1
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Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG. Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis. Nat Commun 2024; 15:1493. [PMID: 38374043 PMCID: PMC10876948 DOI: 10.1038/s41467-024-45665-6] [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: 01/21/2023] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we perform single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.
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Affiliation(s)
- Elvira Mennillo
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Gyehyun Lee
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Iulia Rusu
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ravi K Patel
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | | | - Emily Flynn
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Stephanie Li
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jared L Bain
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christopher Andersen
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Arjun Rao
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Stanley Tamaki
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Tsui
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Alan Shen
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Madison L Lotstein
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Maha Rahim
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mohammad Naser
- Biological Imaging Development CoLab, University of California San Francisco, San Francisco, CA, USA
| | | | - Walter Eckalbar
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Soo-Jin Cho
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Kendall Beck
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Najwa El-Nachef
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sara Lewin
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Daniel R Selvig
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan P Terdiman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Uma Mahadevan
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David Y Oh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gabriela K Fragiadakis
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | | | - Alexis J Combes
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Michael G Kattah
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
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2
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Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG. Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis. bioRxiv 2024:2023.01.21.525036. [PMID: 36711576 PMCID: PMC9882264 DOI: 10.1101/2023.01.21.525036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we performed single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.
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3
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Locher V, Park S, Bunis DG, Makredes S, Mayer M, Burt TD, Fragiadakis GK, Halkias J. Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans. JCI Insight 2023; 8:e164672. [PMID: 37856221 PMCID: PMC10721317 DOI: 10.1172/jci.insight.164672] [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: 08/29/2022] [Accepted: 10/11/2023] [Indexed: 10/21/2023] Open
Abstract
The development of human prenatal adaptive immunity progresses faster than previously appreciated, with the emergence of memory CD4+ T cells alongside regulatory T cells by midgestation. We previously identified a prenatal specific population of promyelocytic leukemia zinc finger-positive (PLZF+) CD4+ T cells with heightened effector potential that were enriched in the developing intestine and accumulated in the cord blood of infants exposed to prenatal inflammation. However, the signals that drive their tissue distribution and effector maturation are unknown. Here, we define the transcriptional and functional heterogeneity of human prenatal PLZF+CD4+ T cells and identify the compartmentalization of T helper-like (Th-like) effector function across the small intestine (SI) and mesenteric lymph nodes (MLNs). IL-7 was more abundant in the SI relative to the MLNs and drove the preferential expansion of naive PLZF+CD4+ T cells via enhanced STAT5 and MEK/ERK signaling. Exposure to IL-7 was sufficient to induce the acquisition of CD45RO expression and rapid effector function in a subset of PLZF+CD4+ T cells, identifying a human analog of memory phenotype CD4+ T cells. Further, IL-7 modulated the differentiation of Th1- and Th17-like PLZF+CD4+ T cells and thus likely contributes to the anatomic compartmentalization of human prenatal CD4+ T cell effector function.
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Affiliation(s)
- Veronica Locher
- Division of Neonatology, Department of Pediatrics, and
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
| | - Sara Park
- Division of Neonatology, Department of Pediatrics, and
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
| | - Daniel G. Bunis
- Bakar ImmunoX Initiative and
- CoLabs, UCSF, San Francisco, California, USA
| | - Stephanie Makredes
- Division of Neonatology, Department of Pediatrics, and
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
| | - Margareta Mayer
- Division of Neonatology, Department of Pediatrics, and
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
| | - Trevor D. Burt
- Division of Neonatology and the Children’s Health & Discovery Initiative, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Gabriela K. Fragiadakis
- Bakar ImmunoX Initiative and
- CoLabs, UCSF, San Francisco, California, USA
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Joanna Halkias
- Division of Neonatology, Department of Pediatrics, and
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
- Bakar ImmunoX Initiative and
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4
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Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Network I, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf J, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar W, Maecker H, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Augustine AD, Sekaly RP, Ehrlich LIR, Fourati S, Peters B, Kleinstein SH, Guan L. Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants. bioRxiv 2023:2023.11.03.565292. [PMID: 37986828 PMCID: PMC10659275 DOI: 10.1101/2023.11.03.565292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Hospitalized COVID-19 patients exhibit diverse clinical outcomes, with some individuals diverging over time even though their initial disease severity appears similar. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity. In this study, we carried out deep immunophenotyping and conducted longitudinal multi-omics modeling integrating ten distinct assays on a total of 1,152 IMPACC participants and identified several immune cascades that were significant drivers of differential clinical outcomes. Increasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, NETosis, and T-cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma immunoglobulins and B cells, as well as dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to the failure of viral clearance in patients with fatal illness. Our longitudinal multi-omics profiling study revealed novel temporal coordination across diverse omics that potentially explain disease progression, providing insights that inform the targeted development of therapies for hospitalized COVID-19 patients, especially those critically ill.
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Hackney JA, Shivram H, Vander Heiden J, Overall C, Orozco L, Gao X, Kim E, West N, Qamra A, Chang D, Chakrabarti A, Choy DF, Combes AJ, Courau T, Fragiadakis GK, Rao AA, Ray A, Tsui J, Hu K, Kuhn NF, Krummel MF, Erle DJ, Kangelaris K, Sarma A, Lyon Z, Calfee CS, Woodruff PG, Ghale R, Mick E, Byrne A, Zha BS, Langelier C, Hendrickson CM, van der Wijst MGP, Hartoularos GC, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Ye CJ, Ramalingam T, McBride JM, Cai F, Teterina A, Bao M, Tsai L, Rosas IO, Regev A, Kapadia SB, Bauer RN, Rosenberger CM. A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling. iScience 2023; 26:107813. [PMID: 37810211 PMCID: PMC10551843 DOI: 10.1016/j.isci.2023.107813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/12/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023] Open
Abstract
Altered myeloid inflammation and lymphopenia are hallmarks of severe infections. We identified the upregulated EN-RAGE gene program in airway and blood myeloid cells from patients with acute lung injury from SARS-CoV-2 or other causes across 7 cohorts. This program was associated with greater clinical severity and predicted future mechanical ventilation and death. EN-RAGEhi myeloid cells express features consistent with suppressor cell functionality, including low HLA-DR and high PD-L1. Sustained EN-RAGE program expression in airway and blood myeloid cells correlated with clinical severity and increasing expression of T cell dysfunction markers. IL-6 upregulated many EN-RAGE program genes in monocytes in vitro. IL-6 signaling blockade by tocilizumab in a placebo-controlled clinical trial led to rapid normalization of EN-RAGE and T cell gene expression. This identifies IL-6 as a key driver of myeloid dysregulation associated with worse clinical outcomes in COVID-19 patients and provides insights into shared pathophysiological mechanisms in non-COVID-19 ARDS.
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Affiliation(s)
- Jason A Hackney
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Haridha Shivram
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Chris Overall
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Luz Orozco
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xia Gao
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eugene Kim
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nathan West
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Aditi Qamra
- Hoffman-La Roche Limited, 7070 Mississauga Road, Mississauga, ON L5N 5M8, Canada
| | - Diana Chang
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - David F Choy
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Alexis J Combes
- University of California San Francisco, San Francisco, CA, USA
| | - Tristan Courau
- University of California San Francisco, San Francisco, CA, USA
| | | | - Arjun Arkal Rao
- University of California San Francisco, San Francisco, CA, USA
| | - Arja Ray
- University of California San Francisco, San Francisco, CA, USA
| | - Jessica Tsui
- University of California San Francisco, San Francisco, CA, USA
| | - Kenneth Hu
- University of California San Francisco, San Francisco, CA, USA
| | - Nicholas F Kuhn
- University of California San Francisco, San Francisco, CA, USA
| | | | - David J Erle
- University of California San Francisco, San Francisco, CA, USA
| | | | - Aartik Sarma
- University of California San Francisco, San Francisco, CA, USA
| | - Zoe Lyon
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Rajani Ghale
- University of California San Francisco, San Francisco, CA, USA
| | - Eran Mick
- University of California San Francisco, San Francisco, CA, USA
| | - Ashley Byrne
- University of California San Francisco, San Francisco, CA, USA
| | | | | | | | - Monique G P van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Tianna Grant
- University of California San Francisco, San Francisco, CA, USA
| | - Raymund Bueno
- University of California San Francisco, San Francisco, CA, USA
| | - David S Lee
- University of California San Francisco, San Francisco, CA, USA
| | | | - Yang Sun
- University of California San Francisco, San Francisco, CA, USA
| | - Richard Perez
- University of California San Francisco, San Francisco, CA, USA
| | | | - Alyssa Ward
- University of California San Francisco, San Francisco, CA, USA
| | - Chun Jimmie Ye
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Fang Cai
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Anastasia Teterina
- Hoffman-La Roche Limited, 7070 Mississauga Road, Mississauga, ON L5N 5M8, Canada
| | - Min Bao
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Larry Tsai
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ivan O Rosas
- Baylor College of Medicine, 7200 Cambridge St, Houston, TX 77030, USA
| | - Aviv Regev
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Rebecca N Bauer
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
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6
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Patel RK, Jaszczak RG, Im K, Carey ND, Courau T, Bunis DG, Samad B, Avanesyan L, Chew NW, Stenske S, Jespersen JM, Publicover J, Edwards AW, Naser M, Rao AA, Lupin-Jimenez L, Krummel MF, Cooper S, Baron JL, Combes AJ, Fragiadakis GK. Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data. Front Immunol 2023; 14:1167241. [PMID: 37731497 PMCID: PMC10507399 DOI: 10.3389/fimmu.2023.1167241] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/04/2023] [Indexed: 09/22/2023] Open
Abstract
In the past decade, high-dimensional single-cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the data generated by these approaches often requires clustering algorithms and dimensionality reduction representation, which are computationally intense and difficult to evaluate and optimize. Here, we present Cytometry Clustering Optimization and Evaluation (Cyclone), an analysis pipeline integrating dimensionality reduction, clustering, evaluation, and optimization of clustering resolution, and downstream visualization tools facilitating the analysis of a wide range of cytometry data. We benchmarked and validated Cyclone on mass cytometry (CyTOF), full-spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF) in a variety of biological contexts, including infectious diseases and cancer. In each instance, Cyclone not only recapitulates gold standard immune cell identification but also enables the unsupervised identification of lymphocytes and mononuclear phagocyte subsets that are associated with distinct biological features. Altogether, the Cyclone pipeline is a versatile and accessible pipeline for performing, optimizing, and evaluating clustering on a variety of cytometry datasets, which will further power immunology research and provide a scaffold for biological discovery.
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Affiliation(s)
- Ravi K. Patel
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Rebecca G. Jaszczak
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Kwok Im
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
| | - Nicholas D. Carey
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
| | - Tristan Courau
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, United States
| | - Daniel G. Bunis
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Bushra Samad
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Lia Avanesyan
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- The Ibrahim El-Hefni Liver Biorepository at California Pacific Medical Center (IELBC), San Francisco, CA, United States
- Division of General and Transplant Hepatology, California Pacific Medical Center & Research Institute, San Francisco, CA, United States
| | - Nayvin W. Chew
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
| | - Sarah Stenske
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
| | - Jillian M. Jespersen
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
| | - Jean Publicover
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
| | - Austin W. Edwards
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Mohammad Naser
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Arjun A. Rao
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Leonard Lupin-Jimenez
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
| | - Matthew F. Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, United States
| | - Stewart Cooper
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- The Ibrahim El-Hefni Liver Biorepository at California Pacific Medical Center (IELBC), San Francisco, CA, United States
- Division of General and Transplant Hepatology, California Pacific Medical Center & Research Institute, San Francisco, CA, United States
| | - Jody L. Baron
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- The Ibrahim El-Hefni Liver Biorepository at California Pacific Medical Center (IELBC), San Francisco, CA, United States
| | - Alexis J. Combes
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, United States
| | - Gabriela K. Fragiadakis
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
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7
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Flynn E, Almonte-Loya A, Fragiadakis GK. Single-Cell Multiomics. Annu Rev Biomed Data Sci 2023; 6:313-337. [PMID: 37159875 DOI: 10.1146/annurev-biodatasci-020422-050645] [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] [Indexed: 05/11/2023]
Abstract
Single-cell RNA sequencing methods have led to improved understanding of the heterogeneity and transcriptomic states present in complex biological systems. Recently, the development of novel single-cell technologies for assaying additional modalities, specifically genomic, epigenomic, proteomic, and spatial data, allows for unprecedented insight into cellular biology. While certain technologies collect multiple measurements from the same cells simultaneously, even when modalities are separately assayed in different cells, we can apply novel computational methods to integrate these data. The application of computational integration methods to multimodal paired and unpaired data results in rich information about the identities of the cells present and the interactions between different levels of biology, such as between genetic variation and transcription. In this review, we both discuss the single-cell technologies for measuring these modalities and describe and characterize a variety of computational integration methods for combining the resulting data to leverage multimodal information toward greater biological insight.
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Affiliation(s)
- Emily Flynn
- CoLabs, University of California, San Francisco, California, USA;
| | - Ana Almonte-Loya
- CoLabs, University of California, San Francisco, California, USA;
- Biomedical Informatics Program, University of California, San Francisco, California, USA
| | - Gabriela K Fragiadakis
- CoLabs, University of California, San Francisco, California, USA;
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
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8
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Neyton LPA, Patel RK, Sarma A, Willmore A, Haller SC, Kangelaris KN, Eckalbar WL, Erle DJ, Krummel MF, Hendrickson CM, Woodruff PG, Langelier CR, Calfee CS, Fragiadakis GK. Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19. Res Sq 2023:rs.3.rs-3168149. [PMID: 37577607 PMCID: PMC10418533 DOI: 10.21203/rs.3.rs-3168149/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Dexamethasone is the standard of care for critically ill patients with COVID-19, but the mechanisms by which it decreases mortality and its immunological effects in this setting are not understood. We performed bulk and single-cell RNA sequencing of the lower respiratory tract and blood, and plasma cytokine profiling to study the effect of dexamethasone on systemic and pulmonary immune cells. We find decreased signatures of antigen presentation, T cell recruitment, and viral injury in patients treated with dexamethasone. We identify compartment- and cell- specific differences in the effect of dexamethasone in patients with severe COVID-19 that are reproducible in publicly available datasets. Our results highlight the importance of studying compartmentalized inflammation in critically ill patients.
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Affiliation(s)
- Lucile P A Neyton
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Ravi K Patel
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Aartik Sarma
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Andrew Willmore
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Sidney C Haller
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Walter L Eckalbar
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - David J Erle
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Lung Biology Center, University of California, San Francisco, CA, USA
| | - Matthew F Krummel
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Carolyn M Hendrickson
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Prescott G Woodruff
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Charles R Langelier
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Carolyn S Calfee
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Anesthesia, University of California, San Francisco, CA, USA
| | - Gabriela K Fragiadakis
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
- Division of Rheumatology, University of California, San Francisco, CA, USA
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9
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Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio OM, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, Li JZ, Ding VW, Matsumoto S, Maishan M, Sreekumar B, Simoneau C, Nazarenko I, Tomlinson MG, Khan K, von Gottberg A, Sigal A, Looney MR, Fragiadakis GK, Jablons DM, Langelier CR, Matthay M, Krummel M, Erle DJ, Combes AJ, Sil A, Ott M, Kratz JR, Roose JP. SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants. Stem Cell Reports 2023; 18:636-653. [PMID: 36827975 PMCID: PMC9948283 DOI: 10.1016/j.stemcr.2023.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/25/2023] Open
Abstract
Ancestral SARS coronavirus-2 (SARS-CoV-2) and variants of concern (VOC) caused a global pandemic with a spectrum of disease severity. The mechanistic explaining variations related to airway epithelium are relatively understudied. Here, we biobanked airway organoids (AO) by preserving stem cell function. We optimized viral infection with H1N1/PR8 and comprehensively characterized epithelial responses to SARS-CoV-2 infection in phenotypically stable AO from 20 different subjects. We discovered Tetraspanin-8 (TSPAN8) as a facilitator of SARS-CoV-2 infection. TSPAN8 facilitates SARS-CoV-2 infection rates independently of ACE2-Spike interaction. In head-to-head comparisons with Ancestral SARS-CoV-2, Delta and Omicron VOC displayed lower overall infection rates of AO but triggered changes in epithelial response. All variants shared highest tropism for ciliated and goblet cells. TSPAN8-blocking antibodies diminish SARS-CoV-2 infection and may spur novel avenues for COVID-19 therapy.
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Affiliation(s)
- Lisiena Hysenaj
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Samantha Little
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Kayla Kulhanek
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Melia Magnen
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kriti Bahl
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Oghenekevwe M Gbenedio
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Morgan Prinz
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Lauren Rodriguez
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher Andersen
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Arjun Arkal Rao
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alan Shen
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Leonard C Lupin-Jimenez
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Luke R Bonser
- Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nina K Serwas
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eran Mick
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Mir M Khalid
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Taha Y Taha
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Renuka Kumar
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jack Z Li
- Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Vivianne W Ding
- Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Shotaro Matsumoto
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mazharul Maishan
- Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bharath Sreekumar
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Camille Simoneau
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Irina Nazarenko
- Institute for Infection Prevention and Hospital Epidemiology, University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; German Cancer Consortium, Partner Site Freiburg and German Cancer Research Center, Heidelberg, Germany
| | - Michael G Tomlinson
- School of Biosciences, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, Midlands, UK
| | - Khajida Khan
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; SAMRC Antibody Immunity Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Max Planck Institute for Infection Biology, Berlin, Germany; Centre for the AIDS Program of Research, Durban, South Africa
| | - Mark R Looney
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA
| | - Gabriela K Fragiadakis
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David M Jablons
- Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charles R Langelier
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Michael Matthay
- Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew Krummel
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David J Erle
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Pulmonary and Critical Care, San Francisco, San Francisco, CA, USA
| | - Alexis J Combes
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institute of Virology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute COVID-19 Research Group, University of California, San Francisco, San Francisco, CA, USA
| | - Johannes R Kratz
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA; Department of Surgery, Division of Cardiothoracic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
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10
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Patel RK, Jaszczak RG, Kwok I, Carey ND, Courau T, Bunis D, Samad B, Avanesyan L, Chew NW, Stenske S, Jespersen JM, Publicover J, Edwards A, Naser M, Rao AA, Lupin-Jimenez L, Krummel MF, Cooper S, Baron J, Combes AJ, Fragiadakis GK. Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data. bioRxiv 2023:2023.03.08.531782. [PMID: 36945648 PMCID: PMC10028883 DOI: 10.1101/2023.03.08.531782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
In the past decade, high-dimensional single cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the data generated by these approaches often requires clustering algorithms and dimensionality reduction representation which are computationally intense and difficult to evaluate and optimize. Here we present Cyclone, an analysis pipeline integrating dimensionality reduction, clustering, evaluation and optimization of clustering resolution, and downstream visualization tools facilitating the analysis of a wide range of cytometry data. We benchmarked and validated Cyclone on mass cytometry (CyTOF), full spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF) in a variety of biological contexts, including infectious diseases and cancer. In each instance, Cyclone not only recapitulates gold standard immune cell identification, but also enables the unsupervised identification of lymphocytes and mononuclear phagocytes subsets that are associated with distinct biological features. Altogether, the Cyclone pipeline is a versatile and accessible pipeline for performing, optimizing, and evaluating clustering on variety of cytometry datasets which will further power immunology research and provide a scaffold for biological discovery.
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11
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Wastyk HC, Perelman D, Topf M, Fragiadakis GK, Robinson JL, Sonnenburg JL, Gardner CD, Sonnenburg ED. Randomized controlled trial demonstrates response to a probiotic intervention for metabolic syndrome that may correspond to diet. Gut Microbes 2023; 15:2178794. [PMID: 36803658 PMCID: PMC9980610 DOI: 10.1080/19490976.2023.2178794] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
An individual's immune and metabolic status is coupled to their microbiome. Probiotics offer a promising, safe route to influence host health, possibly via the microbiome. Here, we report an 18-week, randomized prospective study that explores the effects of a probiotic vs. placebo supplement on 39 adults with elevated parameters of metabolic syndrome. We performed longitudinal sampling of stool and blood to profile the human microbiome and immune system. While we did not see changes in metabolic syndrome markers in response to the probiotic across the entire cohort, there were significant improvements in triglycerides and diastolic blood pressure in a subset of probiotic arm participants. Conversely, the non-responders had increased blood glucose and insulin levels over time. The responders had a distinct microbiome profile at the end of the intervention relative to the non-responders and placebo arm. Importantly, diet was a key differentiating factor between responders and non-responders. Our results show participant-specific effects of a probiotic supplement on improving parameters of metabolic syndrome and suggest that dietary factors may enhance stability and efficacy of the supplement.
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Affiliation(s)
- Hannah C. Wastyk
- Department of Bioengineering, Stanford School of Medicine, Stanford, CA, USA
| | - Dalia Perelman
- Stanford Prevention Research Center, Department of Medicine, Stanford School of 4Medicine, Stanford, CA, USA
| | - Madeline Topf
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA
| | | | - Jennifer L. Robinson
- Stanford Prevention Research Center, Department of Medicine, Stanford School of 4Medicine, Stanford, CA, USA
| | - Justin L. Sonnenburg
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA,Center for Human Microbiome Studies, Stanford School of Medicine, Stanford University, Stanford, CA, USA,Chan Zuckerberg Biohub, San Francisco, CA, USA,CONTACT Justin L. Sonnenburg Microbiology & Immunology, Stanford School of Medicine, Stanford, CA94305, USA
| | - Christopher D. Gardner
- Stanford Prevention Research Center, Department of Medicine, Stanford School of 4Medicine, Stanford, CA, USA,Christopher D. Gardner Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA94305, USA
| | - Erica D. Sonnenburg
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA,Center for Human Microbiome Studies, Stanford School of Medicine, Stanford University, Stanford, CA, USA,Erica D. Sonnenburg Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, 94305, USA
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12
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Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LI, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, Altman MC, Becker PM, Rouphael N, Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LI, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, McEnaney K, Barton B, Lentucci C, Saluvan M, Chang AC, Hoch A, Albert M, Shaheen T, Kho AT, Thomas S, Chen J, Murphy MD, Cooney M, Presnell S, Fragiadakis GK, Patel R, Guan L, Gygi J, Pawar S, Brito A, Khalil Z, Maguire C, Fourati S, Overton JA, Vita R, Westendorf K, Salehi-Rad R, Leligdowicz A, Matthay MA, Singer JP, Kangelaris KN, Hendrickson CM, Krummel MF, Langelier CR, Woodruff PG, Powell DL, Kim JN, Simmons B, Goonewardene IM, Smith CM, Martens M, Mosier J, Kimura H, Sherman AC, Walsh SR, Issa NC, Dela Cruz C, Farhadian S, Iwasaki A, Ko AI, Chinthrajah S, Ahuja N, Rogers AJ, Artandi M, Siegel SA, Lu Z, Drevets DA, Brown BR, Anderson ML, Guirgis FW, Thyagarajan RV, Rousseau JF, Wylie D, Busch J, Gandhi S, Triplett TA, Yendewa G, Giddings O, Anderson EJ, Mehta AK, Sevransky JE, Khor B, Rahman A, Stadlbauer D, Dutta J, Xie H, Kim-Schulze S, Gonzalez-Reiche AS, van de Guchte A, Farrugia K, Khan Z, Maecker HT, Elashoff D, Brook J, Ramires-Sanchez E, Llamas M, Rivera A, Perdomo C, Ward DC, Magyar CE, Fulcher JA, Abe-Jones Y, Asthana S, Beagle A, Bhide S, Carrillo SA, Chak S, Fragiadakis GK, Ghale R, Gonzalez A, Jauregui A, Jones N, Lea T, Lee D, Lota R, Milush J, Nguyen V, Pierce L, Prasad PA, Rao A, Samad B, Shaw C, Sigman A, Sinha P, Ward A, Willmore A, Zhan J, Rashid S, Rodriguez N, Tang K, Altamirano LT, Betancourt L, Curiel C, Sutter N, Paz MT, Tietje-Ulrich G, Leroux C, Connors J, Bernui M, Kutzler MA, Edwards C, Lee E, Lin E, Croen B, Semenza NC, Rogowski B, Melnyk N, Woloszczuk K, Cusimano G, Bell MR, Furukawa S, McLin R, Marrero P, Sheidy J, Tegos GP, Nagle C, Mege N, Ulring K, Seyfert-Margolis V, Conway M, Francisco D, Molzahn A, Erickson H, Wilson CC, Schunk R, Sierra B, Hughes T, Smolen K, Desjardins M, van Haren S, Mitre X, Cauley J, Li X, Tong A, Evans B, Montesano C, Licona JH, Krauss J, Chang JBP, Izaguirre N, Chaudhary O, Coppi A, Fournier J, Mohanty S, Muenker MC, Nelson A, Raddassi K, Rainone M, Ruff WE, Salahuddin S, Schulz WL, Vijayakumar P, Wang H, Wunder Jr. E, Young HP, Zhao Y, Saksena M, Altman D, Kojic E, Srivastava K, Eaker LQ, Bermúdez-González MC, Beach KF, Sominsky LA, Azad AR, Carreño JM, Singh G, Raskin A, Tcheou J, Bielak D, Kawabata H, Mulder LCF, Kleiner G, Lee AS, Do ED, Fernandes A, Manohar M, Hagan T, Blish CA, Din HN, Roque J, Yang S, Brunton A, Sullivan PE, Strnad M, Lyski ZL, Coulter FJ, Booth JL, Sinko LA, Moldawer LL, Borresen B, Roth-Manning B, Song LZ, Nelson E, Lewis-Smith M, Smith J, Tipan PG, Siles N, Bazzi S, Geltman J, Hurley K, Gabriele G, Sieg S, Vaysman T, Bristow L, Hussaini L, Hellmeister K, Samaha H, Cheng A, Spainhour C, Scherer EM, Johnson B, Bechnak A, Ciric CR, Hewitt L, Carter E, Mcnair N, Panganiban B, Huerta C, Usher J, Ribeiro SP, Altman MC, Becker PM, Rouphael N. Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. EBioMedicine 2022; 83:104208. [PMID: 35952496 PMCID: PMC9359694 DOI: 10.1016/j.ebiom.2022.104208] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 03/24/2022] [Revised: 07/11/2022] [Accepted: 07/25/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Better understanding of the association between characteristics of patients hospitalized with coronavirus disease 2019 (COVID-19) and outcome is needed to further improve upon patient management. METHODS Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) is a prospective, observational study of 1164 patients from 20 hospitals across the United States. Disease severity was assessed using a 7-point ordinal scale based on degree of respiratory illness. Patients were prospectively surveyed for 1 year after discharge for post-acute sequalae of COVID-19 (PASC) through quarterly surveys. Demographics, comorbidities, radiographic findings, clinical laboratory values, SARS-CoV-2 PCR and serology were captured over a 28-day period. Multivariable logistic regression was performed. FINDINGS The median age was 59 years (interquartile range [IQR] 20); 711 (61%) were men; overall mortality was 14%, and 228 (20%) required invasive mechanical ventilation. Unsupervised clustering of ordinal score over time revealed distinct disease course trajectories. Risk factors associated with prolonged hospitalization or death by day 28 included age ≥ 65 years (odds ratio [OR], 2.01; 95% CI 1.28-3.17), Hispanic ethnicity (OR, 1.71; 95% CI 1.13-2.57), elevated baseline creatinine (OR 2.80; 95% CI 1.63- 4.80) or troponin (OR 1.89; 95% 1.03-3.47), baseline lymphopenia (OR 2.19; 95% CI 1.61-2.97), presence of infiltrate by chest imaging (OR 3.16; 95% CI 1.96-5.10), and high SARS-CoV2 viral load (OR 1.53; 95% CI 1.17-2.00). Fatal cases had the lowest ratio of SARS-CoV-2 antibody to viral load levels compared to other trajectories over time (p=0.001). 589 survivors (51%) completed at least one survey at follow-up with 305 (52%) having at least one symptom consistent with PASC, most commonly dyspnea (56% among symptomatic patients). Female sex was the only associated risk factor for PASC. INTERPRETATION Integration of PCR cycle threshold, and antibody values with demographics, comorbidities, and laboratory/radiographic findings identified risk factors for 28-day outcome severity, though only female sex was associated with PASC. Longitudinal clinical phenotyping offers important insights, and provides a framework for immunophenotyping for acute and long COVID-19. FUNDING NIH.
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Affiliation(s)
- Al Ozonoff
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | - Joanna Schaenman
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, United States
| | | | - Carly E. Milliren
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | - Carolyn S. Calfee
- University of California San Francisco School of Medicine, San Francisco, CA, United States
| | - Charles B. Cairns
- Drexel University/Tower Health Hospital, Philadelphia, PA, United States
| | - Monica Kraft
- University of Arizona, Tucson, AZ, United States
| | - Lindsey R. Baden
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, United States
| | - Albert C. Shaw
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Denise A. Esserman
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Shanshan Liu
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David A. Hafler
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Ruth R. Montgomery
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Steven H. Kleinstein
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Ofer Levy
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, United States
| | | | - Elias K. Haddad
- Drexel University/Tower Health Hospital, Philadelphia, PA, United States
| | - David J. Erle
- University of California San Francisco School of Medicine, San Francisco, CA, United States
| | | | | | | | | | | | | | - Jordan P. Metcalf
- Oklahoma University Health Sciences Center, Oklahoma, OK, United States
| | - Mark A. Atkinson
- University of Florida, Gainesville and University of South Florida, Tampa, FL, United States
| | - Scott C. Brakenridge
- University of Florida, Gainesville and University of South Florida, Tampa, FL, United States
| | - David Corry
- Baylor College of Medicine, and the Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX, United States
| | - Farrah Kheradmand
- Baylor College of Medicine, and the Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX, United States
| | | | - Esther Melamed
- The University of Texas at Austin, Austin, TX, United States
| | | | - Rafick Sekaly
- Case Western Reserve University, Cleveland, OH, United States
| | - Joann Diray-Arce
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alison D. Augustine
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, United States
| | - Elaine F. Reed
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, United States
| | | | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, United States
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13
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Belonwu SA, Li Y, Bunis DG, Rao AA, Solsberg CW, Oskotsky T, Taubes AL, Grone B, Zalocusky KA, Fragiadakis GK, Huang Y, Sirota M. Bioinformatics Analysis of Publicly Available Single-Nuclei Transcriptomics Alzheimer’s Disease Datasets Reveals APOE Genotype-Specific Changes Across Cell Types in Two Brain Regions. Front Aging Neurosci 2022; 14:749991. [PMID: 35572130 PMCID: PMC9093608 DOI: 10.3389/fnagi.2022.749991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Alzheimer’s Disease (AD) is a complex neurodegenerative disease that gravely affects patients and imposes an immense burden on caregivers. Apolipoprotein E4 (APOE4) has been identified as the most common genetic risk factor for AD, yet the molecular mechanisms connecting APOE4 to AD are not well understood. Past transcriptomic analyses in AD have revealed APOE genotype-specific transcriptomic differences; however, these differences have not been explored at a single-cell level. To elucidate more complex APOE genotype-specific disease-relevant changes masked by the bulk analysis, we leverage the first two single-nucleus RNA sequencing AD datasets from human brain samples, including nearly 55,000 cells from the prefrontal and entorhinal cortices. In each brain region, we performed a case versus control APOE genotype-stratified differential gene expression analysis and pathway network enrichment in astrocytes, microglia, neurons, oligodendrocytes, and oligodendrocyte progenitor cells. We observed more global transcriptomic changes in APOE4 positive AD cells and identified differences across APOE genotypes primarily in glial cell types. Our findings highlight the differential transcriptomic perturbations of APOE isoforms at a single-cell level in AD pathogenesis and have implications for precision medicine development in the diagnosis and treatment of AD.
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Affiliation(s)
- Stella A. Belonwu
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Yaqiao Li
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Daniel G. Bunis
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- CoLabs, University of California, San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, United States
| | - Arjun Arkal Rao
- CoLabs, University of California, San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Caroline Warly Solsberg
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
- Memory and Aging Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Alice L. Taubes
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institute of Neurological Disease, San Francisco, CA, United States
| | - Brian Grone
- Gladstone Institute of Neurological Disease, San Francisco, CA, United States
| | - Kelly A. Zalocusky
- Gladstone Institute of Neurological Disease, San Francisco, CA, United States
| | - Gabriela K. Fragiadakis
- CoLabs, University of California, San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, United States
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Yadong Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institute of Neurological Disease, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Marina Sirota,
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14
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Fragiadakis GK, Bjornson-Hooper ZB, Madhireddy D, Sachs K, Chen H, McIlwain DR, Spitzer MH, Bendall SC, Nolan GP. Variation of Immune Cell Responses in Humans Reveals Sex-Specific Coordinated Signaling Across Cell Types. Front Immunol 2022; 13:867016. [PMID: 35419006 PMCID: PMC8995898 DOI: 10.3389/fimmu.2022.867016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 12/28/2022] Open
Abstract
Assessing the health and competence of the immune system is central to evaluating vaccination responses, autoimmune conditions, cancer prognosis, and treatment. With an increasing number of studies examining immune dysregulation, there is a growing need for a curated reference of variation in immune parameters in healthy individuals. We used mass cytometry (CyTOF) to profile blood from 86 humans in response to 15 ex vivo immune stimuli. We present reference ranges for cell-specific immune markers and highlight differences that appear across sex and age. We identified modules of immune features that suggest there exists an underlying structure to the immune system based on signaling pathway responses across cell types. We observed increased MAPK signaling in inflammatory pathways in innate immune cells and greater overall coordination of immune cell responses in females. In contrast, males exhibited stronger pSTAT1 and pTBK1 responses. These reference data are publicly available as a resource for immune profiling studies.
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Affiliation(s)
- Gabriela K Fragiadakis
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States.,Department of Medicine, Division of Rheumatology, University of California San Francisco, San Francisco, CA, United States.,CoLabs, University of California San Francisco, San Francisco, CA, United States.,Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
| | | | - Deepthi Madhireddy
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
| | - Karen Sachs
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
| | - Han Chen
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
| | - David R McIlwain
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
| | - Matthew H Spitzer
- Immunology Program, Stanford University, Stanford, CA, United States.,Department of Otolaryngology - Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, United States.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, United States.,Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States.,Department of Pathology, Stanford University, Stanford, CA, United States
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15
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Bjornson-Hooper ZB, Fragiadakis GK, Spitzer MH, Chen H, Madhireddy D, Hu K, Lundsten K, McIlwain DR, Nolan GP. A Comprehensive Atlas of Immunological Differences Between Humans, Mice, and Non-Human Primates. Front Immunol 2022; 13:867015. [PMID: 35359965 PMCID: PMC8962947 DOI: 10.3389/fimmu.2022.867015] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [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: 01/31/2022] [Accepted: 02/16/2022] [Indexed: 01/01/2023] Open
Abstract
Animal models are an integral part of the drug development and evaluation process. However, they are unsurprisingly imperfect reflections of humans, and the extent and nature of many immunological differences are unknown. With the rise of targeted and biological therapeutics, it is increasingly important that we understand the molecular differences in the immunological behavior of humans and model organisms. However, very few antibodies are raised against non-human primate antigens, and databases of cross-reactivity between species are incomplete. Thus, we screened 332 antibodies in five immune cell populations in blood from humans and four non-human primate species generating a comprehensive cross-reactivity catalog that includes cell type-specificity. We used this catalog to create large mass cytometry universal cross-species phenotyping and signaling panels for humans, along with three of the model organisms most similar to humans: rhesus and cynomolgus macaques and African green monkeys; and one of the mammalian models most widely used in drug development: C57BL/6 mice. As a proof-of-principle, we measured immune cell signaling responses across all five species to an array of 15 stimuli using mass cytometry. We found numerous instances of different cellular phenotypes and immune signaling events occurring within and between species, and detailed three examples (double-positive T cell frequency and signaling; granulocyte response to Bacillus anthracis antigen; and B cell subsets). We also explore the correlation of herpes simian B virus serostatus on the immune profile. Antibody panels and the full dataset generated are available online as a resource to enable future studies comparing immune responses across species during the evaluation of therapeutics.
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Affiliation(s)
| | - Gabriela K. Fragiadakis
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
- Department of Medicine, Division of Rheumatology, University of California San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- University of California, San Francisco (UCSF) Data Science CoLab and University of California, San Francisco (UCSF) Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Matthew H. Spitzer
- Immunology Program, Stanford University, Stanford, CA, United States
- Departments of Otolaryngology – Head and Neck Surgery and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Han Chen
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Deepthi Madhireddy
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Kevin Hu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Kelly Lundsten
- BioLegend Inc, Advanced Cytometry, San Diego, CA, United States
| | - David R. McIlwain
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Garry P. Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
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16
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Combes AJ, Samad B, Tsui J, Chew NW, Yan P, Reeder GC, Kushnoor D, Shen A, Davidson B, Barczak AJ, Adkisson M, Edwards A, Naser M, Barry KC, Courau T, Hammoudi T, Argüello RJ, Rao AA, Olshen AB, Cai C, Zhan J, Davis KC, Kelley RK, Chapman JS, Atreya CE, Patel A, Daud AI, Ha P, Diaz AA, Kratz JR, Collisson EA, Fragiadakis GK, Erle DJ, Boissonnas A, Asthana S, Chan V, Krummel MF, Fong L, Nelson A, Kumar R, Lee J, Burra A, Hsu J, Hackett C, Tolentino K, Sjarif J, Johnson P, Shao E, Abrau D, Lupin L, Shaw C, Collins Z, Lea T, Corvera C, Nakakura E, Carnevale J, Alvarado M, Loo K, Chen L, Chow M, Grandis J, Ryan W, El-Sayed I, Jablons D, Woodard G, Meng MW, Porten SP, Okada H, Tempero M, Ko A, Kirkwood K, Vandenberg S, Guevarra D, Oropeza E, Cyr C, Glenn P, Bolen J, Morton A, Eckalbar W. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell 2022; 185:184-203.e19. [PMID: 34963056 PMCID: PMC8862608 DOI: 10.1016/j.cell.2021.12.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [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: 04/08/2021] [Revised: 08/25/2021] [Accepted: 12/03/2021] [Indexed: 01/09/2023]
Abstract
Cancers display significant heterogeneity with respect to tissue of origin, driver mutations, and other features of the surrounding tissue. It is likely that individual tumors engage common patterns of the immune system-here "archetypes"-creating prototypical non-destructive tumor immune microenvironments (TMEs) and modulating tumor-targeting. To discover the dominant immune system archetypes, the University of California, San Francisco (UCSF) Immunoprofiler Initiative (IPI) processed 364 individual tumors across 12 cancer types using standardized protocols. Computational clustering of flow cytometry and transcriptomic data obtained from cell sub-compartments uncovered dominant patterns of immune composition across cancers. These archetypes were profound insofar as they also differentiated tumors based upon unique immune and tumor gene-expression patterns. They also partitioned well-established classifications of tumor biology. The IPI resource provides a template for understanding cancer immunity as a collection of dominant patterns of immune organization and provides a rational path forward to learn how to modulate these to improve therapy.
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Affiliation(s)
- Alexis J. Combes
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA,Correspondence: and
| | - Bushra Samad
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jessica Tsui
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Nayvin W. Chew
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Peter Yan
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Gabriella C. Reeder
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Divyashree Kushnoor
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alan Shen
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Brittany Davidson
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Andrea J. Barczak
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Michael Adkisson
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Austin Edwards
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Mohammad Naser
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kevin C. Barry
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tristan Courau
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Taymour Hammoudi
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Rafael J Argüello
- Aix Marseille University, CNRS, INSERM, CIML, Centre d’Immunologie de Marseille-Luminy, Marseille, FRANCE
| | - Arjun Arkal Rao
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adam B. Olshen
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Cathy Cai
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jenny Zhan
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Katelyn C. Davis
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA
| | - Robin K. Kelley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jocelyn S. Chapman
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Departments of Obstetrics, Gynecology, and Reproductive Sciences, Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Chloe E. Atreya
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA,Department of Medicine, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Amar Patel
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Department of Medicine, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adil I. Daud
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA 94143, USA,Department of Dermatology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Patrick Ha
- Department of Otolaryngology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Aaron A. Diaz
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Johannes R. Kratz
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric A. Collisson
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA,Department of Medicine, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Gabriela K Fragiadakis
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA,Department of Medicine Division of Rheumatology, University of California San Francisco, San Francisco, CA 94143, USA
| | - David J. Erle
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF CoLabs, University of California San Francisco, San Francisco, CA 94143, USA,Lung Biology Center, Department of Medicine and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alexandre Boissonnas
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses - CIMI, Paris, France
| | - Saurabh Asthana
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Vincent Chan
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew F. Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA,ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA,UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA 94143, USA,Correspondence: and
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17
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Belonwu SA, Li Y, Bunis D, Rao AA, Solsberg CW, Tang A, Fragiadakis GK, Dubal DB, Oskotsky T, Sirota M. Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer's Disease Across Two Brain Regions. Mol Neurobiol 2021; 59:276-293. [PMID: 34669146 PMCID: PMC8786804 DOI: 10.1007/s12035-021-02591-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 07/19/2021] [Accepted: 10/04/2021] [Indexed: 11/29/2022]
Abstract
Alzheimer’s disease (AD) is a pervasive neurodegenerative disorder that disproportionately affects women. Since neural anatomy and disease pathophysiology differ by sex, investigating sex-specific mechanisms in AD pathophysiology can inform new therapeutic approaches for both sexes. Previous bulk human brain RNA sequencing studies have revealed sex differences in dysregulated molecular pathways related to energy production, neuronal function, and immune response; however, the sex differences in disease mechanisms are yet to be examined comprehensively on a single-cell level. We leveraged nearly 74,000 cells from human prefrontal and entorhinal cortex samples from the first two publicly available single-cell RNA sequencing AD datasets to perform a case versus control sex-stratified differential gene expression analysis and pathway network enrichment in a cell type-specific manner for each brain region. Our examination at the single-cell level revealed sex differences in AD prominently in glial cells of the prefrontal cortex. In the entorhinal cortex, we observed the same genes and networks to be perturbed in opposing directions between sexes in AD relative to healthy state. Our findings contribute to growing evidence of sex differences in AD-related transcriptomic changes, which can fuel the development of therapies that may prove more effective at reversing AD pathophysiology.
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Affiliation(s)
- Stella A Belonwu
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA.,Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Yaqiao Li
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA.,Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Daniel Bunis
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA.,CoLabs, University of California, San Francisco, San Francisco, CA, USA.,Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA
| | - Arjun Arkal Rao
- CoLabs, University of California, San Francisco, San Francisco, CA, USA.,Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA.,Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Caroline Warly Solsberg
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA.,Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Alice Tang
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA.,Bioengineering Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Gabriela K Fragiadakis
- CoLabs, University of California, San Francisco, San Francisco, CA, USA.,Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, Division of Rheumatology, University of California, San Francisco, San Francisco, CA, USA
| | - Dena B Dubal
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.,Neurosciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA.,Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, 490 Illinois St, San Francisco, CA, 94143, USA. .,Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
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18
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Weiner J, Suwalski P, Holtgrewe M, Rakitko A, Thibeault C, Müller M, Patriki D, Quedenau C, Krüger U, Ilinsky V, Popov I, Balnis J, Jaitovich A, Helbig ET, Lippert LJ, Stubbemann P, Real LM, Macías J, Pineda JA, Fernandez-Fuertes M, Wang X, Karadeniz Z, Saccomanno J, Doehn JM, Hübner RH, Hinzmann B, Salvo M, Blueher A, Siemann S, Jurisic S, Beer JH, Rutishauser J, Wiggli B, Schmid H, Danninger K, Binder R, Corman VM, Mühlemann B, Arjun Arkal R, Fragiadakis GK, Mick E, COMET C, Calfee CS, Erle DJ, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Langelier CR, Venkataramani U, García F, Zyla J, Drosten C, Alice B, Jones TC, Suttorp N, Witzenrath M, Hippenstiel S, Zemojtel T, Skurk C, Poller W, Borodina T, Pa-COVID SG, Ripke S, Sander LE, Beule D, Landmesser U, Guettouche T, Kurth F, Heidecker B. Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01. EClinicalMedicine 2021; 40:101099. [PMID: 34490415 PMCID: PMC8410317 DOI: 10.1016/j.eclinm.2021.101099] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/01/2021] [Accepted: 08/04/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there has been increasing urgency to identify pathophysiological characteristics leading to severe clinical course in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Human leukocyte antigen alleles (HLA) have been suggested as potential genetic host factors that affect individual immune response to SARS-CoV-2. We sought to evaluate this hypothesis by conducting a multicenter study using HLA sequencing. METHODS We analyzed the association between COVID-19 severity and HLAs in 435 individuals from Germany (n = 135), Spain (n = 133), Switzerland (n = 20) and the United States (n = 147), who had been enrolled from March 2020 to August 2020. This study included patients older than 18 years, diagnosed with COVID-19 and representing the full spectrum of the disease. Finally, we tested our results by meta-analysing data from prior genome-wide association studies (GWAS). FINDINGS We describe a potential association of HLA-C*04:01 with severe clinical course of COVID-19. Carriers of HLA-C*04:01 had twice the risk of intubation when infected with SARS-CoV-2 (risk ratio 1.5 [95% CI 1.1-2.1], odds ratio 3.5 [95% CI 1.9-6.6], adjusted p-value = 0.0074). These findings are based on data from four countries and corroborated by independent results from GWAS. Our findings are biologically plausible, as HLA-C*04:01 has fewer predicted bindings sites for relevant SARS-CoV-2 peptides compared to other HLA alleles. INTERPRETATION HLA-C*04:01 carrier state is associated with severe clinical course in SARS-CoV-2. Our findings suggest that HLA class I alleles have a relevant role in immune defense against SARS-CoV-2. FUNDING Funded by Roche Sequencing Solutions, Inc.
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Affiliation(s)
- January Weiner
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Core Unit Bioinformatics Berlin, DE 10178, Germany
| | - Phillip Suwalski
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
- Berliner Simulations- und Trainingszentrum, Charite, Berlin, DE 10117, Germany
| | - Manuel Holtgrewe
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Core Unit Genomics Berlin, DE 10178, Germany
| | - Alexander Rakitko
- Genotek Ltd., Nastavnicheskii pereulok 17/1, R 105120 Moscow, Russian Federation
| | - Charlotte Thibeault
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Melina Müller
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
| | - Dimitri Patriki
- Kantonsspital Baden AG, Department of Medicine, Baden, CH 5404, Switzerland
| | - Claudia Quedenau
- Max Delbrueck Center for Molecular Medicine Berlin, DE 13125, Germany
| | - Ulrike Krüger
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Core Unit Genomics Berlin, DE 10178, Germany
| | - Valery Ilinsky
- Genotek Ltd., Nastavnicheskii pereulok 17/1, R 105120 Moscow, Russian Federation
| | - Iaroslav Popov
- Genotek Ltd., Nastavnicheskii pereulok 17/1, R 105120 Moscow, Russian Federation
| | - Joseph Balnis
- Department of Molecular and Cellular Physiology, Albany Medical College, NY, USA
| | - Ariel Jaitovich
- Department of Molecular and Cellular Physiology, Albany Medical College, NY, USA
| | - Elisa T Helbig
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Lena J Lippert
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Paula Stubbemann
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Luis M Real
- Unidad Clínica de Enfermedades Infecciosas y Microbiología. Hospital Universitario de Valme, Sevilla, ES 41014, Spain
| | - Juan Macías
- Unidad Clínica de Enfermedades Infecciosas y Microbiología. Hospital Universitario de Valme, Sevilla, ES 41014, Spain
| | - Juan A Pineda
- Unidad Clínica de Enfermedades Infecciosas y Microbiología. Hospital Universitario de Valme, Sevilla, ES 41014, Spain
| | - Marta Fernandez-Fuertes
- Unidad Clínica de Enfermedades Infecciosas y Microbiología. Hospital Universitario de Valme, Sevilla, ES 41014, Spain
| | - Xiaomin Wang
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
| | - Zehra Karadeniz
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
| | - Jacopo Saccomanno
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Jan-Moritz Doehn
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Ralf-Harto Hübner
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | | | | | - Anja Blueher
- Roche Sequencing Solutions Pleasanton, USA 94588
| | | | - Stjepan Jurisic
- Kantonsspital Baden AG, Department of Medicine, Baden, CH 5404, Switzerland
| | - Juerg H. Beer
- Kantonsspital Baden AG, Department of Medicine, Baden, CH 5404, Switzerland
| | - Jonas Rutishauser
- Kantonsspital Baden AG, Department of Medicine, Baden, CH 5404, Switzerland
| | - Benedikt Wiggli
- Kantonsspital Baden AG, Department of Medicine, Baden, CH 5404, Switzerland
| | - Hansruedi Schmid
- Kantonsspital Baden AG, Department of Medicine, Baden, CH 5404, Switzerland
| | - Kathrin Danninger
- Department of Cardiology and Intensive Care, Klinikum Wels-Grieskirchen, Wels, Austria
| | - Ronald Binder
- Department of Cardiology and Intensive Care, Klinikum Wels-Grieskirchen, Wels, Austria
| | - Victor M Corman
- Charite Universitaetsmedizin Berlin, Institute of Virology Chariteplatz, 1 d-10117, Berlin, DE, 10117, Germany
| | - Barbara Mühlemann
- Charite Universitaetsmedizin Berlin, Institute of Virology Chariteplatz, 1 d-10117, Berlin, DE, 10117, Germany
| | - Rao Arjun Arkal
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Gabriela K. Fragiadakis
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eran Mick
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Consortium COMET
- COMET (COVID-19 Multiphenotyping for Effective Therapies) Consortium members are listed in the Supplementary Appendix 1
| | - Carolyn S. Calfee
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | - David J. Erle
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- COMET (COVID-19 Multiphenotyping for Effective Therapies) Consortium members are listed in the Supplementary Appendix 1
- Lung Biology Center, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Carolyn M. Hendrickson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Matthew F. Krummel
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Prescott G. Woodruff
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, CA, USA
| | - Charles R. Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Urmila Venkataramani
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Federico García
- Hospital Universitario Clínico San Cecilio, Instituto de Investigación Ibs. Granada, Spain
| | - Joanna Zyla
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Christian Drosten
- Charite Universitaetsmedizin Berlin, Institute of Virology Chariteplatz, 1 d-10117, Berlin, DE, 10117, Germany
| | - Braun Alice
- Charite Universitaetsmedizin Berlin, Dept. of Psychiatry and Psychotherapy Chariteplatz 1 d-10117 Berlin, DE 10117, Germany
| | - Terry C Jones
- Charite Universitaetsmedizin Berlin, Institute of Virology Chariteplatz, 1 d-10117, Berlin, DE, 10117, Germany
- German Center for Infection Research (DZIF), Associated Partner Site, 10117 Berlin, Germany
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing St., Cambridge, CB2 3EJ, U.K
| | - Norbert Suttorp
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Martin Witzenrath
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Stefan Hippenstiel
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Tomasz Zemojtel
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Core Unit Genomics Berlin, DE 10178, Germany
| | - Carsten Skurk
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
| | - Wolfgang Poller
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
| | - Tatiana Borodina
- Max Delbrueck Center for Molecular Medicine Berlin, DE 13125, Germany
| | | | - Stephan Ripke
- Charite Universitaetsmedizin Berlin, Dept. of Psychiatry and Psychotherapy Chariteplatz 1 d-10117 Berlin, DE 10117, Germany
- Massachusetts General Hospital, Analytic and Translational Genetics, Boston, MA 02114, USA
- Stanley Center for Psychiatry Research, Broad Institute of MIT and Harvard Cambridge MA 02142, USA
| | - Leif E Sander
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Core Unit Bioinformatics Berlin, DE 10178, Germany
| | - Ulf Landmesser
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
- Berlin Institute of Health at Charité, Berlin, Germany
| | | | - Florian Kurth
- Charite Universitaetsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine Berlin, DE 10117, Germany
| | - Bettina Heidecker
- Department of Cardiology, Charite Universitaetsmedizin Berlin, DE 12203, Germany
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19
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van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Le Voyer T, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ. Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19. Sci Transl Med 2021; 13:eabh2624. [PMID: 34429372 PMCID: PMC8601717 DOI: 10.1126/scitranslmed.abh2624] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A subset of patients diagnosed with coronavirus disease 2019 (COVID-19) present with autoantibodies specific to type I interferons (IFNs). However, the systemic impacts of type I IFN–specific autoantibodies are not fully understood. Here, van der Wijst et al. longitudinally evaluated the relationship between type I IFN–specific autoantibody abundance and changes to the immune system of individuals with COVID-19. Using single-cell transcriptomics, the authors found that the presence of type I IFN autoantibodies correlated with reduced type I IFN–stimulated gene (ISG) expression in patients with critical COVID-19. Reduced ISG expression, in turn, correlated with increased expression of the inhibitory receptor, leukocyte-associated immunoglobulin-like receptor 1 (LAIR1), on monocytes. Together, these findings suggest that early evidence of type I IFN autoantibodies and increased LAIR1 expression may help distinguish severe cases of COVID-19. Neutralizing autoantibodies against type I interferons (IFNs) have been found in some patients with critical coronavirus disease 2019 (COVID-19), the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the prevalence of these antibodies, their longitudinal dynamics across the disease severity scale, and their functional effects on circulating leukocytes remain unknown. Here, in 284 patients with COVID-19, we found type I IFN–specific autoantibodies in peripheral blood samples from 19% of patients with critical disease and 6% of patients with severe disease. We found no type I IFN autoantibodies in individuals with moderate disease. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 patients with COVID-19 and 26 non–COVID-19 controls revealed a lack of type I IFN–stimulated gene (ISG-I) responses in myeloid cells from patients with critical disease. This was especially evident in dendritic cell populations isolated from patients with critical disease producing type I IFN–specific autoantibodies. Moreover, we found elevated expression of the inhibitory receptor leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) on the surface of monocytes isolated from patients with critical disease early in the disease course. LAIR1 expression is inversely correlated with ISG-I expression response in patients with COVID-19 but is not expressed in healthy controls. The deficient ISG-I response observed in patients with critical COVID-19 with and without type I IFN–specific autoantibodies supports a unifying model for disease pathogenesis involving ISG-I suppression through convergent mechanisms.
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Affiliation(s)
- Monique G P van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713AV Groningen, Netherlands.,Institute of Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sara E Vazquez
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA.,Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - George C Hartoularos
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France.,University of Paris, Imagine Institute, 75015 Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Tianna Grant
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Raymund Bueno
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David S Lee
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John R Greenland
- Department of Medicine, University of California, San Francisco, San Francisco Medical Service, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, USA
| | - Yang Sun
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Richard Perez
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.,School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anton Ogorodnikov
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alyssa Ward
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Kara L Lynch
- Zuckerberg San Francisco General, San Francisco, CA 94110, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cassandra Yun
- Zuckerberg San Francisco General, San Francisco, CA 94110, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diane V Havlir
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gabriel Chamie
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Carina Marquez
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bryan Greenhouse
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20814, USA
| | - Philip J Norris
- Zuckerberg San Francisco General, San Francisco, CA 94110, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Larry J Dumont
- Vitalant Research Institute, Denver, CO 80230, USA.,University of Colorado School of Medicine, Aurora, CO 80045, USA.,Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | | | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Adrian Gervais
- University of Paris, Imagine Institute, 75015 Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Tom Le Voyer
- University of Paris, Imagine Institute, 75015 Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Alexander Whatley
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yichen Si
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ashley Byrne
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Alexis J Combes
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA.,UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Arjun Arkal Rao
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA.,UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yun S Song
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.,Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gabriela K Fragiadakis
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.,UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kirsten Kangelaris
- Division of Hospital Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Carolyn S Calfee
- Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine and the Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David J Erle
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.,ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.,Zuckerberg San Francisco General, San Francisco, CA 94110, USA
| | - Carolyn Hendrickson
- Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine and the Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew F Krummel
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Prescott G Woodruff
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine and the Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charles R Langelier
- Division of Infectious Disease, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France.,University of Paris, Imagine Institute, 75015 Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute, New York, NY 10065, USA
| | - Joseph L Derisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chun Jimmie Ye
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.,Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.,Departments of Epidemiology and Biostatistics and Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.,Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
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20
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Wang VE, Blaser BW, Patel RK, Behbehani GK, Rao AA, Durbin-Johnson B, Jiang T, Logan AC, Settles M, Mannis GN, Olin R, Damon LE, Martin TG, Sayre PH, Gaensler KM, McMahon E, Flanders M, Weinberg V, Ye CJ, Carbone DP, Munster PN, Fragiadakis GK, McCormick F, Andreadis C. Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis. Blood Cancer Discov 2021; 2:434-449. [PMID: 34514432 DOI: 10.1158/2643-3230.bcd-21-0055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Acute myeloid leukemia patients refractory to induction therapy or relapsed within one year have poor outcomes. Autocrine production of hepatocyte growth factor by myeloid blasts drives leukemogenesis in pre-clinical models. A phase Ib trial evaluated ficlatuzumab, a first-in-class anti-HGF antibody, in combination with cytarabine in this high-risk population. Dose-limiting toxicities were not observed, and 20 mg/kg was established as the recommended phase II dose. The most frequent treatment-related adverse event was febrile neutropenia. Among 17 evaluable patients, the overall response rate was 53%, all complete remissions. Phospho-proteomic mass cytometry showed potent on-target suppression of p-MET after ficlatuzumab treatment and that attenuation of p-S6 was associated with clinical response. Multiplexed single cell RNA sequencing using prospectively acquired patient specimens identified interferon response genes as adverse predictive factors. The ficlatuzumab and cytarabine combination is well-tolerated with favorable efficacy. High-dimensional analyses at single-cell resolution represent promising approaches for identifying biomarkers of response and mechanisms of resistance in prospective clinical studies.
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Affiliation(s)
- Victoria E Wang
- Department of Medicine, University of California, San Francisco, CA 94158, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Bradley W Blaser
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Ravi K Patel
- CoLabs, University of California, San Francisco, CA 94143, USA
| | - Gregory K Behbehani
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Arjun A Rao
- CoLabs, University of California, San Francisco, CA 94143, USA
| | | | - Tommy Jiang
- Department of Medicine, University of California, San Francisco, CA 94158, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Aaron C Logan
- Department of Medicine, University of California, San Francisco, CA 94158, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Matthew Settles
- Bioinformatics Core, Genome Center, University of California, Davis, CA 95616, USA
| | - Gabriel N Mannis
- Department of Medicine, University of California, San Francisco, CA 94158, USA
| | - Rebecca Olin
- Department of Medicine, University of California, San Francisco, CA 94158, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Lloyd E Damon
- Department of Medicine, University of California, San Francisco, CA 94158, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Thomas G Martin
- Department of Medicine, University of California, San Francisco, CA 94158, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Peter H Sayre
- Department of Medicine, University of California, San Francisco, CA 94158, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Karin M Gaensler
- Department of Medicine, University of California, San Francisco, CA 94158, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Emma McMahon
- Department of Medicine, University of California, San Francisco, CA 94158, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Michael Flanders
- Department of Medicine, University of California, San Francisco, CA 94158, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Vivian Weinberg
- Department of Medicine, University of California, San Francisco, CA 94158, USA
| | - Chun J Ye
- Department of Medicine, University of California, San Francisco, CA 94158, USA
| | - David P Carbone
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Pamela N Munster
- Department of Medicine, University of California, San Francisco, CA 94158, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Gabriela K Fragiadakis
- CoLabs, University of California, San Francisco, CA 94143, USA.,Bakar ImmunoX Initiative, University of California, San Francisco, CA 94143, USA.,Department of Medicine, Division of Rheumatology, University of California, San Francisco, CA 94143, USA
| | - Frank McCormick
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Charalambos Andreadis
- Department of Medicine, University of California, San Francisco, CA 94158, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
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21
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Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Yu FB, Topf M, Gonzalez CG, Van Treuren W, Han S, Robinson JL, Elias JE, Sonnenburg ED, Gardner CD, Sonnenburg JL. Gut-microbiota-targeted diets modulate human immune status. Cell 2021; 184:4137-4153.e14. [PMID: 34256014 DOI: 10.1016/j.cell.2021.06.019] [Citation(s) in RCA: 390] [Impact Index Per Article: 130.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 04/13/2021] [Accepted: 06/11/2021] [Indexed: 12/21/2022]
Abstract
Diet modulates the gut microbiome, which in turn can impact the immune system. Here, we determined how two microbiota-targeted dietary interventions, plant-based fiber and fermented foods, influence the human microbiome and immune system in healthy adults. Using a 17-week randomized, prospective study (n = 18/arm) combined with -omics measurements of microbiome and host, including extensive immune profiling, we found diet-specific effects. The high-fiber diet increased microbiome-encoded glycan-degrading carbohydrate active enzymes (CAZymes) despite stable microbial community diversity. Although cytokine response score (primary outcome) was unchanged, three distinct immunological trajectories in high-fiber consumers corresponded to baseline microbiota diversity. Alternatively, the high-fermented-food diet steadily increased microbiota diversity and decreased inflammatory markers. The data highlight how coupling dietary interventions to deep and longitudinal immune and microbiome profiling can provide individualized and population-wide insight. Fermented foods may be valuable in countering the decreased microbiome diversity and increased inflammation pervasive in industrialized society.
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Affiliation(s)
- Hannah C Wastyk
- Department of Bioengineering, Stanford School of Medicine, Stanford, CA 94305, USA
| | | | - Dalia Perelman
- Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Dylan Dahan
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Bryan D Merrill
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Madeline Topf
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Carlos G Gonzalez
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - William Van Treuren
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Shuo Han
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Jennifer L Robinson
- Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA
| | | | - Erica D Sonnenburg
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA; Center for Human Microbiome Studies, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Christopher D Gardner
- Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA.
| | - Justin L Sonnenburg
- Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA; Center for Human Microbiome Studies, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA.
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22
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Hendley AM, Rao AA, Leonhardt L, Ashe S, Smith JA, Giacometti S, Peng XL, Jiang H, Berrios DI, Pawlak M, Li LY, Lee J, Collisson EA, Anderson MS, Fragiadakis GK, Yeh JJ, Ye CJ, Kim GE, Weaver VM, Hebrok M. Single-cell transcriptome analysis defines heterogeneity of the murine pancreatic ductal tree. eLife 2021; 10:e67776. [PMID: 34009124 PMCID: PMC8184217 DOI: 10.7554/elife.67776] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 02/23/2021] [Accepted: 05/18/2021] [Indexed: 12/25/2022] Open
Abstract
To study disease development, an inventory of an organ's cell types and understanding of physiologic function is paramount. Here, we performed single-cell RNA-sequencing to examine heterogeneity of murine pancreatic duct cells, pancreatobiliary cells, and intrapancreatic bile duct cells. We describe an epithelial-mesenchymal transitory axis in our three pancreatic duct subpopulations and identify osteopontin as a regulator of this fate decision as well as human duct cell dedifferentiation. Our results further identify functional heterogeneity within pancreatic duct subpopulations by elucidating a role for geminin in accumulation of DNA damage in the setting of chronic pancreatitis. Our findings implicate diverse functional roles for subpopulations of pancreatic duct cells in maintenance of duct cell identity and disease progression and establish a comprehensive road map of murine pancreatic duct cell, pancreatobiliary cell, and intrapancreatic bile duct cell homeostasis.
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Affiliation(s)
- Audrey M Hendley
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
- Center for Bioengineering and Tissue Regeneration, University of California, San FranciscoSan FranciscoUnited States
| | - Arjun A Rao
- CoLabs, University of California, San FranciscoSan FranciscoUnited States
- Bakar ImmunoX Initiative, University of California, San FranciscoSan FranciscoUnited States
| | - Laura Leonhardt
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Sudipta Ashe
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Jennifer A Smith
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Simone Giacometti
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Xianlu L Peng
- Department of Pharmacology, University of North Carolina at Chapel HillChapel HillUnited States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel HillChapel HillUnited States
| | - Honglin Jiang
- Division of Hematology and Oncology, Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
| | - David I Berrios
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Mathias Pawlak
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's HospitalBostonUnited States
| | - Lucia Y Li
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Jonghyun Lee
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Eric A Collisson
- Division of Hematology and Oncology, Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
| | - Mark S Anderson
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Gabriela K Fragiadakis
- CoLabs, University of California, San FranciscoSan FranciscoUnited States
- Bakar ImmunoX Initiative, University of California, San FranciscoSan FranciscoUnited States
- Department of Medicine, Division of Rheumatology, University of California, San FranciscoSan FranciscoUnited States
| | - Jen Jen Yeh
- Department of Pharmacology, University of North Carolina at Chapel HillChapel HillUnited States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel HillChapel HillUnited States
- Department of Surgery, University of North Carolina at Chapel HillChapel HillUnited States
| | - Chun Jimmie Ye
- Parker Institute for Cancer ImmunotherapySan FranciscoUnited States
| | - Grace E Kim
- Department of Pathology, University of California, San FranciscoSan FranciscoUnited States
| | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, University of California, San FranciscoSan FranciscoUnited States
| | - Matthias Hebrok
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
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23
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van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Le Voyer T, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ. Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19: Anti-IFN antibodies in critical COVID-19 correlate with poor ISG response and upregulation of LAIR1 surface protein in PBMCs. bioRxiv 2021:2021.03.09.434529. [PMID: 33758859 PMCID: PMC7987018 DOI: 10.1101/2021.03.09.434529] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Type I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocytes remain unknown. Here, in 284 COVID-19 patients, we found IFN-I autoantibodies in 19% of critical, 6% of severe and none of the moderate cases. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 COVID-19 patients, 15 non-COVID-19 patients and 11 non-hospitalized healthy controls, revealed a lack of IFN-I stimulated gene (ISG-I) response in myeloid cells from critical cases, including those producing anti-IFN-I autoantibodies. Moreover, surface protein analysis showed an inverse correlation of the inhibitory receptor LAIR-1 with ISG-I expression response early in the disease course. This aberrant ISG-I response in critical patients with and without IFN-I autoantibodies, supports a unifying model for disease pathogenesis involving ISG-I suppression via convergent mechanisms.
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Affiliation(s)
- Monique G P van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
| | - Sara E Vazquez
- Medical Scientist Training Program, University of California. San Francisco, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - George C Hartoularos
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Tianna Grant
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
| | - Raymund Bueno
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
| | - David S Lee
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- ImmunoX Initiative, University of California, San Francisco, CA, USA
| | - John R Greenland
- Department of Medicine, San Francisco VA Health Care System, University of California, San Francisco, CA, USA
| | - Yang Sun
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- ImmunoX Initiative, University of California, San Francisco, CA, USA
| | - Richard Perez
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Anton Ogorodnikov
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
| | - Alyssa Ward
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Kara L Lynch
- Zuckerberg San Francisco General, San Francisco, CA, USA
| | - Cassandra Yun
- Zuckerberg San Francisco General, San Francisco, CA, USA
| | - Diane V Havlir
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Gabriel Chamie
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Carina Marquez
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Bryan Greenhouse
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Philip J Norris
- Zuckerberg San Francisco General, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Larry J Dumont
- Vitalant Research Institute, Denver, CO, USA
- University of Colorado School of Medicine, Aurora, CO, USA
- Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | | | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Adrian Gervais
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Tom Le Voyer
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Alexander Whatley
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - Yichen Si
- Department of Biostaticstics, University of Michigan
| | | | - Alexis J Combes
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, CA, USA
| | - Arjun Arkal Rao
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, CA, USA
| | - Yun S Song
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
- Department of Statistics, University of California, Berkeley, CA, USA
| | - Gabriela K Fragiadakis
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, CA, USA
| | - Kirsten Kangelaris
- Division of Infectious Disease, Department of Medicine, University of California, San Francisco, CA, USA
| | - Carolyn S Calfee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - David J Erle
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- Zuckerberg San Francisco General, San Francisco, CA, USA
| | - Carolyn Hendrickson
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Matthew F Krummel
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Prescott G Woodruff
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Charles R Langelier
- Division of Infectious Disease, Department of Medicine, University of California, San Francisco, CA, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Joseph L Derisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, CA, USA
- Endocrine Division, Department of Medicine, University of California, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Institute of Human Genetics, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, California, USA
- ImmunoX Initiative, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Departments of Epidemiology and Biostatistics, Bioengineering and Therapeutic Sciences
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
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24
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Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Chew NW, Cleary SJ, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, Im KW, Serwas NK, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. Global absence and targeting of protective immune states in severe COVID-19. Nature 2021; 591:124-130. [PMID: 33494096 PMCID: PMC8567458 DOI: 10.1038/s41586-021-03234-7] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [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: 10/23/2020] [Accepted: 01/12/2021] [Indexed: 12/26/2022]
Abstract
Although infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has pleiotropic and systemic effects in some individuals1-3, many others experience milder symptoms. Here, to gain a more comprehensive understanding of the distinction between severe and mild phenotypes in the pathology of coronavirus disease 2019 (COVID-19) and its origins, we performed a whole-blood-preserving single-cell analysis protocol to integrate contributions from all major immune cell types of the blood-including neutrophils, monocytes, platelets, lymphocytes and the contents of the serum. Patients with mild COVID-19 exhibit a coordinated pattern of expression of interferon-stimulated genes (ISGs)3 across every cell population, whereas these ISG-expressing cells are systemically absent in patients with severe disease. Paradoxically, individuals with severe COVID-19 produce very high titres of anti-SARS-CoV-2 antibodies and have a lower viral load compared to individuals with mild disease. Examination of the serum from patients with severe COVID-19 shows that these patients uniquely produce antibodies that functionally block the production of the ISG-expressing cells associated with mild disease, by activating conserved signalling circuits that dampen cellular responses to interferons. Overzealous antibody responses pit the immune system against itself in many patients with COVID-19, and perhaps also in individuals with other viral infections. Our findings reveal potential targets for immunotherapies in patients with severe COVID-19 to re-engage viral defence.
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Affiliation(s)
- Alexis J Combes
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA.
| | - Tristan Courau
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Nicholas F Kuhn
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
| | - Kenneth H Hu
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
| | - Arja Ray
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
| | - William S Chen
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Nayvin W Chew
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Simon J Cleary
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Divyashree Kushnoor
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Gabriella C Reeder
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Alan Shen
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Tsui
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Kamir J Hiam-Galvez
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Department of Otolaryngology, University of California San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Priscila Muñoz-Sandoval
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Wandi S Zhu
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - David S Lee
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Yang Sun
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ran You
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
| | - Mélia Magnen
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Lauren Rodriguez
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Department of Otolaryngology, University of California San Francisco, San Francisco, CA, USA
| | - K W Im
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Nina K Serwas
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
| | - Aleksandra Leligdowicz
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Colin R Zamecnik
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Rita P Loudermilk
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Michael R Wilson
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Chun J Ye
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gabriela K Fragiadakis
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mark R Looney
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Vincent Chan
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
| | - Alyssa Ward
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sidney Carrillo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Michael Matthay
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - David J Erle
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Prescott G Woodruff
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Charles Langelier
- Division of Infectious Disease, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten Kangelaris
- Division of Hospital Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Carolyn M Hendrickson
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Carolyn Calfee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Arjun Arkal Rao
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA.
| | - Matthew F Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA.
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25
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Abstract
Complex datasets provide opportunities for discoveries beyond their initial scope. Effective and rapid data sharing and management practices are crucial to realize this potential; however, they are harder to implement than post-publication access. Here, we introduce the concept of a "data sharing trust" to maximize the value of large datasets.
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Affiliation(s)
- Vincent Chan
- Department of Microbiology and Immunology, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0511, USA; Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0511, USA; ImmunoX Initiative, Department of Microbiology and Immunology, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0511, USA
| | - Pier Federico Gherardini
- Parker Institute for Cancer Immunotherapy, 1 Letterman Drive, Suite D3500, San Francisco, CA 94129-1504
| | - Matthew F Krummel
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0511, USA; ImmunoX Initiative, Department of Microbiology and Immunology, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0511, USA.
| | - Gabriela K Fragiadakis
- ImmunoX Initiative, Department of Microbiology and Immunology, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0511, USA; UCSF CoLabs, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0511, USA; Division of Rheumatology, Department of Medicine, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0511, USA.
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26
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Bunis DG, Andrews J, Fragiadakis GK, Burt TD, Sirota M. dittoSeq: Universal User-Friendly Single-Cell and Bulk RNA Sequencing Visualization Toolkit. Bioinformatics 2020; 36:5535-5536. [PMID: 33313640 PMCID: PMC8016464 DOI: 10.1093/bioinformatics/btaa1011] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/16/2020] [Accepted: 11/24/2020] [Indexed: 11/14/2022] Open
Abstract
SUMMARY A visualization suite for major forms of bulk and single-cell RNAseq data in R. dittoSeq is color blindness-friendly by default, robustly documented to power ease-of-use, and allows highly customizable generation of both daily-use and publication-quality figures. AVAILABILITY AND IMPLEMENTATION dittoSeq is an R package available through Bioconductor via an open source MIT license. SUPPLEMENTARY INFORMATION Supplementary Code and figures are available at Bioinformatics online. Full vignettes are available through Bioconductor, https://bioconductor.org/packages/dittoSeq/, and github, github.com/dtm2451/dittoSeq/.
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Affiliation(s)
- Daniel G Bunis
- San Francisco, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research University of California, San Francisco, CA, USA.,Bakar Computational Health Sciences Institute University of California, San Francisco, San Francisco, CA, USA
| | - Jared Andrews
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Gabriela K Fragiadakis
- Department of Medicine Division of Rheumatology, University of California, San Francisco, San Francisco, CA, USA
| | - Trevor D Burt
- San Francisco, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research University of California, San Francisco, CA, USA.,Department of Pediatrics Division of Neonatology, University of California, San Francisco, San Francisco, CA, USA.,Department of Pediatrics, Division of Neonatology and the Children's Health and Discovery Initiative, Duke University School of Medicine, Durham, NC, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute University of California, San Francisco, San Francisco, CA, USA.,Department of Pediatrics Division of Neonatology, University of California, San Francisco, San Francisco, CA, USA
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27
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Rahil Z, Leylek R, Schürch CM, Chen H, Bjornson-Hooper Z, Christensen SR, Gherardini PF, Bhate SS, Spitzer MH, Fragiadakis GK, Mukherjee N, Kim N, Jiang S, Yo J, Gaudilliere B, Affrime M, Bock B, Hensley SE, Idoyaga J, Aghaeepour N, Kim K, Nolan GP, McIlwain DR. Landscape of coordinated immune responses to H1N1 challenge in humans. J Clin Invest 2020; 130:5800-5816. [PMID: 33044226 PMCID: PMC7598057 DOI: 10.1172/jci137265] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 02/17/2020] [Accepted: 07/31/2020] [Indexed: 12/18/2022] Open
Abstract
Influenza is a significant cause of morbidity and mortality worldwide. Here we show changes in the abundance and activation states of more than 50 immune cell subsets in 35 individuals over 11 time points during human A/California/2009 (H1N1) virus challenge monitored using mass cytometry along with other clinical assessments. Peak change in monocyte, B cell, and T cell subset frequencies coincided with peak virus shedding, followed by marked activation of T and NK cells. Results led to the identification of CD38 as a critical regulator of plasmacytoid dendritic cell function in response to influenza virus. Machine learning using study-derived clinical parameters and single-cell data effectively classified and predicted susceptibility to infection. The coordinated immune cell dynamics defined in this study provide a framework for identifying novel correlates of protection in the evaluation of future influenza therapeutics.
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Affiliation(s)
- Zainab Rahil
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Rebecca Leylek
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Christian M. Schürch
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Han Chen
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Zach Bjornson-Hooper
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Shannon R. Christensen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Salil S. Bhate
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | | | - Gabriela K. Fragiadakis
- UCSF Data Science CoLab and UCSF Department of Medicine, UCSF, San Francisco, California, USA
| | - Nilanjan Mukherjee
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Nelson Kim
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Sizun Jiang
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jennifer Yo
- ARK Clinical Research, Long Beach, California, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California, USA
| | | | | | - Scott E. Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Juliana Idoyaga
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Kenneth Kim
- ARK Clinical Research, Long Beach, California, USA
| | - Garry P. Nolan
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - David R. McIlwain
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- WCCT Global, Cypress, California, USA
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28
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Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Cleary SJ, Chew NW, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. Global Absence and Targeting of Protective Immune States in Severe COVID-19. bioRxiv 2020. [PMID: 33140050 DOI: 10.1101/2020.10.28.359935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holistic understanding of the severe/mild distinction in COVID-19 pathology, and its origins. We performed a whole-blood preserving single-cell analysis protocol to integrate contributions from all major cell types including neutrophils, monocytes, platelets, lymphocytes and the contents of serum. Patients with mild COVID-19 disease display a coordinated pattern of interferon-stimulated gene (ISG) expression across every cell population and these cells are systemically absent in patients with severe disease. Severe COVID-19 patients also paradoxically produce very high anti-SARS-CoV-2 antibody titers and have lower viral load as compared to mild disease. Examination of the serum from severe patients demonstrates that they uniquely produce antibodies with multiple patterns of specificity against interferon-stimulated cells and that those antibodies functionally block the production of the mild disease-associated ISG-expressing cells. Overzealous and auto-directed antibody responses pit the immune system against itself in many COVID-19 patients and this defines targets for immunotherapies to allow immune systems to provide viral defense. One Sentence Summary In severe COVID-19 patients, the immune system fails to generate cells that define mild disease; antibodies in their serum actively prevents the successful production of those cells.
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29
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Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Cleary SJ, Chew NW, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. Global Absence and Targeting of Protective Immune States in Severe COVID-19. Res Sq 2020. [PMID: 33140041 PMCID: PMC7605560 DOI: 10.21203/rs.3.rs-97042/v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holistic understanding of the severe/mild distinction in COVID-19 pathology, and its origins. We performed a whole-blood preserving single-cell analysis protocol to integrate contributions from all major cell types including neutrophils, monocytes, platelets, lymphocytes and the contents of serum. Patients with mild COVID-19 disease display a coordinated pattern of interferon-stimulated gene (ISG) expression across every cell population and these cells are systemically absent in patients with severe disease. Severe COVID-19 patients also paradoxically produce very high anti-SARS-CoV-2 antibody titers and have lower viral load as compared to mild disease. Examination of the serum from severe patients demonstrates that they uniquely produce antibodies with multiple patterns of specificity against interferon-stimulated cells and that those antibodies functionally block the production of the mild disease-associated ISG-expressing cells. Overzealous and auto-directed antibody responses pit the immune system against itself in many COVID-19 patients and this defines targets for immunotherapies to allow immune systems to provide viral defense. In severe COVID-19 patients, the immune system fails to generate cells that define mild disease; antibodies in their serum actively prevents the successful production of those cells.
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Affiliation(s)
- Alexis J Combes
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,UCSF CoLabs, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Tristan Courau
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,UCSF CoLabs, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Nicholas F Kuhn
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Kenneth H Hu
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Arja Ray
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - William S Chen
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Department of Radiation Oncology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Simon J Cleary
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Nayvin W Chew
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,UCSF CoLabs, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Divyashree Kushnoor
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,UCSF CoLabs, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Gabriella C Reeder
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,UCSF CoLabs, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Alan Shen
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,UCSF CoLabs, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Jessica Tsui
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,UCSF CoLabs, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Kamir J Hiam-Galvez
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Departments of Otolaryngology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Department of Microbiology & Immunology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Priscila Muñoz-Sandoval
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Department of Microbiology & Immunology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Sandler Asthma Basic Research Center, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Wandi S Zhu
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Department of Microbiology & Immunology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Sandler Asthma Basic Research Center, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - David S Lee
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Institute of Human Genetics and Division of Rheumatology, Department of Medicine, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Yang Sun
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Institute of Human Genetics and Division of Rheumatology, Department of Medicine, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Ran You
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Mélia Magnen
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Lauren Rodriguez
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Departments of Otolaryngology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Aleksandra Leligdowicz
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Colin R Zamecnik
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Weill Institute for Neurosciences, Department of Neurology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Rita P Loudermilk
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Weill Institute for Neurosciences, Department of Neurology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Michael R Wilson
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Weill Institute for Neurosciences, Department of Neurology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Chun J Ye
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Institute of Human Genetics and Division of Rheumatology, Department of Medicine, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Gabriela K Fragiadakis
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,UCSF CoLabs, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Institute of Human Genetics and Division of Rheumatology, Department of Medicine, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Mark R Looney
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Vincent Chan
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Alyssa Ward
- Institute of Human Genetics and Division of Rheumatology, Department of Medicine, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Sidney Carrillo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | | | - Michael Matthay
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - David J Erle
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,UCSF CoLabs, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Prescott G Woodruff
- ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Charles Langelier
- Division of Infectious Disease, Department of Medicine, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Kirsten Kangelaris
- Division of Hospital Medicine, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Carolyn M Hendrickson
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Carolyn Calfee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and the Cardiovascular Research Institute, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Arjun Arkal Rao
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,UCSF CoLabs, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
| | - Matthew F Krummel
- Department of Pathology, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA.,ImmunoX Initiative, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, CA 94143-0511, USA
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30
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Fragiadakis GK, Wastyk HC, Robinson JL, Sonnenburg ED, Sonnenburg JL, Gardner CD. Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight. Am J Clin Nutr 2020; 111:1127-1136. [PMID: 32186326 PMCID: PMC7266695 DOI: 10.1093/ajcn/nqaa046] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [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: 04/24/2019] [Accepted: 02/24/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND With the rising rates of obesity and associated metabolic disorders, there is a growing need for effective long-term weight-loss strategies, coupled with an understanding of how they interface with human physiology. Interest is growing in the potential role of gut microbes as they pertain to responses to different weight-loss diets; however, the ways that diet, the gut microbiota, and long-term weight loss influence one another is not well understood. OBJECTIVES Our primary objective was to determine if baseline microbiota composition or diversity was associated with weight-loss success. A secondary objective was to track the longitudinal associations of changes to lower-carbohydrate or lower-fat diets and concomitant weight loss with the composition and diversity of the gut microbiota. METHODS We used 16S ribosomal RNA gene amplicon sequencing to profile microbiota composition over a 12-mo period in 49 participants as part of a larger randomized dietary intervention study of participants consuming either a healthy low-carbohydrate or a healthy low-fat diet. RESULTS While baseline microbiota composition was not predictive of weight loss, each diet resulted in substantial changes in the microbiota 3-mo after the start of the intervention; some of these changes were diet specific (14 taxonomic changes specific to the healthy low-carbohydrate diet, 12 taxonomic changes specific to the healthy low-fat diet) and others tracked with weight loss (7 taxonomic changes in both diets). After these initial shifts, the microbiota returned near its original baseline state for the remainder of the intervention, despite participants maintaining their diet and weight loss for the entire study. CONCLUSIONS These results suggest a resilience to perturbation of the microbiota's starting profile. When considering the established contribution of obesity-associated microbiotas to weight gain in animal models, microbiota resilience may need to be overcome for long-term alterations to human physiology. This trial was registered at clinicaltrials.gov as NCT01826591.
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Affiliation(s)
| | - Hannah C Wastyk
- Department of Bioengineering, Stanford School of Medicine, Stanford, CA, USA
| | - Jennifer L Robinson
- Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Erica D Sonnenburg
- Microbiology and Immunology, Stanford School of Medicine, Stanford, CA, USA,Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA
| | - Justin L Sonnenburg
- Microbiology and Immunology, Stanford School of Medicine, Stanford, CA, USA,Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA,Chan Zuckerberg Biohub, San Francisco, CA, USA,Address correspondence to JLS (e-mail: )
| | - Christopher D Gardner
- Stanford Prevention Research Center, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA,Address correspondence to CDG (e-mail: )
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31
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Ko ME, Williams CM, Fread KI, Goggin SM, Rustagi RS, Fragiadakis GK, Nolan GP, Zunder ER. FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets. Nat Protoc 2020; 15:398-420. [PMID: 31932774 DOI: 10.1038/s41596-019-0246-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/29/2019] [Indexed: 12/12/2022]
Abstract
High-dimensional single-cell technologies present new opportunities for biological discovery, but the complex nature of the resulting datasets makes it challenging to perform comprehensive analysis. One particular challenge is the analysis of single-cell time course datasets: how to identify unique cell populations and track how they change across time points. To facilitate this analysis, we developed FLOW-MAP, a graphical user interface (GUI)-based software tool that uses graph layout analysis with sequential time ordering to visualize cellular trajectories in high-dimensional single-cell datasets obtained from flow cytometry, mass cytometry or single-cell RNA sequencing (scRNAseq) experiments. Here we provide a detailed description of the FLOW-MAP algorithm and how to use the open-source R package FLOWMAPR via its GUI or with text-based commands. This approach can be applied to many dynamic processes, including in vitro stem cell differentiation, in vivo development, oncogenesis, the emergence of drug resistance and cell signaling dynamics. To demonstrate our approach, we perform a step-by-step analysis of a single-cell mass cytometry time course dataset from mouse embryonic stem cells differentiating into the three germ layers: endoderm, mesoderm and ectoderm. In addition, we demonstrate FLOW-MAP analysis of a previously published scRNAseq dataset. Using both synthetic and experimental datasets for comparison, we perform FLOW-MAP analysis side by side with other single-cell analysis methods, to illustrate when it is advantageous to use the FLOW-MAP approach. The protocol takes between 30 min and 1.5 h to complete.
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Affiliation(s)
- Melissa E Ko
- Cancer Biology Program, Stanford School of Medicine, Stanford, CA, USA
| | - Corey M Williams
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Kristen I Fread
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Sarah M Goggin
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Rohit S Rustagi
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | | | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Eli R Zunder
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
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32
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Abstract
The gut microbiota is a complex and plastic network of diverse organisms intricately connected with human physiology. Recent advances in profiling approaches of both the microbiota and the immune system now enable a deeper exploration of immunity-microbiota connections. An important next step is to elucidate a human-relevant "map" of microbial-immune wiring while focusing on animal studies to probe a prioritized subset of interactions. Here, we provide an overview of this field's current status and discuss two approaches for establishing priorities for detailed investigation: (1) longitudinal intervention studies in humans probing the dynamics of both the microbiota and the immune system and (2) the study of traditional populations to assess lost features of human microbial identity whose absence may be contributing to the rise of immunological disorders. These human-centered approaches offer a judicious path forward to understand the impact of the microbiota in immune development and function.
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Affiliation(s)
- Sean P Spencer
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA.
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33
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Bongen E, Lucian H, Khatri A, Fragiadakis GK, Bjornson ZB, Nolan GP, Utz PJ, Khatri P. Sex Differences in the Blood Transcriptome Identify Robust Changes in Immune Cell Proportions with Aging and Influenza Infection. Cell Rep 2019; 29:1961-1973.e4. [PMID: 31722210 PMCID: PMC6856718 DOI: 10.1016/j.celrep.2019.10.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/12/2019] [Accepted: 10/03/2019] [Indexed: 02/09/2023] Open
Abstract
Sex differences in autoimmunity and infection suggest that a better understanding of molecular sex differences will improve the diagnosis and treatment of immune-related disease. We identified 144 differentially expressed genes, referred to as immune sex expression signature (iSEXS), between human males and females using an integrated multi-cohort analysis of blood transcriptome profiles from six discovery cohorts from five continents with 458 healthy individuals. We validated iSEXS in 11 additional cohorts of 524 peripheral blood samples. When we separated iSEXS into genes located on sex chromosomes (XY-iSEXS) or autosomes (autosomal-iSEXS), both modules distinguished males and females. iSEXS reflects sex differences in immune cell proportions, with female-associated genes showing higher expression by CD4+ T cells and male-associated genes showing higher expression by myeloid cells. Autosomal-iSEXS detected an increase in monocytes with age in females, reflected sex-differential immune cell dynamics during influenza infection, and predicted antibody response in males, but not females.
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Affiliation(s)
- Erika Bongen
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Haley Lucian
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Avani Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gabriela K Fragiadakis
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zachary B Bjornson
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
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34
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Aghaeepour N, Simonds EF, Knapp DJHF, Bruggner RV, Sachs K, Culos A, Gherardini PF, Samusik N, Fragiadakis GK, Bendall SC, Gaudilliere B, Angst MS, Eaves CJ, Weiss WA, Fantl WJ, Nolan GP. GateFinder: projection-based gating strategy optimization for flow and mass cytometry. Bioinformatics 2019; 34:4131-4133. [PMID: 29850785 DOI: 10.1093/bioinformatics/bty430] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/22/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using lower-parameter methods remains challenging. Results Here, we present GateFinder, an algorithm that enriches high-dimensional cell types with simple, stepwise polygon gates requiring only two markers at a time. A series of case studies of complex cell types illustrates how simplified enrichment strategies can enable more efficient assays, reveal novel biomarkers and clarify underlying biology. Availability and implementation The GateFinder algorithm is implemented as a free and open-source package for BioConductor: https://nalab.stanford.edu/gatefinder. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nima Aghaeepour
- Baxter Laboratory in Stem Cell Biology.,Department of Anesthesiology, Stanford University, Stanford, CA, USA
| | - Erin F Simonds
- Department of Neurology, University of California, San Francisco, CA, USA
| | - David J H F Knapp
- Terry Fox Laboratory, British Columbia Cancer Research Center, Vancouver, BC, Canada
| | | | | | - Anthony Culos
- Department of Anesthesiology, Stanford University, Stanford, CA, USA
| | | | | | | | - Sean C Bendall
- Baxter Laboratory in Stem Cell Biology.,Department of Pathology
| | - Brice Gaudilliere
- Baxter Laboratory in Stem Cell Biology.,Department of Anesthesiology, Stanford University, Stanford, CA, USA
| | - Martin S Angst
- Department of Anesthesiology, Stanford University, Stanford, CA, USA
| | - Connie J Eaves
- Terry Fox Laboratory, British Columbia Cancer Research Center, Vancouver, BC, Canada
| | - William A Weiss
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Wendy J Fantl
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
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35
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Jha AR, Davenport ER, Gautam Y, Bhandari D, Tandukar S, Ng KM, Fragiadakis GK, Holmes S, Gautam GP, Leach J, Sherchand JB, Bustamante CD, Sonnenburg JL. Gut microbiome transition across a lifestyle gradient in Himalaya. PLoS Biol 2018; 16:e2005396. [PMID: 30439937 PMCID: PMC6237292 DOI: 10.1371/journal.pbio.2005396] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [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: 01/17/2018] [Accepted: 10/15/2018] [Indexed: 01/04/2023] Open
Abstract
The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles. However, it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle. Whether shifts away from the foraging lifestyle that characterize much of humanity's past influence the gut microbiome, and to what degree, remains unclear. Here, we characterize the stool bacterial composition of four Himalayan populations to investigate how the gut community changes in response to shifts in traditional human lifestyles. These groups led seminomadic hunting-gathering lifestyles until transitioning to varying levels of agricultural dependence upon farming. The Tharu began farming 250-300 years ago, the Raute and Raji transitioned 30-40 years ago, and the Chepang retain many aspects of a foraging lifestyle. We assess the contributions of dietary and environmental factors on their gut-associated microbes and find that differences in the lifestyles of Himalayan foragers and farmers are strongly correlated with microbial community variation. Furthermore, the gut microbiomes of all four traditional Himalayan populations are distinct from that of the Americans, indicating that industrialization may further exacerbate differences in the gut community. The Chepang foragers harbor an elevated abundance of taxa associated with foragers around the world. Conversely, the gut microbiomes of the populations that have transitioned to farming are more similar to those of Americans, with agricultural dependence and several associated lifestyle and environmental factors correlating with the extent of microbiome divergence from the foraging population. The gut microbiomes of Raute and Raji reveal an intermediate state between the Chepang and Tharu, indicating that divergence from a stereotypical foraging microbiome can occur within a single generation. Our results also show that environmental factors such as drinking water source and solid cooking fuel are significantly associated with the gut microbiome. Despite the pronounced differences in gut bacterial composition across populations, we found little differences in alpha diversity across lifestyles. These findings in genetically similar populations living in the same geographical region establish the key role of lifestyle in determining human gut microbiome composition and point to the next challenging steps of determining how large-scale gut microbiome reconfiguration impacts human biology.
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Affiliation(s)
- Aashish R. Jha
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
- Center for Computational, Evolutionary, and Human Genetics, Stanford University, Stanford, California, United States of America
| | - Emily R. Davenport
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Yoshina Gautam
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | - Dinesh Bhandari
- Public Health Research Laboratory, Institute of Medicine, Maharajgunj, Kathmandu, Nepal
| | - Sarmila Tandukar
- Public Health Research Laboratory, Institute of Medicine, Maharajgunj, Kathmandu, Nepal
| | - Katharine M. Ng
- Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
| | - Gabriela K. Fragiadakis
- Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | | | - Jeff Leach
- Human Food Project, Terlingua, Texas, United States of America
- Department of Twin Research and Genetic Epidemiology, King’s College London, St. Thomas’ Hospital, London, United Kingdom
| | | | - Carlos D. Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
- Center for Computational, Evolutionary, and Human Genetics, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- Center for Human Microbiome Studies, Stanford University, Stanford, California, United States of America
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36
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Fragiadakis GK, Smits SA, Sonnenburg ED, Van Treuren W, Reid G, Knight R, Manjurano A, Changalucha J, Dominguez-Bello MG, Leach J, Sonnenburg JL. Links between environment, diet, and the hunter-gatherer microbiome. Gut Microbes 2018; 10:216-227. [PMID: 30118385 PMCID: PMC6546328 DOI: 10.1080/19490976.2018.1494103] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The study of traditional populations provides a view of human-associated microbes unperturbed by industrialization, as well as a window into the microbiota that co-evolved with humans. Here we discuss our recent work characterizing the microbiota from the Hadza hunter-gatherers of Tanzania. We found seasonal shifts in bacterial taxa, diversity, and carbohydrate utilization by the microbiota. When compared to the microbiota composition from other populations around the world, the Hadza microbiota shares bacterial families with other traditional societies that are rare or absent from microbiotas of industrialized nations. We present additional observations from the Hadza microbiota and their lifestyle and environment, including microbes detected on hands, water, and animal sources, how the microbiota varies with sex and age, and the short-term effects of introducing agricultural products into the diet. In the context of our previously published findings and of these additional observations, we discuss a path forward for future work.
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Affiliation(s)
- Gabriela K. Fragiadakis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Samuel A. Smits
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - William Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gregor Reid
- Department of Microbiology & Immunology, Department of Surgery, Western University, Lawson Health Research Institute, London, Ontario, Canada
| | - Rob Knight
- Departments of Pediatrics and Computer Science & Engineering and Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Alphaxard Manjurano
- Parasitic Diseases Programme and Laboratory Sciences Programme, National Institute for Medical Research, Mwanza Centre, Mwanza, Tanzania
| | - John Changalucha
- Sexual and Reproductive Health Programme and Laboratory Sciences Programme, National Institute for Medical Research, Mwanza Centre, Mwanza, Tanzania
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Department of AnthropologyRutgers, The State University of New Jersey, New Brunswick, NJUSA
| | - Jeff Leach
- Human Food Project, Terlingua, Texas, USA,The Department of Twin Research and Genetic EpidemiologyKing’s College London, St Thomas’ Hospital, London, UK
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Chan Zuckerberg Biohub, San Francisco, CA, USA,CONTACT Justin L. Sonnenburg
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37
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Blazkova J, Gupta S, Liu Y, Gaudilliere B, Ganio EA, Bolen CR, Saar-Dover R, Fragiadakis GK, Angst MS, Hasni S, Aghaeepour N, Stevenson D, Baldwin N, Anguiano E, Chaussabel D, Altman MC, Kaplan MJ, Davis MM, Furman D. Multicenter Systems Analysis of Human Blood Reveals Immature Neutrophils in Males and During Pregnancy. J Immunol 2017; 198:2479-2488. [PMID: 28179497 PMCID: PMC5337813 DOI: 10.4049/jimmunol.1601855] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/11/2017] [Indexed: 12/22/2022]
Abstract
Despite clear differences in immune system responses and in the prevalence of autoimmune diseases between males and females, there is little understanding of the processes involved. In this study, we identified a gene signature of immature-like neutrophils, characterized by the overexpression of genes encoding for several granule-containing proteins, which was found at higher levels (up to 3-fold) in young (20-30 y old) but not older (60 to >89 y old) males compared with females. Functional and phenotypic characterization of peripheral blood neutrophils revealed more mature and responsive neutrophils in young females, which also exhibited an elevated capacity in neutrophil extracellular trap formation at baseline and upon microbial or sterile autoimmune stimuli. The expression levels of the immature-like neutrophil signature increased linearly with pregnancy, an immune state of increased susceptibility to certain infections. Using mass cytometry, we also find increased frequencies of immature forms of neutrophils in the blood of women during late pregnancy. Thus, our findings show novel sex differences in innate immunity and identify a common neutrophil signature in males and in pregnant women.
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Affiliation(s)
- Jana Blazkova
- Division of Translational Medicine, Department of Systems Biology, Sidra Medical and Research Center, 26999 Doha, Qatar
| | - Sarthak Gupta
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Yudong Liu
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Christopher R Bolen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Ron Saar-Dover
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Gabriela K Fragiadakis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Sarfaraz Hasni
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - David Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | | | | | - Damien Chaussabel
- Division of Translational Medicine, Department of Systems Biology, Sidra Medical and Research Center, 26999 Doha, Qatar
| | - Matthew C Altman
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
- Institute for Immunity, Transplantation of Infection, Stanford University School of Medicine, Stanford, CA 94305; and
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - David Furman
- Division of Translational Medicine, Department of Systems Biology, Sidra Medical and Research Center, 26999 Doha, Qatar;
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
- Institute for Immunity, Transplantation of Infection, Stanford University School of Medicine, Stanford, CA 94305; and
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38
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Furman D, Chang J, Lartigue L, Bolen CR, Haddad F, Gaudilliere B, Ganio EA, Fragiadakis GK, Spitzer MH, Douchet I, Daburon S, Moreau JF, Nolan GP, Blanco P, Déchanet-Merville J, Dekker CL, Jojic V, Kuo CJ, Davis MM, Faustin B. Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states. Nat Med 2017; 23:174-184. [PMID: 28092664 DOI: 10.1038/nm.4267] [Citation(s) in RCA: 265] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 12/13/2016] [Indexed: 12/13/2022]
Abstract
Low-grade, chronic inflammation has been associated with many diseases of aging, but the mechanisms responsible for producing this inflammation remain unclear. Inflammasomes can drive chronic inflammation in the context of an infectious disease or cellular stress, and they trigger the maturation of interleukin-1β (IL-1β). Here we find that the expression of specific inflammasome gene modules stratifies older individuals into two extremes: those with constitutive expression of IL-1β, nucleotide metabolism dysfunction, elevated oxidative stress, high rates of hypertension and arterial stiffness; and those without constitutive expression of IL-1β, who lack these characteristics. Adenine and N4-acetylcytidine, nucleotide-derived metabolites that are detectable in the blood of the former group, prime and activate the NLRC4 inflammasome, induce the production of IL-1β, activate platelets and neutrophils and elevate blood pressure in mice. In individuals over 85 years of age, the elevated expression of inflammasome gene modules was associated with all-cause mortality. Thus, targeting inflammasome components may ameliorate chronic inflammation and various other age-associated conditions.
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Affiliation(s)
- David Furman
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.,Department of Systems Biology, Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Junlei Chang
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Lydia Lartigue
- INSERM U916 VINCO, Institut Bergonié, Bordeaux Cedex, France
| | - Christopher R Bolen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - François Haddad
- Institute of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Brice Gaudilliere
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Edward A Ganio
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Gabriela K Fragiadakis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew H Spitzer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Isabelle Douchet
- CIRID, UMR CNRS 5164, Université Bordeaux 2, Bordeaux Cedex, France
| | - Sophie Daburon
- CIRID, UMR CNRS 5164, Université Bordeaux 2, Bordeaux Cedex, France
| | | | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Patrick Blanco
- CIRID, UMR CNRS 5164, Université Bordeaux 2, Bordeaux Cedex, France
| | | | - Cornelia L Dekker
- Department of Pediatrics, Division of Infectious Diseases, Stanford University, Stanford, California, USA
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin Faustin
- CIRID, UMR CNRS 5164, Université Bordeaux 2, Bordeaux Cedex, France
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39
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Sogi KM, Holsclaw CM, Fragiadakis GK, Nomura DK, Leary JA, Bertozzi CR. Biosynthesis and Regulation of Sulfomenaquinone, a Metabolite Associated with Virulence in Mycobacterium tuberculosis. ACS Infect Dis 2016; 2:800-806. [PMID: 27933784 DOI: 10.1021/acsinfecdis.6b00106] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Sulfomenaquinone (SMK) is a recently identified metabolite that is unique to the Mycobacterium tuberculosis (M. tuberculosis) complex and is shown to modulate its virulence. Here, we report the identification of the SMK biosynthetic operon that, in addition to a previously identified sulfotransferase stf3, includes a putative cytochrome P450 gene (cyp128) and a gene of unknown function, rv2269c. We demonstrate that cyp128 and stf3 are sufficient for the biosynthesis of SMK from menaquinone and rv2269c exhibits promoter activity in M. tuberculosis. Loss of Stf3 expression, but not that of Cyp128, is correlated with elevated levels of menaquinone-9, an essential component in the electron-transport chain in M. tuberculosis. Finally, we showed in a mouse model of infection that the loss of cyp128 exhibits a hypervirulent phenotype similar to that in previous studies of the stf3 mutant. These findings provide a platform for defining the molecular basis of SMK's role in M. tuberculosis pathogenesis.
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Affiliation(s)
| | | | | | - Daniel K. Nomura
- Department
of Nutritional Science and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
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40
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Fragiadakis GK, Baca QJ, Gherardini PF, Ganio EA, Gaudilliere DK, Tingle M, Lancero HL, McNeil LS, Spitzer MH, Wong RJ, Shaw GM, Darmstadt GL, Sylvester KG, Winn VD, Carvalho B, Lewis DB, Stevenson DK, Nolan GP, Aghaeepour N, Angst MS, Gaudilliere BL. Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy. J Immunol 2016; 197:4482-4492. [PMID: 27793998 DOI: 10.4049/jimmunol.1601195] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/20/2016] [Indexed: 12/17/2022]
Abstract
Preterm labor and infections are the leading causes of neonatal deaths worldwide. During pregnancy, immunological cross talk between the mother and her fetus is critical for the maintenance of pregnancy and the delivery of an immunocompetent neonate. A precise understanding of healthy fetomaternal immunity is the important first step to identifying dysregulated immune mechanisms driving adverse maternal or neonatal outcomes. This study combined single-cell mass cytometry of paired peripheral and umbilical cord blood samples from mothers and their neonates with a graphical approach developed for the visualization of high-dimensional data to provide a high-resolution reference map of the cellular composition and functional organization of the healthy fetal and maternal immune systems at birth. The approach enabled mapping of known phenotypical and functional characteristics of fetal immunity (including the functional hyperresponsiveness of CD4+ and CD8+ T cells and the global blunting of innate immune responses). It also allowed discovery of new properties that distinguish the fetal and maternal immune systems. For example, examination of paired samples revealed differences in endogenous signaling tone that are unique to a mother and her offspring, including increased ERK1/2, MAPK-activated protein kinase 2, rpS6, and CREB phosphorylation in fetal Tbet+CD4+ T cells, CD8+ T cells, B cells, and CD56loCD16+ NK cells and decreased ERK1/2, MAPK-activated protein kinase 2, and STAT1 phosphorylation in fetal intermediate and nonclassical monocytes. This highly interactive functional map of healthy fetomaternal immunity builds the core reference for a growing data repository that will allow inferring deviations from normal associated with adverse maternal and neonatal outcomes.
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Affiliation(s)
- Gabriela K Fragiadakis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Quentin J Baca
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Pier Federico Gherardini
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Dyani K Gaudilliere
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Martha Tingle
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Hope L Lancero
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Leslie S McNeil
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Matthew H Spitzer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | - Gary L Darmstadt
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | - Karl G Sylvester
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94305; and
| | - Brendan Carvalho
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - David B Lewis
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305.,Division of Allergy, Immunology, and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Brice L Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305;
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41
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Gaudillière B, Fragiadakis GK, Bruggner RV, Nicolau M, Finck R, Tingle M, Silva J, Ganio EA, Yeh CG, Maloney WJ, Huddleston JI, Goodman SB, Davis MM, Bendall SC, Fantl WJ, Angst MS, Nolan GP. Clinical recovery from surgery correlates with single-cell immune signatures. Sci Transl Med 2016; 6:255ra131. [PMID: 25253674 DOI: 10.1126/scitranslmed.3009701] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Delayed recovery from surgery causes personal suffering and substantial societal and economic costs. Whether immune mechanisms determine recovery after surgical trauma remains ill-defined. Single-cell mass cytometry was applied to serial whole-blood samples from 32 patients undergoing hip replacement to comprehensively characterize the phenotypic and functional immune response to surgical trauma. The simultaneous analysis of 14,000 phosphorylation events in precisely phenotyped immune cell subsets revealed uniform signaling responses among patients, demarcating a surgical immune signature. When regressed against clinical parameters of surgical recovery, including functional impairment and pain, strong correlations were found with STAT3 (signal transducer and activator of transcription), CREB (adenosine 3',5'-monophosphate response element-binding protein), and NF-κB (nuclear factor κB) signaling responses in subsets of CD14(+) monocytes (R = 0.7 to 0.8, false discovery rate <0.01). These sentinel results demonstrate the capacity of mass cytometry to survey the human immune system in a relevant clinical context. The mechanistically derived immune correlates point to diagnostic signatures, and potential therapeutic targets, that could postoperatively improve patient recovery.
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Affiliation(s)
- Brice Gaudillière
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA. Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford, CA 94305, USA
| | - Gabriela K Fragiadakis
- Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford, CA 94305, USA. Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Robert V Bruggner
- Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford, CA 94305, USA. Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA
| | - Monica Nicolau
- Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford, CA 94305, USA. Department of Mathematics, Stanford University, Stanford, CA 94305, USA. Center for Cancer Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Rachel Finck
- Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford, CA 94305, USA. Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Martha Tingle
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julian Silva
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christine G Yeh
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Maloney
- Department of Orthopedic Surgery, Stanford University, Redwood City, CA 94063, USA
| | - James I Huddleston
- Department of Orthopedic Surgery, Stanford University, Redwood City, CA 94063, USA
| | - Stuart B Goodman
- Department of Orthopedic Surgery, Stanford University, Redwood City, CA 94063, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Sean C Bendall
- Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford, CA 94305, USA. Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Wendy J Fantl
- Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford, CA 94305, USA. Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Garry P Nolan
- Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford, CA 94305, USA. Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
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42
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Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE. The effect of microbial colonization on the host proteome varies by gastrointestinal location. ISME J 2015; 10:1170-81. [PMID: 26574685 DOI: 10.1038/ismej.2015.187] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 09/02/2015] [Accepted: 09/18/2015] [Indexed: 01/06/2023]
Abstract
Endogenous intestinal microbiota have wide-ranging and largely uncharacterized effects on host physiology. Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to define the mouse intestinal proteome in the stomach, jejunum, ileum, cecum and proximal colon under three colonization states: germ-free (GF), monocolonized with Bacteroides thetaiotaomicron and conventionally raised (CR). Our analysis revealed distinct proteomic abundance profiles along the gastrointestinal (GI) tract. Unsupervised clustering showed that host protein abundance primarily depended on GI location rather than colonization state and specific proteins and functions that defined these locations were identified by random forest classifications. K-means clustering of protein abundance across locations revealed substantial differences in host protein production between CR mice relative to GF and monocolonized mice. Finally, comparison with fecal proteomic data sets suggested that the identities of stool proteins are not biased to any region of the GI tract, but are substantially impacted by the microbiota in the distal colon.
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Affiliation(s)
- Joshua S Lichtman
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Emily Alsentzer
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Mia Jaffe
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Sprockett
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Evan Masutani
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Elvis Ikwa
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Gabriela K Fragiadakis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Bevan Emma Huang
- Digital Productivity Flagship, Commonwealth Scientific and Industrial Research Organization, Dutton Park, Queensland, Australia
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
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43
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Gaudillière B, Ganio EA, Tingle M, Lancero HL, Fragiadakis GK, Baca QJ, Aghaeepour N, Wong RJ, Quaintance C, El-Sayed YY, Shaw GM, Lewis DB, Stevenson DK, Nolan GP, Angst MS. Implementing Mass Cytometry at the Bedside to Study the Immunological Basis of Human Diseases: Distinctive Immune Features in Patients with a History of Term or Preterm Birth. Cytometry A 2015; 87:817-29. [PMID: 26190063 PMCID: PMC4758855 DOI: 10.1002/cyto.a.22720] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [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] [Indexed: 11/12/2022]
Abstract
Single-cell technologies have immense potential to shed light on molecular and biological processes that drive human diseases. Mass cytometry (or Cytometry by Time Of Flight mass spectrometry, CyTOF) has already been employed in clinical studies to comprehensively survey patients' circulating immune system. As interest in the "bedside" application of mass cytometry is growing, the delineation of relevant methodological issues is called for. This report uses a newly generated dataset to discuss important methodological considerations when mass cytometry is implemented in a clinical study. Specifically, the use of whole blood samples versus peripheral blood mononuclear cells (PBMCs), design of mass-tagged antibody panels, technical and analytical implications of sample barcoding, and application of traditional and unsupervised approaches to analyze high-dimensional mass cytometry datasets are discussed. A mass cytometry assay was implemented in a cross-sectional study of 19 women with a history of term or preterm birth to determine whether immune traits in peripheral blood differentiate the two groups in the absence of pregnancy. Twenty-seven phenotypic and 11 intracellular markers were simultaneously analyzed in whole blood samples stimulated with lipopolysaccharide (LPS at 0, 0.1, 1, 10, and 100 ng mL(-1)) to examine dose-dependent signaling responses within the toll-like receptor 4 (TLR4) pathway. Complementary analyses, grounded in traditional or unsupervised gating strategies of immune cell subsets, indicated that the prpS6 and pMAPKAPK2 responses in classical monocytes are accentuated in women with a history of preterm birth (FDR<1%). The results suggest that women predisposed to preterm birth may be prone to mount an exacerbated TLR4 response during the course of pregnancy. This important hypothesis-generating finding points to the power of single-cell mass cytometry to detect biologically important differences in a relatively small patient cohort.
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Affiliation(s)
- Brice Gaudillière
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, School of Medicine, Stanford, California 94305
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
| | - Edward A. Ganio
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, School of Medicine, Stanford, California 94305
| | - Martha Tingle
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, School of Medicine, Stanford, California 94305
| | - Hope L. Lancero
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, School of Medicine, Stanford, California 94305
| | - Gabriela K. Fragiadakis
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
| | - Quentin J. Baca
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, School of Medicine, Stanford, California 94305
| | - Nima Aghaeepour
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
| | - Ronald J. Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
| | - Cele Quaintance
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
| | - Yasser Y. El-Sayed
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, California 94305
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
| | - David B. Lewis
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
| | - David K. Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
| | - Garry P. Nolan
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
| | - Martin S. Angst
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, School of Medicine, Stanford, California 94305
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44
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Spitzer MH, Gherardini PF, Fragiadakis GK, Bhattacharya N, Yuan RT, Hotson AN, Finck R, Carmi Y, Zunder ER, Fantl WJ, Bendall SC, Engleman EG, Nolan GP. IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system. Science 2015; 349:1259425. [PMID: 26160952 DOI: 10.1126/science.1259425] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Immune cells function in an interacting hierarchy that coordinates the activities of various cell types according to genetic and environmental contexts. We developed graphical approaches to construct an extensible immune reference map from mass cytometry data of cells from different organs, incorporating landmark cell populations as flags on the map to compare cells from distinct samples. The maps recapitulated canonical cellular phenotypes and revealed reproducible, tissue-specific deviations. The approach revealed influences of genetic variation and circadian rhythms on immune system structure, enabled direct comparisons of murine and human blood cell phenotypes, and even enabled archival fluorescence-based flow cytometry data to be mapped onto the reference framework. This foundational reference map provides a working definition of systemic immune organization to which new data can be integrated to reveal deviations driven by genetics, environment, or pathology.
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Affiliation(s)
- Matthew H Spitzer
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA.
| | - Pier Federico Gherardini
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Gabriela K Fragiadakis
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | | | - Robert T Yuan
- Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA
| | - Andrew N Hotson
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Rachel Finck
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Yaron Carmi
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Eli R Zunder
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Wendy J Fantl
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Stanford University, Stanford, CA 94305, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA
| | - Edgar G Engleman
- Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA
| | - Garry P Nolan
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA.
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45
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Behbehani GK, Thom C, Zunder ER, Finck R, Gaudilliere B, Fragiadakis GK, Fantl WJ, Nolan GP. Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining. Cytometry A 2014; 85:1011-9. [PMID: 25274027 DOI: 10.1002/cyto.a.22573] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [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: 06/17/2014] [Revised: 08/19/2014] [Accepted: 09/15/2014] [Indexed: 12/29/2022]
Abstract
Fluorescent cellular barcoding and mass-tag cellular barcoding are cytometric methods that enable high sample throughput, minimize inter-sample variation, and reduce reagent consumption. Previously employed barcoding protocols require that barcoding be performed after surface marker staining, complicating combining the technique with measurement of alcohol-sensitive surface epitopes. This report describes a method of barcoding fixed cells after a transient partial permeabilization with 0.02% saponin that results in efficient and consistent barcode staining with fluorescent or mass-tagged reagents while preserving surface marker staining. This approach simplifies barcoding protocols and allows direct comparison of surface marker staining of multiple samples without concern for variations in the antibody cocktail volume, antigen-antibody ratio, or machine sensitivity. Using this protocol, cellular barcoding can be used to reliably detect subtle differences in surface marker expression.
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Affiliation(s)
- Gregory K Behbehani
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California; Divisions of Hematology and Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
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