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Sugawara S, Hueber B, Woolley G, Terry K, Kroll K, Manickam C, Ram DR, Ndhlovu LC, Goepfert P, Jost S, Reeves RK. Multiplex interrogation of the NK cell signalome reveals global downregulation of CD16 signaling during lentivirus infection through an IL-18/ADAM17-dependent mechanism. PLoS Pathog 2023; 19:e1011629. [PMID: 37669308 PMCID: PMC10503717 DOI: 10.1371/journal.ppat.1011629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 09/15/2023] [Accepted: 08/21/2023] [Indexed: 09/07/2023] Open
Abstract
Despite their importance, natural killer (NK) cell responses are frequently dysfunctional during human immunodeficiency virus-1 (HIV-1) and simian immunodeficiency virus (SIV) infections, even irrespective of antiretroviral therapies, with poorly understood underlying mechanisms. NK cell surface receptor modulation in lentivirus infection has been extensively studied, but a deeper interrogation of complex cell signaling is mostly absent, largely due to the absence of any comprehensive NK cell signaling assay. To fill this knowledge gap, we developed a novel multiplex signaling analysis to broadly assess NK cell signaling. Using this assay, we elucidated that NK cells exhibit global signaling reduction from CD16 both in people living with HIV-1 (PLWH) and SIV-infected rhesus macaques. Intriguingly, antiretroviral treatment did not fully restore diminished CD16 signaling in NK cells from PLWH. As a putative mechanism, we demonstrated that NK cells increased surface ADAM17 expression via elevated plasma IL-18 levels during HIV-1 infection, which in turn reduced surface CD16 downregulation. We also illustrated that CD16 expression and signaling can be restored by ADAM17 perturbation. In summary, our multiplex NK cell signaling analysis delineated unique NK cell signaling perturbations specific to lentiviral infections, resulting in their dysfunction. Our analysis also provides mechanisms that will inform the restoration of dysregulated NK cell functions, offering potential insights for the development of new NK cell-based immunotherapeutics for HIV-1 disease.
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Affiliation(s)
- Sho Sugawara
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Brady Hueber
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Griffin Woolley
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Karen Terry
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Kyle Kroll
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Cordelia Manickam
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Daniel R. Ram
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, United States of America
| | - Paul Goepfert
- University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Stephanie Jost
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - R. Keith Reeves
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
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Wu C, Liang JA, Brenchley JM, Shin T, Fan X, Mortlock RD, Abraham D, Allan DS, Thomas ML, Hong S, Dunbar CE. Barcode clonal tracking of tissue-resident immune cells in rhesus macaque highlights distinct clonal distribution pattern of tissue NK cells. Front Immunol 2022; 13:994498. [PMID: 36605190 PMCID: PMC9808525 DOI: 10.3389/fimmu.2022.994498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 11/12/2022] Open
Abstract
Tissue resident (TR) immune cells play important roles in facilitating tissue homeostasis, coordinating immune responses against infections and tumors, and maintaining immunological memory. While studies have shown these cells are distinct phenotypically and functionally from cells found in the peripheral blood (PB), the clonal relationship between these populations across tissues has not been comprehensively studied in primates or humans. We utilized autologous transplantation of rhesus macaque hematopoietic stem and progenitor cells containing high diversity barcodes to track the clonal distribution of T, B, myeloid and natural killer (NK) cell populations across tissues, including liver, spleen, lung, and gastrointestinal (GI) tract, in comparison with PB longitudinally post-transplantation, in particular we focused on NK cells which do not contain endogenous clonal markers and have not been previously studied in this context. T cells demonstrated tissue-specific clonal expansions as expected, both overlapping and distinct from blood T cells. In contrast, B and myeloid cells showed a much more homogeneous clonal pattern across various tissues and the blood. The clonal distribution of TR NK was more heterogenous between individual animals. In some animals, as we have previously reported, we observed large PB clonal expansions in mature CD56-CD16+ NK cells. Notably, we found a separate set of highly expanded PB clones in CD16-CD56- (DN) NK subset that were also contributing to TR NK cells in all tissues examined, both in TR CD56-CD16+ and DN populations but absent in CD56+16- TR NK across all tissues analyzed. Additionally, we observed sets of TR NK clones specific to individual tissues such as lung or GI tract and sets of TR NK clones shared across liver and spleen, distinct from other tissues. Combined with prior functional data that suggests NK memory is restricted to liver or other TR NK cells, these clonally expanded TR NK cells may be of interest for future investigation into NK cell tissue immunological memory, with implications for development of NK based immunotherapies and an understanding of NK memory.
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Affiliation(s)
- Chuanfeng Wu
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Jialiu A. Liang
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Jason M. Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Taehoon Shin
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Xing Fan
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Ryland D. Mortlock
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Diana M. Abraham
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - David S.J. Allan
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Marvin L. Thomas
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, United States
| | - So Gun Hong
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States,*Correspondence: Cynthia E. Dunbar,
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Murphy JM, Ngai L, Mortha A, Crome SQ. Tissue-Dependent Adaptations and Functions of Innate Lymphoid Cells. Front Immunol 2022; 13:836999. [PMID: 35359972 PMCID: PMC8960279 DOI: 10.3389/fimmu.2022.836999] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/11/2022] [Indexed: 12/21/2022] Open
Abstract
Tissue-resident immune cells reside in distinct niches across organs, where they contribute to tissue homeostasis and rapidly respond to perturbations in the local microenvironment. Innate lymphoid cells (ILCs) are a family of innate immune cells that regulate immune and tissue homeostasis. Across anatomical locations throughout the body, ILCs adopt tissue-specific fates, differing from circulating ILC populations. Adaptations of ILCs to microenvironmental changes have been documented in several inflammatory contexts, including obesity, asthma, and inflammatory bowel disease. While our understanding of ILC functions within tissues have predominantly been based on mouse studies, development of advanced single cell platforms to study tissue-resident ILCs in humans and emerging patient-based data is providing new insights into this lymphocyte family. Within this review, we discuss current concepts of ILC fate and function, exploring tissue-specific functions of ILCs and their contribution to health and disease across organ systems.
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Affiliation(s)
- Julia M Murphy
- Department of Immunology, University of Toronto, Toronto, ON, Canada.,Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Louis Ngai
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Arthur Mortha
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Sarah Q Crome
- Department of Immunology, University of Toronto, Toronto, ON, Canada.,Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
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Valle-Noguera A, Ochoa-Ramos A, Gomez-Sánchez MJ, Cruz-Adalia A. Type 3 Innate Lymphoid Cells as Regulators of the Host-Pathogen Interaction. Front Immunol 2021; 12:748851. [PMID: 34659248 PMCID: PMC8511434 DOI: 10.3389/fimmu.2021.748851] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/13/2021] [Indexed: 12/16/2022] Open
Abstract
Type 3 Innate lymphoid cells (ILC3s) have been described as tissue-resident cells and characterized throughout the body, especially in mucosal sites and classical first barrier organs such as skin, gut and lungs, among others. A significant part of the research has focused on their role in combating pathogens, mainly extracellular pathogens, with the gut as the principal organ. However, some recent discoveries in the field have unveiled their activity in other organs, combating intracellular pathogens and as part of the response to viruses. In this review we have compiled the latest studies on the role of ILC3s and the molecular mechanisms involved in defending against different microbes at the mucosal surface, most of these studies have made use of conditional transgenic mice. The present review therefore attempts to provide an overview of the function of ILC3s in infections throughout the body, focusing on their specific activity in different organs.
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Affiliation(s)
- Ana Valle-Noguera
- Department of Immunology, School of Medicine, Universidad Complutense de Madrid; 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Anne Ochoa-Ramos
- Department of Immunology, School of Medicine, Universidad Complutense de Madrid; 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Maria José Gomez-Sánchez
- Department of Immunology, School of Medicine, Universidad Complutense de Madrid; 12 de Octubre Health Research Institute (imas12), Madrid, Spain
| | - Aranzazu Cruz-Adalia
- Department of Immunology, School of Medicine, Universidad Complutense de Madrid; 12 de Octubre Health Research Institute (imas12), Madrid, Spain
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Kazer SW, Walker BD, Shalek AK. Evolution and Diversity of Immune Responses during Acute HIV Infection. Immunity 2021; 53:908-924. [PMID: 33207216 DOI: 10.1016/j.immuni.2020.10.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/03/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023]
Abstract
Understanding the earliest immune responses following HIV infection is critical to inform future vaccines and therapeutics. Here, we review recent prospective human studies in at-risk populations that have provided insight into immune responses during acute infection, including additional relevant data from non-human primate (NHP) studies. We discuss the timing, nature, and function of the diverse immune responses induced, the onset of immune dysfunction, and the effects of early anti-retroviral therapy administration. Treatment at onset of viremia mitigates peripheral T and B cell dysfunction, limits seroconversion, and enhances cellular antiviral immunity despite persistence of infection in lymphoid tissues. We highlight pertinent areas for future investigation, and how application of high-throughput technologies, alongside targeted NHP studies, may elucidate immune response features to target in novel preventions and cures.
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Affiliation(s)
- Samuel W Kazer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA; HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Alex K Shalek
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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