1
|
Lee MJ, de los Rios Kobara I, Barnard TR, Vales Torres X, Tobin NH, Ferbas KG, Rimoin AW, Yang OO, Aldrovandi GM, Wilk AJ, Fulcher JA, Blish CA. NK Cell-Monocyte Cross-talk Underlies NK Cell Activation in Severe COVID-19. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1693-1705. [PMID: 38578283 PMCID: PMC11102029 DOI: 10.4049/jimmunol.2300731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
NK cells in the peripheral blood of severe COVID-19 patients exhibit a unique profile characterized by activation and dysfunction. Previous studies have identified soluble factors, including type I IFN and TGF-β, that underlie this dysregulation. However, the role of cell-cell interactions in modulating NK cell function during COVID-19 remains unclear. To address this question, we combined cell-cell communication analysis on existing single-cell RNA sequencing data with in vitro primary cell coculture experiments to dissect the mechanisms underlying NK cell dysfunction in COVID-19. We found that NK cells are predicted to interact most strongly with monocytes and that this occurs via both soluble factors and direct interactions. To validate these findings, we performed in vitro cocultures in which NK cells from healthy human donors were incubated with monocytes from COVID-19+ or healthy donors. Coculture of healthy NK cells with monocytes from COVID-19 patients recapitulated aspects of the NK cell phenotype observed in severe COVID-19, including decreased expression of NKG2D, increased expression of activation markers, and increased proliferation. When these experiments were performed in a Transwell setting, we found that only CD56bright CD16- NK cells were activated in the presence of severe COVID-19 patient monocytes. O-link analysis of supernatants from Transwell cocultures revealed that cultures containing severe COVID-19 patient monocytes had significantly elevated levels of proinflammatory cytokines and chemokines, as well as TGF-β. Collectively, these results demonstrate that interactions between NK cells and monocytes in the peripheral blood of COVID-19 patients contribute to NK cell activation and dysfunction in severe COVID-19.
Collapse
Affiliation(s)
- Madeline J. Lee
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
- Stanford Immunology Program, Stanford University School of Medicine, Palo Alto, CA
| | - Izumi de los Rios Kobara
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
- Stanford Immunology Program, Stanford University School of Medicine, Palo Alto, CA
| | - Trisha R. Barnard
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
| | - Xariana Vales Torres
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
- Stanford Immunology Program, Stanford University School of Medicine, Palo Alto, CA
| | - Nicole H. Tobin
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Kathie G. Ferbas
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Anne W. Rimoin
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA
| | - Otto O. Yang
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Grace M. Aldrovandi
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Aaron J. Wilk
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Palo Alto, CA
| | - Jennifer A. Fulcher
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Catherine A. Blish
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
- Chan Zuckerberg Biohub, San Francisco, CA
| |
Collapse
|
2
|
Knoll R, Bonaguro L, dos Santos JC, Warnat-Herresthal S, Jacobs-Cleophas MCP, Blümel E, Reusch N, Horne A, Herbert M, Nuesch-Germano M, Otten T, van der Heijden WA, van de Wijer L, Shalek AK, Händler K, Becker M, Beyer MD, Netea MG, Joosten LAB, van der Ven AJAM, Schultze JL, Aschenbrenner AC. Identification of drug candidates targeting monocyte reprogramming in people living with HIV. Front Immunol 2023; 14:1275136. [PMID: 38077315 PMCID: PMC10703486 DOI: 10.3389/fimmu.2023.1275136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/18/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction People living with HIV (PLHIV) are characterized by functional reprogramming of innate immune cells even after long-term antiretroviral therapy (ART). In order to assess technical feasibility of omics technologies for application to larger cohorts, we compared multiple omics data layers. Methods Bulk and single-cell transcriptomics, flow cytometry, proteomics, chromatin landscape analysis by ATAC-seq as well as ex vivo drug stimulation were performed in a small number of blood samples derived from PLHIV and healthy controls from the 200-HIV cohort study. Results Single-cell RNA-seq analysis revealed that most immune cells in peripheral blood of PLHIV are altered in their transcriptomes and that a specific functional monocyte state previously described in acute HIV infection is still existing in PLHIV while other monocyte cell states are only occurring acute infection. Further, a reverse transcriptome approach on a rather small number of PLHIV was sufficient to identify drug candidates for reversing the transcriptional phenotype of monocytes in PLHIV. Discussion These scientific findings and technological advancements for clinical application of single-cell transcriptomics form the basis for the larger 2000-HIV multicenter cohort study on PLHIV, for which a combination of bulk and single-cell transcriptomics will be included as the leading technology to determine disease endotypes in PLHIV and to predict disease trajectories and outcomes.
Collapse
Affiliation(s)
- Rainer Knoll
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Jéssica C. dos Santos
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Stefanie Warnat-Herresthal
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Maartje C. P. Jacobs-Cleophas
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Edda Blümel
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Nico Reusch
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Arik Horne
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Systems Hematology, Stem Cells & Precision Medicine, Max Delbrück Center - Berlin Institute for Medical Systems Biology (MDCBIMSB), Berlin, Germany
| | - Miriam Herbert
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- In Vivo Cell Biology of Infection, Max Planck Institute for Infection Biology (MPIIB), Berlin, Germany
| | - Melanie Nuesch-Germano
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Twan Otten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Wouter A. van der Heijden
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lisa van de Wijer
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alex K. Shalek
- Broad Institute at Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, United States
- Ragon Institute of Mass General Hospital (MGH), MIT, and Harvard, Cambridge, MA, United States
- Department of Chemistry, Institute for Medical Engineering and Science, Koch Institute, Cambridge, MA, United States
| | - Kristian Händler
- Platform for Single Cell Genomics and Epigenomics (PRECISE), DZNE and University of Bonn, Bonn, Germany
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Matthias Becker
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Marc D. Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics (PRECISE), DZNE and University of Bonn, Bonn, Germany
| | - Mihai G. Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Leo A. B. Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andre J. A. M. van der Ven
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Joachim L. Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics (PRECISE), DZNE and University of Bonn, Bonn, Germany
| | - Anna C. Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| |
Collapse
|
3
|
Trifone C, Baquero L, Czernikier A, Benencio P, Leng L, Laufer N, Quiroga MF, Bucala R, Ghiglione Y, Turk G. Macrophage Migration Inhibitory Factor (MIF) Promotes Increased Proportions of the Highly Permissive Th17-like Cell Profile during HIV Infection. Viruses 2022; 14:v14102218. [PMID: 36298774 PMCID: PMC9611675 DOI: 10.3390/v14102218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
In this study, we evaluate the role of the MIF/CD74 axis in the functionality of CD4+ T lymphocytes (CD4TL) during HIV infection. MDMs from healthy donors were infected with a R5-tropic or Transmitted/Founder (T/F) HIV strain. At day 11 post-MDM infection, allogeneic co-cultures with uninfected CD4TLs plus MIF stimulus were performed. Cytokine production was evaluated by ELISA. MIF plasma levels of people with HIV (PWH) were evaluated by ELISA. The phenotype and infection rate of CD4TLs from PWH were analyzed after MIF stimulus. Intracellular cytokines and transcription factors were evaluated by flow cytometry. Data were analyzed by parametric or non-parametric methods. The MIF stimulation of HIV-infected MDMs induced an increased expression of IL-6, IL-1β and IL-8. In CD4TL/MDM co-cultures, the MIF treatment increased IL-17A/RORγt-expressing CD4TLs. Higher concentrations of IL-17A in supernatants were also observed. These results were recapitulated using transmitted/founder (T/F) HIV-1 strains. The MIF treatment appeared to affect memory CD4TLs more than naïve CD4TLs. MIF blocking showed a negative impact on IL17A+CD4TL proportions. Higher MIF concentrations in PWH-derived plasma were correlated with higher IL-17A+CD4TL percentages. Finally, MIF stimulation in PWH-derived PBMCs led to an increase in Th17-like population. MIF may contribute to viral pathogenesis by generating a microenvironment enriched in activating mediators and Th17-like CD4TLs, which are known to be highly susceptible to HIV-1 infection and relevant to viral persistence. These observations establish a basis for considering MIF as a possible therapeutic target.
Collapse
Affiliation(s)
- César Trifone
- Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET—Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - Lucía Baquero
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET—Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - Alejandro Czernikier
- Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET—Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - Paula Benencio
- Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET—Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - Lin Leng
- Department of Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Natalia Laufer
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET—Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - María Florencia Quiroga
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET—Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - Richard Bucala
- Department of Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yanina Ghiglione
- Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET—Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - Gabriela Turk
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET—Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
- Correspondence: ; Tel.: +54-11-4508-3689 (ext. 130); Fax: +54-11-4508-3705
| |
Collapse
|