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Balachandran H, Kroll K, Terry K, Manickam C, Jones R, Woolley G, Hayes T, Martinot AJ, Sharma A, Lewis M, Jost S, Reeves RK. NK cells modulate in vivo control of SARS-CoV-2 replication and suppression of lung damage. PLoS Pathog 2024; 20:e1012439. [PMID: 39133756 DOI: 10.1371/journal.ppat.1012439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/22/2024] [Indexed: 08/18/2024] Open
Abstract
Natural killer (NK) cells play a critical role in virus control. However, it has remained largely unclear whether NK cell mobilization in SARS-CoV-2 infections is beneficial or pathologic. To address this deficit, we employed a validated experimental NK cell depletion non-human primate (NHP) model with SARS-CoV-2 Delta variant B.1.617.2 challenge. Viral loads (VL), NK cell numbers, activation, proliferation, and functional measures were evaluated in blood and tissues. In non-depleted (control) animals, infection rapidly induced NK cell expansion, activation, and increased tissue trafficking associated with VL. Strikingly, we report that experimental NK cell depletion leads to higher VL, longer duration of viral shedding, significantly increased levels of pro-inflammatory cytokines in the lungs, and overt lung damage. Overall, we find the first significant and conclusive evidence for NK cell-mediated control of SARS-CoV-2 virus replication and disease pathology. These data indicate that adjunct therapies for infection could largely benefit from NK cell-targeted approaches.
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Affiliation(s)
- Harikrishnan Balachandran
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, 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
| | - 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
| | - 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
| | - Rhianna Jones
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, 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
| | - Tammy Hayes
- Department of Infectious Diseases and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| | - Amanda J Martinot
- Department of Infectious Diseases and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| | - Ankur Sharma
- BIOQUAL, Inc., Rockville, Maryland, United States of America
| | - Mark Lewis
- BIOQUAL, Inc., Rockville, Maryland, 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
| | - 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 School of Medicine, Durham, North Carolina, United States of America
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2
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Derby N, Biswas S, Yusova S, Luevano-Santos C, Pacheco MC, Meyer KA, Johnson BI, Fischer M, Fancher KA, Fisher C, Abraham YM, McMahon CJ, Lutz SS, Smedley JV, Burwitz BJ, Sodora DL. SIV Infection Is Associated with Transient Acute-Phase Steatosis in Hepatocytes In Vivo. Viruses 2024; 16:296. [PMID: 38400071 PMCID: PMC10892327 DOI: 10.3390/v16020296] [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: 11/01/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Metabolic-dysfunction-associated fatty liver disease (MAFLD) is a major cause of morbidity and mortality in HIV-infected individuals, even those receiving optimal antiretroviral therapy. Here, we utilized the SIV rhesus macaque model and advanced laparoscopic techniques for longitudinal collection of liver tissue to elucidate the timing of pathologic changes. The livers of both SIV-infected (N = 9) and SIV-naïve uninfected (N = 8) macaques were biopsied and evaluated at four time points (weeks -4, 2, 6, and 16-20 post-infection) and at necropsy (week 32). SIV DNA within the macaques' livers varied by over 4 logs at necropsy, and liver SIV DNA significantly correlated with SIV RNA in the plasma throughout the study. Acute phase liver pathology (2 weeks post-infection) was characterized by evidence for fat accumulation (microvesicular steatosis), a transient elevation in both AST and cholesterol levels within the serum, and increased hepatic expression of the PPARA gene associated with cholesterol metabolism and beta oxidation. By contrast, the chronic phase of the SIV infection (32 weeks post-infection) was associated with sinusoidal dilatation, while steatosis resolved and concentrations of AST and cholesterol remained similar to those in uninfected macaques. These findings suggest differential liver pathologies associated with the acute and chronic phases of infection and the possibility that therapeutic interventions targeting metabolic function may benefit liver health in people newly diagnosed with HIV.
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Affiliation(s)
- Nina Derby
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA
| | - Sreya Biswas
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
- Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Sofiya Yusova
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
- Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Cristina Luevano-Santos
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA
| | | | - Kimberly A. Meyer
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA
| | - Brooke I. Johnson
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA
| | - Miranda Fischer
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
- Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Katherine A. Fancher
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA
| | - Cole Fisher
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA
| | - Yohannes M. Abraham
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA
| | - Conor J. McMahon
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
- Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Savannah S. Lutz
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
- Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Jeremy V. Smedley
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
- Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Benjamin J. Burwitz
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
- Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Donald L. Sodora
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98109, USA
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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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Natural Killer Cells Regulate Acute SIV Replication, Dissemination, and Inflammation, but Do Not Impact Independent Transmission Events. J Virol 2023; 97:e0151922. [PMID: 36511699 PMCID: PMC9888193 DOI: 10.1128/jvi.01519-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Natural killer (NK) cells are potent effector cells of the innate immune system possessing both cytotoxic and immunoregulatory capabilities, which contribute to their crucial role in controlling human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) infections. However, despite significant evidence for NK cell modulation of HIV disease, their specific contribution to transmission and control of acute infection remains less clear. To elucidate the contribution of NK cells during acute SIV infection, we performed an acute necropsy study, where rhesus macaques (RM) were subjected to preinfection depletion of systemic NK cells using established methods of IL-15 neutralization, followed by subsequent challenge with barcoded SIVmac239X. Our study showed that depletion was highly effective, resulting in near total ablation of all NK cell subsets in blood, liver, oral, and rectal mucosae, and lymph nodes (LN) that persisted through the duration of the study. Meanwhile, frequencies and phenotypes of T cells remained virtually unchanged, indicating that our method of NK cell depletion had minimal off-target effects. Importantly, NK cell-depleted RM demonstrated an early and sustained 1 to 2 log increase in viremia over controls, but sequence analysis suggested no difference in the number of independent transmission events. Acute bulk, central memory (CM), and CCR5+ CD4+ T cell depletion was similar between experimental and control groups, while CD8+ T cell activation was higher in NK cell-depleted RM as measured by Ki67 and PD-1 expression. Using 27-plex Luminex analyses, we also found modestly increased inflammatory cytokines in NK cell-depleted RM compared to control animals. In the effort to determine the impact of NK cells on HIV/SIV transmission and acute viremia, future studies will be necessary to better harness these cells for future viral therapies. Collectively, these data suggest NK cells are important modulators of lentivirus dissemination and disease but may not have the capacity to independently eliminate individual transmission events. IMPORTANCE Natural killer (NK) cells as major effector cells of the innate immune system can contribute significantly to human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) control. However, a specific role for NK cells in blocking lentivirus transmission remains incompletely clear. In this study, we depleted NK cells prior to challenge with a barcoded SIV. Importantly, our studied showed systemic NK cell depletion was associated with a significant increase in acute viremia, but did not impact the number of independent transmission events. Collectively, these data suggest NK cells are critical modulators of early lentivirus replication but may not regulate individual transmission events at mucosal portals of entry.
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Fisher BS, Fancher KA, Gustin AT, Fisher C, Wood MP, Gale M, Burwitz BJ, Smedley J, Klatt NR, Derby N, Sodora DL. Liver Bacterial Dysbiosis With Non-Tuberculosis Mycobacteria Occurs in SIV-Infected Macaques and Persists During Antiretroviral Therapy. Front Immunol 2022; 12:793842. [PMID: 35082782 PMCID: PMC8784802 DOI: 10.3389/fimmu.2021.793842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/16/2021] [Indexed: 01/26/2023] Open
Abstract
Liver disease is a significant contributor to morbidity and mortality in HIV-infected individuals, even during successful viral suppression with combination antiretroviral therapy (cART). Similar to HIV infection, SIV infection of rhesus macaques is associated with gut microbiome dysbiosis and microbial translocation that can be detected systemically in the blood. As microbes leaving the intestines must first pass through the liver via the portal vein, we evaluated the livers of both SIV-infected (SIV+) and SIV-infected cART treated (SIV+cART) rhesus macaques for evidence of microbial changes compared to uninfected macaques. Dysbiosis was observed in both the SIV+ and SIV+cART macaques, encompassing changes in the relative abundance of several genera, including a reduction in the levels of Lactobacillus and Staphylococcus. Most strikingly, we found an increase in the relative abundance and absolute quantity of bacteria within the Mycobacterium genus in both SIV+ and SIV+cART macaques. Multi-gene sequencing identified a species of atypical mycobacteria similar to the opportunistic pathogen M. smegmatis. Phosphatidyl inositol lipoarabinomannan (PILAM) (a glycolipid cell wall component found in atypical mycobacteria) stimulation in primary human hepatocytes resulted in an upregulation of inflammatory transcriptional responses, including an increase in the chemokines associated with neutrophil recruitment (CXCL1, CXCL5, and CXCL6). These studies provide key insights into SIV associated changes in hepatic microbial composition and indicate a link between microbial components and immune cell recruitment in SIV+ and SIV+cART treated macaques.
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Affiliation(s)
- Bridget S. Fisher
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Katherine A. Fancher
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Andrew T. Gustin
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA, United States
| | - Cole Fisher
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Matthew P. Wood
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA, United States
| | - Benjamin J. Burwitz
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| | - Jeremy Smedley
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, United States
| | - Nichole R. Klatt
- Department of Surgery, University of Minnesota, Minneapolis, MN, United States
| | - Nina Derby
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Donald L. Sodora
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
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Abstract
Purpose of Review Observations of differing bacterial, intestinal microbiomes in people living with HIV have propelled interest in contributions of the microbiome to HIV disease. Non-human primate (NHP) models of HIV infection provide a controlled setting for assessing contributions of the microbiome by standardizing environmental confounders. We provide an overview of the findings of microbiome contributions to aspects of HIV disease derived from these animal models. Recent Findings Observations of differing bacterial, intestinal microbiomes are inconsistently observed in the NHP model following SIV infection. Differences in lentiviral susceptibility and vaccine efficacy have been attributed to variations in the intestinal microbiome; however, by-and-large, these differences have not been experimentally assessed. Summary Although compelling associations exist, clearly defined contributions of the microbiome to HIV and SIV disease are lacking. The empirical use of comprehensive multi-omics assessments and longitudinal and interventional study designs in NHP models is necessary to define this contribution more clearly.
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Affiliation(s)
- Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA
| | - Alexandra M Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, USA.
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