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Vivanco Gonzalez N, Oliveria JP, Tebaykin D, Ivison GT, Mukai K, Tsai MM, Borges L, Nadeau KC, Galli SJ, Tsai AG, Bendall SC. An optimized protocol for phenotyping human granulocytes by mass cytometry. STAR Protoc 2022; 3:101280. [PMID: 35434655 PMCID: PMC9010787 DOI: 10.1016/j.xpro.2022.101280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Nora Vivanco Gonzalez
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
- Corresponding author
| | - John-Paul Oliveria
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON, L8S4K1, Canada
| | - Dmitry Tebaykin
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Geoffrey T. Ivison
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Kaori Mukai
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Stanford, CA, United States
| | - Mindy M. Tsai
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Stanford, CA, United States
| | - Luciene Borges
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, School of Medicine, Stanford University, Stanford, CA, United States
| | - Stephen J. Galli
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Stanford, CA, United States
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Albert G. Tsai
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Sean C. Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
- Corresponding author
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2
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Ivison GT, Vendrame E, Martínez-Colón GJ, Ranganath T, Vergara R, Zhao NQ, Martin MP, Bendall SC, Carrington M, Cyktor JC, McMahon DK, Eron J, Jones RB, Mellors JW, Bosch RJ, Gandhi RT, Holmes S, Blish CA. Natural Killer Cell Receptors and Ligands Are Associated With Markers of HIV-1 Persistence in Chronically Infected ART Suppressed Patients. Front Cell Infect Microbiol 2022; 12:757846. [PMID: 35223535 PMCID: PMC8866573 DOI: 10.3389/fcimb.2022.757846] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
The latent HIV-1 reservoir represents a major barrier to achieving a long-term antiretroviral therapy (ART)-free remission or cure for HIV-1. Natural Killer (NK) cells are innate immune cells that play a critical role in controlling viral infections and have been shown to be involved in preventing HIV-1 infection and, in those who are infected, delaying time to progression to AIDS. However, their role in limiting HIV-1 persistence on long term ART is still uncharacterized. To identify associations between markers of HIV-1 persistence and the NK cell receptor-ligand repertoire, we used twin mass cytometry panels to characterize the peripheral blood NK receptor-ligand repertoire in individuals with long-term antiretroviral suppression enrolled in the AIDS Clinical Trial Group A5321 study. At the time of testing, participants had been on ART for a median of 7 years, with virological suppression <50 copies/mL since at most 48 weeks on ART. We found that the NK cell receptor and ligand repertoires did not change across three longitudinal samples over one year-a median of 25 weeks and 50 weeks after the initial sampling. To determine the features of the receptor-ligand repertoire that associate with markers of HIV-1 persistence, we performed a LASSO normalized regression. This analysis revealed that the NK cell ligands CD58, HLA-B, and CRACC, as well as the killer cell immunoglobulin-like receptors (KIRs) KIR2DL1, KIR2DL3, and KIR2DS4 were robustly predictive of markers of HIV-1 persistence, as measured by total HIV-1 cell-associated DNA, HIV-1 cell-associated RNA, and single copy HIV-RNA assays. To characterize the roles of cell populations defined by multiple markers, we augmented the LASSO analysis with FlowSOM clustering. This analysis found that a less mature NK cell phenotype (CD16+CD56dimCD57-LILRB1-NKG2C-) was associated with lower HIV-1 cell associated DNA. Finally, we found that surface expression of HLA-Bw6 measured by CyTOF was associated with lower HIV-1 persistence. Genetic analysis revealed that this was driven by lower HIV-1 persistence in HLA-Bw4/6 heterozygotes. These findings suggest that there may be a role for NK cells in controlling HIV-1 persistence in individuals on long-term ART, which must be corroborated by future studies.
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Affiliation(s)
- Geoffrey T Ivison
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States.,Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Elena Vendrame
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Giovanny J Martínez-Colón
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Thanmayi Ranganath
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Rosemary Vergara
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Nancy Q Zhao
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Maureen P Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National, Cancer Institute, Frederick, MD, United States.,Laboratory of Integrative Cancer, Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National, Cancer Institute, Frederick, MD, United States.,Laboratory of Integrative Cancer, Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States.,Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Boston, MA, United States
| | - Joshua C Cyktor
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States
| | - Deborah K McMahon
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States
| | - Joseph Eron
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ronald J Bosch
- Center for Biostatistics in AIDS Research, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Rajesh T Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Center for AIDS Research, Harvard University, Boston, MA, United States
| | - Susan Holmes
- Department of Statistics, School of Humanities and Sciences, Stanford University, Stanford, CA, United States
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Chan Zuckerberg Biohub, San Francisco, CA, United States
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3
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Barnes SE, Zera KA, Ivison GT, Buckwalter MS, Engleman EG. Brain profiling in murine colitis and human epilepsy reveals neutrophils and TNFα as mediators of neuronal hyperexcitability. J Neuroinflammation 2021; 18:199. [PMID: 34511110 PMCID: PMC8436533 DOI: 10.1186/s12974-021-02262-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/30/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Patients with chronic inflammatory disorders such as inflammatory bowel disease frequently experience neurological complications including epilepsy, depression, attention deficit disorders, migraines, and dementia. However, the mechanistic basis for these associations is unknown. Given that many patients are unresponsive to existing medications or experience debilitating side effects, novel therapeutics that target the underlying pathophysiology of these conditions are urgently needed. METHODS Because intestinal disorders such as inflammatory bowel disease are robustly associated with neurological symptoms, we used three different mouse models of colitis to investigate the impact of peripheral inflammatory disease on the brain. We assessed neuronal hyperexcitability, which is associated with many neurological symptoms, by measuring seizure threshold in healthy and colitic mice. We profiled the neuroinflammatory phenotype of colitic mice and used depletion and neutralization assays to identify the specific mediators responsible for colitis-induced neuronal hyperexcitability. To determine whether our findings in murine models overlapped with a human phenotype, we performed gene expression profiling, pathway analysis, and deconvolution on microarray data from hyperexcitable human brain tissue from patients with epilepsy. RESULTS We observed that murine colitis induces neuroinflammation characterized by increased pro-inflammatory cytokine production, decreased tight junction protein expression, and infiltration of monocytes and neutrophils into the brain. We also observed sustained neuronal hyperexcitability in colitic mice. Colitis-induced neuronal hyperexcitability was ameliorated by neutrophil depletion or TNFα blockade. Gene expression profiling of hyperexcitable brain tissue resected from patients with epilepsy also revealed a remarkably similar pathology to that seen in the brains of colitic mice, including neutrophil infiltration and high TNFα expression. CONCLUSIONS Our results reveal neutrophils and TNFα as central regulators of neuronal hyperexcitability of diverse etiology. Thus, there is a strong rationale for evaluating anti-inflammatory agents, including clinically approved TNFα inhibitors, for the treatment of neurological and psychiatric symptoms present in, and potentially independent of, a diagnosed inflammatory disorder.
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Affiliation(s)
- Sarah E Barnes
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kristy A Zera
- Department of Neurology, Stanford University, Stanford, CA, USA
| | - Geoffrey T Ivison
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Infectious Diseases, Stanford University, Stanford, CA, USA
| | | | - Edgar G Engleman
- Department of Pathology, Stanford University, Stanford, CA, USA.
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4
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Vendrame E, McKechnie JL, Ranganath T, Zhao NQ, Rustagi A, Vergara R, Ivison GT, Kronstad LM, Simpson LJ, Blish CA. Profiling of the Human Natural Killer Cell Receptor-Ligand Repertoire. J Vis Exp 2020. [PMID: 33283785 DOI: 10.3791/61912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Natural killer (NK) cells are among the first responders to viral infections. The ability of NK cells to rapidly recognize and kill virally infected cells is regulated by their expression of germline-encoded inhibitory and activating receptors. The engagement of these receptors by their cognate ligands on target cells determines whether the intercellular interaction will result in NK cell killing. This protocol details the design and optimization of two complementary mass cytometry (CyTOF) panels. One panel was designed to phenotype NK cells based on receptor expression. The other panel was designed to interrogate expression of known ligands for NK cell receptors on several immune cell subsets. Together, these two panels allow for the profiling of the human NK cell receptor-ligand repertoire. Furthermore, this protocol also details the process by which we stain samples for CyTOF. This process has been optimized for improved reproducibility and standardization. An advantage of CyTOF is its ability to measure over 40 markers in each panel, with minimal signal overlap, allowing researchers to capture the breadth of the NK cell receptor-ligand repertoire. Palladium barcoding also reduces inter-sample variation, as well as consumption of reagents, making it easier to stain samples with each panel in parallel. Limitations of this protocol include the relatively low throughput of CyTOF and the inability to recover cells after analysis. These panels were designed for the analysis of clinical samples from patients suffering from acute and chronic viral infections, including dengue virus, human immunodeficiency virus (HIV), and influenza. However, they can be utilized in any setting to investigate the human NK cell receptor-ligand repertoire. Importantly, these methods can be applied broadly to the design and execution of future CyTOF panels.
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Affiliation(s)
- Elena Vendrame
- Department of Medicine, Stanford University School of Medicine
| | - Julia L McKechnie
- Department of Medicine, Stanford University School of Medicine; Program in Immunology, Stanford University School of Medicine
| | | | - Nancy Q Zhao
- Department of Medicine, Stanford University School of Medicine; Program in Immunology, Stanford University School of Medicine
| | - Arjun Rustagi
- Department of Medicine, Stanford University School of Medicine
| | | | - Geoffrey T Ivison
- Department of Medicine, Stanford University School of Medicine; Program in Immunology, Stanford University School of Medicine
| | - Lisa M Kronstad
- Department of Medicine, Stanford University School of Medicine
| | - Laura J Simpson
- Department of Medicine, Stanford University School of Medicine
| | - Catherine A Blish
- Department of Medicine, Stanford University School of Medicine; Program in Immunology, Stanford University School of Medicine; Chan-Zuckerberg BioHub;
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5
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Vivanco Gonzalez N, Oliveria JP, Tebaykin D, Ivison GT, Mukai K, Tsai MM, Borges L, Nadeau KC, Galli SJ, Tsai AG, Bendall SC. Mass Cytometry Phenotyping of Human Granulocytes Reveals Novel Basophil Functional Heterogeneity. iScience 2020; 23:101724. [PMID: 33205028 PMCID: PMC7653073 DOI: 10.1016/j.isci.2020.101724] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/18/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023] Open
Abstract
Basophils, the rarest granulocyte, play critical roles in parasite- and allergen-induced inflammation. We applied mass cytometry (CyTOF) to simultaneously asses 44 proteins to phenotype and functionally characterize neutrophils, eosinophils, and basophils from 19 healthy donors. There was minimal heterogeneity seen in eosinophils and neutrophils, but data-driven analyses revealed four unique subpopulations within phenotypically basophilic granulocytes (PBG; CD45+HLA-DR−CD123+). Through CyTOF and fluorescence-activated cell sorting (FACS), we classified these four PBG subpopulations as (I) CD16lowFcεRIhighCD244high (88.5 ± 1.2%), (II) CD16highFcεRIhighCD244high (9.1 ± 0.4%), (III) CD16lowFcεRIlowCD244low (2.3 ± 1.3), and (IV) CD16highFcεRIlowCD244low (0.4 ± 0.1%). Prospective isolation confirmed basophilic-morphology of PBG I–III, but neutrophilic-morphology of PBG IV. Functional interrogation via IgE-crosslinking or IL-3 stimulation demonstrated that PBG I–II had significant increases in CD203c expression, whereas PBG III–IV remained unchanged compared with media-alone conditions. Thus, PBG III–IV could serve roles in non-IgE-mediated immunity. Our findings offer new perspectives in human basophil heterogeneity and the varying functional potential of these new subsets in health and disease. Unsupervised clustering revealed 4 basophil populations, driven by CD16, CD244, and FcεRI The rarest basophil subpopulation IV was morphologically neutrophils Anti-IgE and IL-3 stimulation did not induce functional responses in III and IV Basophil subpopulation heterogeneity was observed in healthy and CML samples
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Affiliation(s)
- Nora Vivanco Gonzalez
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
| | - John-Paul Oliveria
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON, L8S4K1, Canada
| | - Dmitry Tebaykin
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
| | - Geoffrey T. Ivison
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
| | - Kaori Mukai
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Mindy M. Tsai
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Luciene Borges
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Stephen J. Galli
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Albert G. Tsai
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
| | - Sean C. Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
- Corresponding author
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Wilk AJ, Rustagi A, Zhao NQ, Roque J, Martínez-Colón GJ, McKechnie JL, Ivison GT, Ranganath T, Vergara R, Hollis T, Simpson LJ, Grant P, Subramanian A, Rogers AJ, Blish CA. A single-cell atlas of the peripheral immune response in patients with severe COVID-19. Nat Med 2020; 26:1070-1076. [PMID: 32514174 PMCID: PMC7382903 DOI: 10.1038/s41591-020-0944-y] [Citation(s) in RCA: 1034] [Impact Index Per Article: 258.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/19/2020] [Indexed: 02/08/2023]
Abstract
There is an urgent need to better understand the pathophysiology of Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2, which has infected more than three million people worldwide1. Approximately 20% of patients with COVID-19 develop severe disease and 5% of patients require intensive care2. Severe disease has been associated with changes in peripheral immune activity, including increased levels of pro-inflammatory cytokines3,4 that may be produced by a subset of inflammatory monocytes5,6, lymphopenia7,8 and T cell exhaustion9,10. To elucidate pathways in peripheral immune cells that might lead to immunopathology or protective immunity in severe COVID-19, we applied single-cell RNA sequencing (scRNA-seq) to profile peripheral blood mononuclear cells (PBMCs) from seven patients hospitalized for COVID-19, four of whom had acute respiratory distress syndrome, and six healthy controls. We identify reconfiguration of peripheral immune cell phenotype in COVID-19, including a heterogeneous interferon-stimulated gene signature, HLA class II downregulation and a developing neutrophil population that appears closely related to plasmablasts appearing in patients with acute respiratory failure requiring mechanical ventilation. Importantly, we found that peripheral monocytes and lymphocytes do not express substantial amounts of pro-inflammatory cytokines. Collectively, we provide a cell atlas of the peripheral immune response to severe COVID-19.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Betacoronavirus/immunology
- COVID-19
- Case-Control Studies
- Coronavirus Infections/genetics
- Coronavirus Infections/immunology
- Coronavirus Infections/pathology
- Cytokines/genetics
- Cytokines/metabolism
- Female
- Gene Expression Profiling/methods
- Humans
- Immunity, Cellular
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
- Leukocytes, Mononuclear/virology
- Male
- Middle Aged
- Pandemics
- Pneumonia, Viral/genetics
- Pneumonia, Viral/immunology
- Pneumonia, Viral/pathology
- RNA-Seq/methods
- SARS-CoV-2
- Sequence Analysis, RNA/methods
- Severity of Illness Index
- Single-Cell Analysis/methods
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Young Adult
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Affiliation(s)
- Aaron J Wilk
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nancy Q Zhao
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonasel Roque
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Julia L McKechnie
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Geoffrey T Ivison
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Thanmayi Ranganath
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Rosemary Vergara
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Taylor Hollis
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura J Simpson
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Philip Grant
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aruna Subramanian
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Angela J Rogers
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Catherine A Blish
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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7
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Wilk AJ, Rustagi A, Zhao NQ, Roque J, Martinez-Colon GJ, McKechnie JL, Ivison GT, Ranganath T, Vergara R, Hollis T, Simpson LJ, Grant P, Subramanian A, Rogers AJ, Blish CA. A single-cell atlas of the peripheral immune response to severe COVID-19. medRxiv 2020. [PMID: 32511639 DOI: 10.1101/2020.04.17.20069930] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
There is an urgent need to better understand the pathophysiology of Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2. Here, we apply single-cell RNA sequencing (scRNA-seq) to peripheral blood mononuclear cells (PBMCs) of 7 patients hospitalized with confirmed COVID-19 and 6 healthy controls. We identify substantial reconfiguration of peripheral immune cell phenotype in COVID-19, including a heterogeneous interferon-stimulated gene (ISG) signature, HLA class II downregulation, and a novel B cell-derived granulocyte population appearing in patients with acute respiratory failure requiring mechanical ventilation. Importantly, peripheral monocytes and lymphocytes do not express substantial amounts of pro-inflammatory cytokines, suggesting that circulating leukocytes do not significantly contribute to the potential COVID-19 cytokine storm. Collectively, we provide the most thorough cell atlas to date of the peripheral immune response to severe COVID-19.
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8
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Sang AX, McPherson MC, Ivison GT, Qu X, Rigdon J, Esquivel CO, Krams SM, Martinez OM. Dual blockade of the PI3K/Akt/mTOR pathway inhibits posttransplant Epstein-Barr virus B cell lymphomas and promotes allograft survival. Am J Transplant 2019; 19:1305-1314. [PMID: 30549430 PMCID: PMC6482059 DOI: 10.1111/ajt.15216] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 09/19/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 01/25/2023]
Abstract
Posttransplant lymphoproliferative disorder (PTLD) is a serious complication of organ transplantation that often manifests as Epstein-Barr virus (EBV)-associated B cell lymphomas. Current treatments for PTLD have limited efficacy and can be associated with graft rejection or systemic toxicities. The mTOR inhibitor, rapamycin, suppresses tumor growth of EBV+ B cell lymphoma cells in vitro and in vivo; however, the efficacy is limited and clinical benefits of mTOR inhibitors for PTLD are variable. Here, we show constitutive activation of multiple nodes within the PI3K/Akt/mTOR pathway in EBV+ PTLD-derived cell lines. Inhibition of either PI3K or Akt, with specific inhibitors CAL-101 and MK-2206, respectively, diminished growth of EBV+ B cell lines from PTLD patients in a dose-dependent manner. Importantly, rapamycin combined with CAL-101 or MK-2206 had a synergistic effect in suppressing cell growth as determined by IC50 isobolographic analysis and Loewe indices. Moreover, these combinations were significantly more effective than rapamycin alone in inhibiting tumor xenograft growth in NOD-SCID mice. Finally, both CAL-101 and MK-2206 also prolonged survival of heterotopic cardiac allografts in C57BL/6 mice. Thus, combination therapy with rapamycin and a PI3K inhibitor, or an Akt inhibitor, can be an efficacious treatment for EBV-associated PTLD, while simultaneously promoting allograft survival.
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Affiliation(s)
- Adam X Sang
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Marla C McPherson
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Geoffrey T Ivison
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiumei Qu
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph Rigdon
- Quantitative Sciences Unit, Stanford University School of Medicine, Stanford, CA, USA
| | - Carlos O Esquivel
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Sheri M Krams
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA,Stanford Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Olivia M Martinez
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA,Stanford Immunology, Stanford University School of Medicine, Stanford, CA, USA
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9
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Abstract
![]()
Nonheme Fe(II)/αKG-dependent
oxygenases catalyze diverse
reactions, typically inserting an O atom from O2 into a
C–H bond. Although the key to their catalytic cycle is the
fact that binding and positioning of primary substrate precede O2 activation, the means by which substrate binding stimulates
turnover is not well understood. Factor Inhibiting HIF (FIH) is a
Fe(II)/αKG-dependent oxygenase that acts as a cellular oxygen
sensor in humans by hydroxylating the target residue Asn803, found in the C-terminal transactivation domain (CTAD) of hypoxia
inducible factor-1. FIH-Gln239 makes two hydrogen bonds
with CTAD-Asn803, positioning this target residue over
the Fe(II). We hypothesized the positioning of the side chain of CTAD-Asn803 by FIH-Gln239 was critical for stimulating O2 activation and subsequent substrate hydroxylation. The steady-state
characterization of five FIH-Gln239 variants (Ala, Asn,
Glu, His, and Leu) tested the role of hydrogen bonding potential and
sterics near the target residue. Each variant exhibited a 20–1200-fold
decrease in kcat and kcat/KM(CTAD), but no change
in KM(CTAD), indicating that the step
after CTAD binding was affected by point mutation. Uncoupled O2 activation was prominent in these variants, as shown by large
coupling ratios (C = [succinate]/[CTAD-OH] = 3–5)
for each of the FIH-Gln239 → X variants. The coupling
ratios decreased in D2O, indicating an isotope-sensitive
inactivation for variants, not observed in the wild type. The data
presented indicate that the proper positioning of CTAD-Asn803 by FIH-Gln239 is necessary to suppress uncoupled turnover
and to support substrate hydroxylation, suggesting substrate positioning
may be crucial for directing O2 reactivity within the broader
class of αKG hydroxylases.
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Affiliation(s)
- John A Hangasky
- Department of Chemistry, University of Massachusetts at Amherst , Amherst, Massachusetts 01003, United States
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