologic disorders. Although pathologic roles for innate immunity are well-described in multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE), protective aspects of the immune response are less understood. In this study, we sought to identify the function of Dectin-1, a C-type lectin receptor (CLR), in CNS autoimmunity. We found that Dectin-1 limited neuroinflammation in EAE while its canonical signaling mediator, Card9, promoted disease. Myeloid cells from the bone-marrow mediated the regulatory function of Dectin-1 in EAE and upregulated expression of Oncostatin M (Osm), a neuroprotective cytokine, through a non-canonical Card9-independent Dectin-1 signaling pathway. We found that the Osm receptor (OsmR) functioned specifically in astrocytes to reduce EAE severity. RNA-seq profiling of the Card9-independent Dectin-1 transcriptional program identified multiple targets with neuroprotective functions, including Osm, which were regulated by NFAT signaling. Our data describe a new mechanism of neuroprotective myeloid-astrocyte crosstalk regulated by a non-canonical Dectin-1 pathway.
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7
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Deerhake ME, Reyes EY, Xu-Vanpala S, Shinohara ML. Single-Cell Transcriptional Heterogeneity of Neutrophils During Acute Pulmonary Cryptococcus neoformans Infection. Front Immunol 2021; 12:670574. [PMID: 33995406 PMCID: PMC8116703 DOI: 10.3389/fimmu.2021.670574] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Neutrophils are critical as the first-line defense against fungal pathogens. Yet, previous studies indicate that neutrophil function is complex during Cryptococcus neoformans (Cn) infection. To better understand the role of neutrophils in acute pulmonary cryptococcosis, we analyzed neutrophil heterogeneity by single-cell transcriptional analysis of immune cells in the lung of Cn-infected mice from a published dataset. We identified neutrophils by reference-based annotation and identified two distinct neutrophil subsets generated during acute Cn infection: A subset with an oxidative stress signature (Ox-PMN) and another with enhanced cytokine gene expression (Cyt-PMN). Based on gene regulatory network and ligand-receptor analysis, we hypothesize that Ox-PMNs interact with the fungus and generate ROS, while Cyt-PMNs are longer-lived neutrophils that indirectly respond to Cn-derived ligands and cytokines to modulate cell-cell communication with dendritic cells and alveolar macrophages. Based on the data, we hypothesized that, during in vivo fungal infection, there is a division of labor in which each activated neutrophil becomes either Ox-PMN or Cyt-PMN.
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Affiliation(s)
- M Elizabeth Deerhake
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
| | - Estefany Y Reyes
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
| | - Shengjie Xu-Vanpala
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
| | - Mari L Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
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8
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Deerhake ME, Danzaki K, Inoue M, Cardakli ED, Nonaka T, Aggarwal N, Barclay WE, Ji RR, Shinohara ML. Dectin-1 limits autoimmune neuroinflammation and promotes myeloid cell-astrocyte crosstalk via Card9-independent expression of Oncostatin M. Immunity 2021; 54:484-498.e8. [PMID: 33581044 PMCID: PMC7956124 DOI: 10.1016/j.immuni.2021.01.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 11/20/2020] [Accepted: 01/12/2021] [Indexed: 12/12/2022]
Abstract
Pathologic roles of innate immunity in neurologic disorders are well described, but their beneficial aspects are less understood. Dectin-1, a C-type lectin receptor (CLR), is largely known to induce inflammation. Here, we report that Dectin-1 limited experimental autoimmune encephalomyelitis (EAE), while its downstream signaling molecule, Card9, promoted the disease. Myeloid cells mediated the pro-resolution function of Dectin-1 in EAE with enhanced gene expression of the neuroprotective molecule, Oncostatin M (Osm), through a Card9-independent pathway, mediated by the transcription factor NFAT. Furthermore, we find that the Osm receptor (OsmR) functioned specifically in astrocytes to reduce EAE severity. Notably, Dectin-1 did not respond to heat-killed Mycobacteria, an adjuvant to induce EAE. Instead, endogenous Dectin-1 ligands, including galectin-9, in the central nervous system (CNS) were involved to limit EAE. Our study reveals a mechanism of beneficial myeloid cell-astrocyte crosstalk regulated by a Dectin-1 pathway and identifies potential therapeutic targets for autoimmune neuroinflammation.
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MESH Headings
- Animals
- Astrocytes/immunology
- Brain/pathology
- CARD Signaling Adaptor Proteins/metabolism
- Cell Communication
- Cells, Cultured
- Disease Models, Animal
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Galectins/metabolism
- Gene Expression Regulation
- Lectins, C-Type/genetics
- Lectins, C-Type/metabolism
- Mice, Inbred C57BL
- Mice, Knockout
- Multiple Sclerosis/immunology
- Myelin-Oligodendrocyte Glycoprotein/immunology
- Myeloid Cells/immunology
- Neurogenic Inflammation/immunology
- Oncostatin M/genetics
- Oncostatin M/metabolism
- Oncostatin M Receptor beta Subunit/metabolism
- Peptide Fragments/immunology
- Receptors, Mitogen/genetics
- Receptors, Mitogen/metabolism
- Signal Transduction
- Mice
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Affiliation(s)
- M Elizabeth Deerhake
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Keiko Danzaki
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Makoto Inoue
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Emre D Cardakli
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Toshiaki Nonaka
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nupur Aggarwal
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - William E Barclay
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ru-Rong Ji
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mari L Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
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9
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Xu-Vanpala S, Deerhake ME, Wheaton JD, Parker ME, Juvvadi PR, MacIver N, Ciofani M, Shinohara ML. Functional heterogeneity of alveolar macrophage population based on expression of CXCL2. Sci Immunol 2020; 5:5/50/eaba7350. [PMID: 32769172 DOI: 10.1126/sciimmunol.aba7350] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 06/15/2020] [Indexed: 12/21/2022]
Abstract
Alveolar macrophages (AMs) are the major lung-resident macrophages and have contradictory functions. AMs maintain tolerance and tissue homeostasis, but they also initiate strong inflammatory responses. However, such opposing roles within the AM population were not known to be simultaneously generated and coexist. Here, we uncovered heterogeneous AM subpopulations generated in response to two distinct pulmonary fungal infections, Cryptococcus neoformans and Aspergillus fumigatus Some AMs are bona fide sentinel cells that produce chemoattractant CXCL2, which also serves as a marker for AM heterogeneity, in the context of pulmonary fungal infections. However, other AMs do not produce CXCL2 and other pro-inflammatory molecules. Instead, they highly produce anti-inflammatory molecules, including interleukin-10 (IL-10) and complement component 1q (C1q). These two AM subpopulations have distinct metabolic profiles and phagocytic capacities. We report that polarization of pro-inflammatory and anti-inflammatory AM subpopulations is regulated at both epigenetic and transcriptional levels and that these AM subpopulations are generally highly plastic. Our studies have uncovered the role of C1q expression in programming and sustaining anti-inflammatory AMs. Our finding of the AM heterogeneity upon fungal infections suggests a possible pharmacological intervention target to treat fungal infections by tipping the balance of AM subpopulations.
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Affiliation(s)
- Shengjie Xu-Vanpala
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - M Elizabeth Deerhake
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joshua D Wheaton
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.,Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Morgan E Parker
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Praveen R Juvvadi
- Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Nancie MacIver
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA.,Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maria Ciofani
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mari L Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA. .,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
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10
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Deerhake ME, Biswas DD, Barclay WE, Shinohara ML. Pattern Recognition Receptors in Multiple Sclerosis and Its Animal Models. Front Immunol 2019; 10:2644. [PMID: 31781124 PMCID: PMC6861384 DOI: 10.3389/fimmu.2019.02644] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 10/25/2019] [Indexed: 12/15/2022] Open
Abstract
Pattern recognition receptors (PRRs) coordinate the innate immune response and have a significant role in the development of multiple sclerosis (MS). Accumulating evidence has identified both pathogenic and protective functions of PRR signaling in MS and its animal model, experimental autoimmune encephalomyelitis (EAE). Additionally, evidence for PRR signaling in non-immune cells and PRR responses to host-derived endogenous ligands has also revealed new pathways controlling the development of CNS autoimmunity. Many PRRs remain uncharacterized in MS and EAE, and understanding the distinct triggers and functions of PRR signaling in CNS autoimmunity requires further investigation. In this brief review, we discuss the diverse pathogenic and protective functions of PRRs in MS and EAE, and highlight major avenues for future research.
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Affiliation(s)
- M Elizabeth Deerhake
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
| | - Debolina D Biswas
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
| | - William E Barclay
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
| | - Mari L Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
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Abstract
Researchers have previously hypothesized autoimmune origins for narcolepsy on the basis of its strong genetic association with an MHC class II allele. In a recent issue of Nature, Latorre et al. (2018) discovered that narcolepsy patients had autoreactive T cells specific to the neuronal antigen hypocretin, providing more evidence of the potential immune origin of the disease.
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Affiliation(s)
- M Elizabeth Deerhake
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA
| | - William E Barclay
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Mari L Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, NC 27705, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27705, USA.
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12
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Amambua-Ngwa A, Tetteh KKA, Manske M, Gomez-Escobar N, Stewart LB, Deerhake ME, Cheeseman IH, Newbold CI, Holder AA, Knuepfer E, Janha O, Jallow M, Campino S, MacInnis B, Kwiatkowski DP, Conway DJ. Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites. PLoS Genet 2012; 8:e1002992. [PMID: 23133397 PMCID: PMC3486833 DOI: 10.1371/journal.pgen.1002992] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 08/13/2012] [Indexed: 11/19/2022] Open
Abstract
Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens, leading to identifiable signatures of balancing selection. To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum, we generated paired-end short-read sequences of parasites in clinical isolates from an endemic Gambian population, which were mapped to the 3D7 strain reference genome to yield high-quality genome-wide coding sequence data for 65 isolates. A minority of genes did not map reliably, including the hypervariable var, rifin, and stevor families, but 5,056 genes (90.9% of all in the genome) had >70% sequence coverage with minimum read depth of 5 for at least 50 isolates, of which 2,853 genes contained 3 or more single nucleotide polymorphisms (SNPs) for analysis of polymorphic site frequency spectra. Against an overall background of negatively skewed frequencies, as expected from historical population expansion combined with purifying selection, the outlying minority of genes with signatures indicating exceptionally intermediate frequencies were identified. Comparing genes with different stage-specificity, such signatures were most common in those with peak expression at the merozoite stage that invades erythrocytes. Members of clag, PfMC-2TM, surfin, and msp3-like gene families were highly represented, the strongest signature being in the msp3-like gene PF10_0355. Analysis of msp3-like transcripts in 45 clinical and 11 laboratory adapted isolates grown to merozoite-containing schizont stages revealed surprisingly low expression of PF10_0355. In diverse clonal parasite lines the protein product was expressed in a minority of mature schizonts (<1% in most lines and ∼10% in clone HB3), and eight sub-clones of HB3 cultured separately had an intermediate spectrum of positive frequencies (0.9 to 7.5%), indicating phase variable expression of this polymorphic antigen. This and other identified targets of balancing selection are now prioritized for functional study.
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Affiliation(s)
| | - Kevin K. A. Tetteh
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Magnus Manske
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Lindsay B. Stewart
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - M. Elizabeth Deerhake
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ian H. Cheeseman
- Medical Research Council Unit, Fajara, Banjul, The Gambia
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christopher I. Newbold
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Anthony A. Holder
- Division of Parasitology, MRC National Institute for Medical Research, London, United Kingdom
| | - Ellen Knuepfer
- Division of Parasitology, MRC National Institute for Medical Research, London, United Kingdom
| | - Omar Janha
- Medical Research Council Unit, Fajara, Banjul, The Gambia
| | | | - Susana Campino
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Dominic P. Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - David J. Conway
- Medical Research Council Unit, Fajara, Banjul, The Gambia
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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