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Blum SM, Zlotoff DA, Smith NP, Kernin IJ, Ramesh S, Zubiri L, Caplin J, Samanta N, Martin SC, Tirard A, Sen P, Song Y, Barth J, Slowikowski K, Nasrallah M, Tantivit J, Manakongtreecheep K, Arnold BY, McGuire J, Pinto CJ, McLoughlin D, Jackson M, Chan P, Lawless A, Sharova T, Nieman LT, Gainor JF, Juric D, Mino-Kenudsen M, Sullivan RJ, Boland GM, Stone JR, Thomas MF, Neilan TG, Reynolds KL, Villani AC. Immune Responses in Checkpoint Myocarditis Across Heart, Blood, and Tumor. bioRxiv 2023:2023.09.15.557794. [PMID: 37790460 PMCID: PMC10542127 DOI: 10.1101/2023.09.15.557794] [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: 10/05/2023]
Abstract
Immune checkpoint inhibitors (ICIs) are widely used anti-cancer therapies that can cause morbid and potentially fatal immune-related adverse events (irAEs). ICI-related myocarditis (irMyocarditis) is uncommon but has the highest mortality of any irAE. The pathogenesis of irMyocarditis and its relationship to anti-tumor immunity remain poorly understood. We sought to define immune responses in heart, tumor, and blood during irMyocarditis and identify biomarkers of clinical severity by leveraging single-cell (sc)RNA-seq coupled with T cell receptor (TCR) sequencing, microscopy, and proteomics analysis of 28 irMyocarditis patients and 23 controls. Our analysis of 284,360 cells from heart and blood specimens identified cytotoxic T cells, inflammatory macrophages, conventional dendritic cells (cDCs), and fibroblasts enriched in irMyocarditis heart tissue. Additionally, potentially targetable, pro-inflammatory transcriptional programs were upregulated across multiple cell types. TCR clones enriched in heart and paired tumor tissue were largely non-overlapping, suggesting distinct T cell responses within these tissues. We also identify the presence of cardiac-expanded TCRs in a circulating, cycling CD8 T cell population as a novel peripheral biomarker of fatality. Collectively, these findings highlight critical biology driving irMyocarditis and putative biomarkers for therapeutic intervention.
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Affiliation(s)
- Steven M. Blum
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Daniel A. Zlotoff
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Cardio-Oncology Program, Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Neal P. Smith
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Isabela J. Kernin
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Swetha Ramesh
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Leyre Zubiri
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Joshua Caplin
- Cardio-Oncology Program, Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Nandini Samanta
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Sidney C. Martin
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Alice Tirard
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Pritha Sen
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Transplant and Immunocompromised Host Program, Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital
| | - Yuhui Song
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
| | - Jaimie Barth
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Kamil Slowikowski
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Mazen Nasrallah
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, North Shore Physicians Group, Department of Medicine, Mass General Brigham Healthcare Center, Lynn, MA, USA
| | - Jessica Tantivit
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Kasidet Manakongtreecheep
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Benjamin Y. Arnold
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - John McGuire
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Christopher J. Pinto
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Clinical Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel McLoughlin
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Clinical Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Monica Jackson
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Clinical Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - PuiYee Chan
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Clinical Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Aleigha Lawless
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Tatyana Sharova
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Linda T. Nieman
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
| | - Justin F. Gainor
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Dejan Juric
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Mari Mino-Kenudsen
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan J. Sullivan
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Genevieve M. Boland
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - James R. Stone
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Molly F. Thomas
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Tomas G. Neilan
- Harvard Medical School, Boston, MA, USA
- Cardio-Oncology Program, Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kerry L. Reynolds
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
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Smith NP, Yan Y, Pan Y, Williams JB, Manakongtreecheep K, Pant S, Zhao J, Tian T, Pan T, Stingley C, Wu K, Zhang J, Kley AL, Sorger PK, Villani AC, Kupper TS. Resident memory T cell development is associated with AP-1 transcription factor upregulation across anatomical niches. bioRxiv 2023:2023.09.29.560006. [PMID: 37873428 PMCID: PMC10592877 DOI: 10.1101/2023.09.29.560006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Tissue-resident memory T (T RM ) cells play a central role in immune responses to pathogens across all barrier tissues after infection. However, the underlying mechanisms that drive T RM differentiation and priming for their recall effector function remains unclear. In this study, we leveraged both newly generated and publicly available single-cell RNA-sequencing (scRNAseq) data generated across 10 developmental time points to define features of CD8 T RM across both skin and small-intestine intraepithelial lymphocytes (siIEL). We employed linear modeling to capture temporally-associated gene programs that increase their expression levels in T cell subsets transitioning from an effector to a memory T cell state. In addition to capturing tissue-specific gene programs, we defined a consensus T RM signature of 60 genes across skin and siIEL that can effectively distinguish T RM from circulating T cell populations, providing a more specific T RM signature than what was previously generated by comparing bulk T RM to naïve or non-tissue resident memory populations. This updated T RM signature included the AP-1 transcription factor family members Fos, Fosb and Fosl2 . Moreover, ATACseq analysis detected an enrichment of AP-1-specific motifs at open chromatin sites in mature T RM . CyCIF tissue imaging detected nuclear co-localization of AP-1 members Fosb and Junb in resting CD8 T RM >100 days post-infection. Taken together, these results reveal a critical role of AP-1 transcription factor members in T RM biology and suggests a novel mechanism for rapid reactivation of resting T RM in tissue upon antigen encounter.
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Alladina J, Smith NP, Kooistra T, Slowikowski K, Kernin IJ, Deguine J, Keen HL, Manakongtreecheep K, Tantivit J, Rahimi RA, Sheng SL, Nguyen ND, Haring AM, Giacona FL, Hariri LP, Xavier RJ, Luster AD, Villani AC, Cho JL, Medoff BD. A human model of asthma exacerbation reveals transcriptional programs and cell circuits specific to allergic asthma. Sci Immunol 2023; 8:eabq6352. [PMID: 37146132 PMCID: PMC10440046 DOI: 10.1126/sciimmunol.abq6352] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/13/2023] [Indexed: 05/07/2023]
Abstract
Asthma is a chronic disease most commonly associated with allergy and type 2 inflammation. However, the mechanisms that link airway inflammation to the structural changes that define asthma are incompletely understood. Using a human model of allergen-induced asthma exacerbation, we compared the lower airway mucosa in allergic asthmatics and allergic non-asthmatic controls using single-cell RNA sequencing. In response to allergen, the asthmatic airway epithelium was highly dynamic and up-regulated genes involved in matrix degradation, mucus metaplasia, and glycolysis while failing to induce injury-repair and antioxidant pathways observed in controls. IL9-expressing pathogenic TH2 cells were specific to asthmatic airways and were only observed after allergen challenge. Additionally, conventional type 2 dendritic cells (DC2 that express CD1C) and CCR2-expressing monocyte-derived cells (MCs) were uniquely enriched in asthmatics after allergen, with up-regulation of genes that sustain type 2 inflammation and promote pathologic airway remodeling. In contrast, allergic controls were enriched for macrophage-like MCs that up-regulated tissue repair programs after allergen challenge, suggesting that these populations may protect against asthmatic airway remodeling. Cellular interaction analyses revealed a TH2-mononuclear phagocyte-basal cell interactome unique to asthmatics. These pathogenic cellular circuits were characterized by type 2 programming of immune and structural cells and additional pathways that may sustain and amplify type 2 signals, including TNF family signaling, altered cellular metabolism, failure to engage antioxidant responses, and loss of growth factor signaling. Our findings therefore suggest that pathogenic effector circuits and the absence of proresolution programs drive structural airway disease in response to type 2 inflammation.
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Affiliation(s)
- Jehan Alladina
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Neal P. Smith
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Tristan Kooistra
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kamil Slowikowski
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Isabela J. Kernin
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Jacques Deguine
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Henry L. Keen
- Iowa Institute of Human Genetics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Kasidet Manakongtreecheep
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Jessica Tantivit
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Rod A. Rahimi
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Susan L. Sheng
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nhan D. Nguyen
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexis M. Haring
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Francesca L. Giacona
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lida P. Hariri
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Ramnik J. Xavier
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew D. Luster
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Josalyn L. Cho
- Division of Pulmonary, Critical Care and Occupational Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Benjamin D. Medoff
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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4
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LaSalle TJ, Gonye ALK, Freeman SS, Kaplonek P, Gushterova I, Kays KR, Manakongtreecheep K, Tantivit J, Rojas-Lopez M, Russo BC, Sharma N, Thomas MF, Lavin-Parsons KM, Lilly BM, Mckaig BN, Charland NC, Khanna HK, Lodenstein CL, Margolin JD, Blaum EM, Lirofonis PB, Revach OY, Mehta A, Sonny A, Bhattacharyya RP, Parry BA, Goldberg MB, Alter G, Filbin MR, Villani AC, Hacohen N, Sade-Feldman M. Longitudinal characterization of circulating neutrophils uncovers phenotypes associated with severity in hospitalized COVID-19 patients. Cell Rep Med 2022; 3:100779. [PMID: 36208629 PMCID: PMC9510054 DOI: 10.1016/j.xcrm.2022.100779] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 09/30/2021] [Revised: 08/02/2022] [Accepted: 09/21/2022] [Indexed: 01/21/2023]
Abstract
Mechanisms of neutrophil involvement in severe coronavirus disease 2019 (COVID-19) remain incompletely understood. Here, we collect longitudinal blood samples from 306 hospitalized COVID-19+ patients and 86 controls and perform bulk RNA sequencing of enriched neutrophils, plasma proteomics, and high-throughput antibody profiling to investigate relationships between neutrophil states and disease severity. We identify dynamic switches between six distinct neutrophil subtypes. At days 3 and 7 post-hospitalization, patients with severe disease display a granulocytic myeloid-derived suppressor cell-like gene expression signature, while patients with resolving disease show a neutrophil progenitor-like signature. Humoral responses are identified as potential drivers of neutrophil effector functions, with elevated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific immunoglobulin G1 (IgG1)-to-IgA1 ratios in plasma of severe patients who survived. In vitro experiments confirm that while patient-derived IgG antibodies induce phagocytosis in healthy donor neutrophils, IgA antibodies predominantly induce neutrophil cell death. Overall, our study demonstrates a dysregulated myelopoietic response in severe COVID-19 and a potential role for IgA-dominant responses contributing to mortality.
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Affiliation(s)
- Thomas J LaSalle
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Health Sciences and Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA.
| | - Anna L K Gonye
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel S Freeman
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Irena Gushterova
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kyle R Kays
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kasidet Manakongtreecheep
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jessica Tantivit
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Maricarmen Rojas-Lopez
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Brian C Russo
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Nihaarika Sharma
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Molly F Thomas
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Brendan M Lilly
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brenna N Mckaig
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nicole C Charland
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Hargun K Khanna
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Carl L Lodenstein
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Justin D Margolin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily M Blaum
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paola B Lirofonis
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Or-Yam Revach
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Arnav Mehta
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Abraham Sonny
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Roby P Bhattacharyya
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Blair Alden Parry
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Marcia B Goldberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA; Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Michael R Filbin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Emergency Medicine, Harvard Medical School, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Moshe Sade-Feldman
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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5
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Leisman DE, Mehta A, Thompson BT, Charland NC, Gonye ALK, Gushterova I, Kays KR, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Filbin MR, Goldberg MB. Alveolar, Endothelial, and Organ Injury Marker Dynamics in Severe COVID-19. Am J Respir Crit Care Med 2022; 205:507-519. [PMID: 34878969 PMCID: PMC8906476 DOI: 10.1164/rccm.202106-1514oc] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [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: 06/24/2021] [Accepted: 12/07/2021] [Indexed: 11/23/2022] Open
Abstract
Rationale: Alveolar and endothelial injury may be differentially associated with coronavirus disease (COVID-19) severity over time. Objectives: To describe alveolar and endothelial injury dynamics and associations with COVID-19 severity, cardiorenovascular injury, and outcomes. Methods: This single-center observational study enrolled patients with COVID-19 requiring respiratory support at emergency department presentation. More than 40 markers of alveolar (including receptor for advanced glycation endproducts [RAGE]), endothelial (including angiopoietin-2), and cardiorenovascular injury (including renin, kidney injury molecule-1, and troponin-I) were serially compared between invasively and spontaneously ventilated patients using mixed-effects repeated-measures models. Ventilatory ratios were calculated for intubated patients. Associations of biomarkers with modified World Health Organization scale at Day 28 were determined with multivariable proportional-odds regression. Measurements and Main Results: Of 225 patients, 74 (33%) received invasive ventilation at Day 0. RAGE was 1.80-fold higher in invasive ventilation patients at Day 0 (95% confidence interval [CI], 1.50-2.17) versus spontaneous ventilation, but decreased over time in all patients. Changes in alveolar markers did not correlate with changes in endothelial, cardiac, or renal injury markers. In contrast, endothelial markers were similar to lower at Day 0 for invasive ventilation versus spontaneous ventilation, but then increased over time only among intubated patients. In intubated patients, angiopoietin-2 was similar (fold difference, 1.02; 95% CI, 0.89-1.17) to nonintubated patients at Day 0 but 1.80-fold higher (95% CI, 1.56-2.06) at Day 3; cardiorenovascular injury markers showed similar patterns. Endothelial markers were not consistently associated with ventilatory ratios. Endothelial markers were more often significantly associated with 28-day outcomes than alveolar markers. Conclusions: Alveolar injury markers increase early. Endothelial injury markers increase later and are associated with cardiorenovascular injury and 28-day outcome. Alveolar and endothelial injury likely contribute at different times to disease progression in severe COVID-19.
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Affiliation(s)
- Daniel E. Leisman
- Department of Anesthesiology, Critical Care, and Pain Medicine
- Department of Medicine
| | - Arnav Mehta
- Massachusetts General Hospital Cancer Center
- Department of Medicine
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Anna L. K. Gonye
- Center for Cancer Research
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
| | - Irena Gushterova
- Center for Cancer Research
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
| | | | | | - Thomas J. LaSalle
- Center for Cancer Research
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
| | | | | | | | - Kasidet Manakongtreecheep
- Center for Cancer Research
- Center for Immunology and Inflammatory Diseases, and
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
| | | | | | - Maricarmen Rojas-Lopez
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine
- Department of Microbiology, and
| | - Brian C. Russo
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine
- Department of Microbiology, and
| | - Nihaarika Sharma
- Center for Cancer Research
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
| | - Jessica Tantivit
- Center for Cancer Research
- Center for Immunology and Inflammatory Diseases, and
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
| | - Molly F. Thomas
- Center for Cancer Research
- Center for Immunology and Inflammatory Diseases, and
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
| | | | - Alexandra-Chloé Villani
- Massachusetts General Hospital Cancer Center
- Department of Medicine
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
| | - Moshe Sade-Feldman
- Massachusetts General Hospital Cancer Center
- Department of Medicine
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
| | - Nir Hacohen
- Massachusetts General Hospital Cancer Center
- Department of Medicine
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
| | - Michael R. Filbin
- Department of Emergency Medicine, and
- Department of Emergency Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
| | - Marcia B. Goldberg
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine
- Department of Microbiology, and
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; and
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6
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Kaplonek P, Wang C, Bartsch Y, Fischinger S, Gorman MJ, Bowman K, Kang J, Dayal D, Martin P, Nowak RP, Villani AC, Hsieh CL, Charland NC, Gonye AL, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Sade-Feldman M, Feldman J, Julg B, Nilles EJ, Musk ER, Menon AS, Fischer ES, McLellan JS, Schmidt A, Goldberg MB, Filbin MR, Hacohen N, Lauffenburger DA, Alter G. Early cross-coronavirus reactive signatures of humoral immunity against COVID-19. Sci Immunol 2021; 6:eabj2901. [PMID: 34652962 PMCID: PMC8943686 DOI: 10.1126/sciimmunol.abj2901] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/06/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022]
Abstract
The introduction of vaccines has inspired hope in the battle against SARS-CoV-2. However, the emergence of viral variants, in the absence of potent antivirals, has left the world struggling with the uncertain nature of this disease. Antibodies currently represent the strongest correlate of immunity against SARS-CoV-2, thus we profiled the earliest humoral signatures in a large cohort of acutely ill (survivors and nonsurvivors) and mild or asymptomatic individuals with COVID-19. Although a SARS-CoV-2–specific immune response evolved rapidly in survivors of COVID-19, nonsurvivors exhibited blunted and delayed humoral immune evolution, particularly with respect to S2-specific antibodies. Given the conservation of S2 across β-coronaviruses, we found that the early development of SARS-CoV-2–specific immunity occurred in tandem with preexisting common β-coronavirus OC43 humoral immunity in survivors, which was also selectively expanded in individuals that develop a paucisymptomatic infection. These data point to the importance of cross-coronavirus immunity as a correlate of protection against COVID-19.
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Affiliation(s)
| | - Chuangqi Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yannic Bartsch
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | | | - Kathryn Bowman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Jaewon Kang
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Diana Dayal
- Space Exploration Technologies Corporation, Hawthorne, CA, USA
| | - Patrick Martin
- Space Exploration Technologies Corporation, Hawthorne, CA, USA
| | - Radoslaw P. Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nicole C. Charland
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anna L.K. Gonye
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Irena Gushterova
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Hargun K. Khanna
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas J. LaSalle
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Brendan M. Lilley
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Carl L. Lodenstein
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kasidet Manakongtreecheep
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Justin D. Margolin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brenna N. McKaig
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Maricarmen Rojas-Lopez
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brian C. Russo
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nihaarika Sharma
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jessica Tantivit
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Molly F. Thomas
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Moshe Sade-Feldman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Boris Julg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Elon R. Musk
- Space Exploration Technologies Corporation, Hawthorne, CA, USA
| | - Anil S. Menon
- Space Exploration Technologies Corporation, Hawthorne, CA, USA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Aaron Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Marcia B. Goldberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Michael R. Filbin
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
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7
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LaSalle TJ, Gonye ALK, Freeman SS, Kaplonek P, Gushterova I, Kays KR, Manakongtreecheep K, Tantivit J, Rojas-Lopez M, Russo BC, Sharma N, Thomas MF, Lavin-Parsons KM, Lilly BM, Mckaig BN, Charland NC, Khanna HK, Lodenstein CL, Margolin JD, Blaum EM, Lirofonis PB, Sonny A, Bhattacharyya RP, Parry BA, Goldberg MB, Alter G, Filbin MR, Villani AC, Hacohen N, Sade-Feldman M. Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with disease severity in hospitalized COVID-19 patients. bioRxiv 2021. [PMID: 34642692 DOI: 10.1101/2021.10.04.463121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Multiple studies have identified an association between neutrophils and COVID-19 disease severity; however, the mechanistic basis of this association remains incompletely understood. Here we collected 781 longitudinal blood samples from 306 hospitalized COVID-19 + patients, 78 COVID-19 âˆ' acute respiratory distress syndrome patients, and 8 healthy controls, and performed bulk RNA-sequencing of enriched neutrophils, plasma proteomics, cfDNA measurements and high throughput antibody profiling assays to investigate the relationship between neutrophil states and disease severity or death. We identified dynamic switches between six distinct neutrophil subtypes using non-negative matrix factorization (NMF) clustering. At days 3 and 7 post-hospitalization, patients with severe disease had an enrichment of a granulocytic myeloid derived suppressor cell-like state gene expression signature, while non-severe patients with resolved disease were enriched for a progenitor-like immature neutrophil state signature. Severe disease was associated with gene sets related to neutrophil degranulation, neutrophil extracellular trap (NET) signatures, distinct metabolic signatures, and enhanced neutrophil activation and generation of reactive oxygen species (ROS). We found that the majority of patients had a transient interferon-stimulated gene signature upon presentation to the emergency department (ED) defined here as Day 0, regardless of disease severity, which persisted only in patients who subsequently died. Humoral responses were identified as potential drivers of neutrophil effector functions, as enhanced antibody-dependent neutrophil phagocytosis and reduced NETosis was associated with elevated SARS-CoV-2-specific IgG1-to-IgA1 ratios in plasma of severe patients who survived. In vitro experiments confirmed that while patient-derived IgG antibodies mostly drove neutrophil phagocytosis and ROS production in healthy donor neutrophils, patient-derived IgA antibodies induced a predominant NETosis response. Overall, our study demonstrates neutrophil dysregulation in severe COVID-19 and a potential role for IgA-dominant responses in driving neutrophil effector functions in severe disease and mortality.
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8
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Li Y, Schneider AM, Mehta A, Sade-Feldman M, Kays KR, Gentili M, Charland NC, Gonye AL, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Parry BA, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Regan J, Flynn JP, Villani AC, Hacohen N, Goldberg MB, Filbin MR, Li JZ. SARS-CoV-2 viremia is associated with distinct proteomic pathways and predicts COVID-19 outcomes. J Clin Invest 2021; 131:148635. [PMID: 34196300 PMCID: PMC8245177 DOI: 10.1172/jci148635] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [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: 02/10/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUNDSARS-CoV-2 plasma viremia has been associated with severe disease and death in COVID-19 in small-scale cohort studies. The mechanisms behind this association remain elusive.METHODSWe evaluated the relationship between SARS-CoV-2 viremia, disease outcome, and inflammatory and proteomic profiles in a cohort of COVID-19 emergency department participants. SARS-CoV-2 viral load was measured using a quantitative reverse transcription PCR-based platform. Proteomic data were generated with Proximity Extension Assay using the Olink platform.RESULTSThis study included 300 participants with nucleic acid test-confirmed COVID-19. Plasma SARS-CoV-2 viremia levels at the time of presentation predicted adverse disease outcomes, with an adjusted OR of 10.6 (95% CI 4.4-25.5, P < 0.001) for severe disease (mechanical ventilation and/or 28-day mortality) and 3.9 (95% CI 1.5-10.1, P = 0.006) for 28-day mortality. Proteomic analyses revealed prominent proteomic pathways associated with SARS-CoV-2 viremia, including upregulation of SARS-CoV-2 entry factors (ACE2, CTSL, FURIN), heightened markers of tissue damage to the lungs, gastrointestinal tract, and endothelium/vasculature, and alterations in coagulation pathways.CONCLUSIONThese results highlight the cascade of vascular and tissue damage associated with SARS-CoV-2 plasma viremia that underlies its ability to predict COVID-19 disease outcomes.FUNDINGMark and Lisa Schwartz; the National Institutes of Health (U19AI082630); the American Lung Association; the Executive Committee on Research at Massachusetts General Hospital; the Chan Zuckerberg Initiative; Arthur, Sandra, and Sarah Irving for the David P. Ryan, MD, Endowed Chair in Cancer Research; an EMBO Long-Term Fellowship (ALTF 486-2018); a Cancer Research Institute/Bristol Myers Squibb Fellowship (CRI2993); the Harvard Catalyst/Harvard Clinical and Translational Science Center (National Center for Advancing Translational Sciences, NIH awards UL1TR001102 and UL1TR002541-01); and by the Harvard University Center for AIDS Research (National Institute of Allergy and Infectious Diseases, 5P30AI060354).
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Affiliation(s)
- Yijia Li
- Brigham and Women’s Hospital and
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Alexis M. Schneider
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Arnav Mehta
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Center for Cancer Research, Department of Medicine, and
| | - Moshe Sade-Feldman
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Cancer Research, Department of Medicine, and
| | - Kyle R. Kays
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Matteo Gentili
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nicole C. Charland
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Anna L.K. Gonye
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Cancer Research, Department of Medicine, and
| | - Irena Gushterova
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Cancer Research, Department of Medicine, and
| | - Hargun K. Khanna
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas J. LaSalle
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Cancer Research, Department of Medicine, and
| | | | - Brendan M. Lilley
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Carl L. Lodenstein
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kasidet Manakongtreecheep
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Justin D. Margolin
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Brenna N. McKaig
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Blair A. Parry
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Maricarmen Rojas-Lopez
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Brian C. Russo
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nihaarika Sharma
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jessica Tantivit
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Molly F. Thomas
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | - Alexandra-Chloé Villani
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Nir Hacohen
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Cancer Research, Department of Medicine, and
| | - Marcia B. Goldberg
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael R. Filbin
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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9
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Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye AL, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB. Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions. Cell Rep Med 2021; 2:100287. [PMID: 33969320 PMCID: PMC8091031 DOI: 10.1016/j.xcrm.2021.100287] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [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] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/08/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023]
Abstract
Mechanisms underlying severe coronavirus disease 2019 (COVID-19) disease remain poorly understood. We analyze several thousand plasma proteins longitudinally in 306 COVID-19 patients and 78 symptomatic controls, uncovering immune and non-immune proteins linked to COVID-19. Deconvolution of our plasma proteome data using published scRNA-seq datasets reveals contributions from circulating immune and tissue cells. Sixteen percent of patients display reduced inflammation yet comparably poor outcomes. Comparison of patients who died to severely ill survivors identifies dynamic immune-cell-derived and tissue-associated proteins associated with survival, including exocrine pancreatic proteases. Using derived tissue-specific and cell-type-specific intracellular death signatures, cellular angiotensin-converting enzyme 2 (ACE2) expression, and our data, we infer whether organ damage resulted from direct or indirect effects of infection. We propose a model in which interactions among myeloid, epithelial, and T cells drive tissue damage. These datasets provide important insights and a rich resource for analysis of mechanisms of severe COVID-19 disease.
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Affiliation(s)
- Michael R. Filbin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Emergency Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Arnav Mehta
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alexis M. Schneider
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kyle R. Kays
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Matteo Gentili
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Bánk G. Fenyves
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Emergency Medicine, Semmelweis University, Budapest, Hungary
| | - Nicole C. Charland
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anna L.K. Gonye
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Irena Gushterova
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Hargun K. Khanna
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas J. LaSalle
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Brendan M. Lilley
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Carl L. Lodenstein
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kasidet Manakongtreecheep
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Justin D. Margolin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brenna N. McKaig
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Maricarmen Rojas-Lopez
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Brian C. Russo
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Nihaarika Sharma
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jessica Tantivit
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Molly F. Thomas
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robert E. Gerszten
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- CardioVascular Institute, Department of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Graham S. Heimberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Paul J. Hoover
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - David J. Lieb
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Brian Lin
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Regenerative Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Debby Ngo
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Karin Pelka
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Miguel Reyes
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher S. Smillie
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Avinash Waghray
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Regenerative Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas E. Wood
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Amanda S. Zajac
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | | | | | - Roby P. Bhattacharyya
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Blair Alden Parry
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Moshe Sade-Feldman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Marcia B. Goldberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
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10
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Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Triglia ET, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams TS, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo AS, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CG. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nat Med 2021; 27:546-559. [PMID: 33654293 PMCID: PMC9469728 DOI: 10.1038/s41591-020-01227-z] [Citation(s) in RCA: 206] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 12/23/2020] [Indexed: 02/01/2023]
Abstract
Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.
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Affiliation(s)
- Christoph Muus
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; John A. Paulson School of Engineering and Applied Sciences, Harvard, University, Cambridge, MA 02138
| | - Malte D. Luecken
- Institute of Computational Biology, Helmholtz Zentrum München, , Neuherberg, Germany
| | - Gokcen Eraslan
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lisa Sikkema
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Avinash Waghray
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA; Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Graham Heimberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yoshihiko Kobayashi
- Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Eeshit Dhaval Vaishnav
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02140, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Christopher Smillie
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Karthik A. Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Elizabeth Thu Duong
- University of California San Diego, Department of Pediatrics, Division of Respiratory Medicine
| | - Evgenij Fiskin
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Elena Torlai Triglia
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Meshal Ansari
- Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Peiwen Cai
- Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA
| | - Brian Lin
- Center for Regenerative Medicine, Massachusetts General Hospital,Boston, MA, USA; Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Justin Buchanan
- Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093. Department of Cellular and Molecular Medicine, University of California-San Diego School of Medicine, La Jolla, CA, 92093
| | - Sijia Chen
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA
| | - Jian Shu
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Adam L. Haber
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA. Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Hattie Chung
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel T. Montoro
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Taylor S. Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
| | - Hananeh Aliee
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Samuel J. Allon
- Institute for Medical Engineering and Science & Department of Chemistry, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard
| | - Zaneta Andrusivova
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology
| | - Ilias Angelidis
- Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin Bassler
- Department for Genomics & Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | | | - Inbal Benhar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard,Cambridge, MA, 02142, USA
| | | | | | - Liam Bolt
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Emelie Braun
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute
| | - Linh T. Bui
- Translational Genomics Research Institute, Phoenix, AZ
| | - Steven Callori
- Department of Medicine, Boston University School of Medicine; Bioinformatic Program, Boston University
| | - Mark Chaffin
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
| | - Evgeny Chichelnitskiy
- Institute of Transplant Immunology, Hannover Medical School, MHH, Carl-Neuberg Str. 1, 30625 Hannover, Germany, phone +40 511 532 9745; fax +40 511 532 8090; German Center for Infectious Diseases DZIF, TTU-IICH 07.801
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, University of California-San Diego, La Jolla, CA, 92093
| | - Thomas M. Conlon
- Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Michael S. Cuoco
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Anna S.E. Cuomo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Marie Deprez
- Université Côte d’Azur, CNRS, IPMC, Sophia-Antipolis, 06560, France
| | - Grant Duclos
- Boston University School of Medicine, Boston, MA 02118, USA
| | | | - David S. Fischer
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Shila Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Astrid Gillich
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Bruno Giotti
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Minzhe Guo
- Divisions of Pulmonary Biology; Perinatal Institute, Cincinnati Children's Hospital Medical Center
| | | | - Arun C. Habermann
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Tyler Harvey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Peng He
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Xiaomeng Hou
- Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093. Department of Cellular and Molecular Medicine, University of California-San Diego School of Medicine, La Jolla, CA, 92093
| | - Lijuan Hu
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute
| | - Yan Hu
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado, Aurora, CO, USA 80045
| | - Alok Jaiswal
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lu Ji
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Theodoro S. Kapellos
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Christin S. Kuo
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Ludvig Larsson
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology
| | | | - Kyungtae Lim
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Monika Litviňuková
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.; Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Leif S. Ludwig
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA Division of Hematology / Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Soeren Lukassen
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany; Berlin Institute of Health (BIH), Center for Digital Health, Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Wendy Luo
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Elo Madissoon
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK; Wellcome Sanger Institute, Cellular Genetics Programme Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Kasidet Manakongtreecheep
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sylvie Leroy
- Université Côte d’Azur, Pulmonology Department, CHU Nice, NICE, France; Institut de Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Christoph H. Mayr
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Group Systems Medicine of Chronic Lung Disease, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Ian M. Mbano
- Africa Health Research Institute,Durban, South Africa. School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of Kwazulu Natal, Durban, South Africa
| | - Alexi M. McAdams
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114
| | - Ahmad N. Nabhan
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Sarah K. Nyquist
- Computational and Systems Biology, CSAIL, Institute for Medical Engineering and Science & Department of Chemistry, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard
| | - Lolita Penland
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Olivier B. Poirion
- Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093. Department of Cellular and Molecular Medicine, University of California-San Diego School of Medicine, La Jolla, CA, 92093
| | - Sergio Poli
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
| | - CanCan Qi
- Dept. of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rachel Queen
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Bioscience West Building, Newcastle upon Tyne NE1 3 BZ, UK
| | - Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA, United States.; Department of Cardiology, University Heart & Vascular Center, University of Hamburg, Hamburg, Germany
| | - Ivan Rosas
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
| | - Jonas C. Schupp
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Conor V. Shea
- Boston University School of Medicine, Boston, MA 02118, USA
| | - Xingyi Shi
- Department of Medicine, Boston University School of Medicine; Bioinformatic Program, Boston University
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford Medicine, Stanford, CA 94305, USA
| | - Rene V. Sit
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Kamil Slowikowski
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Neal P. Smith
- Massachusetts General Hospital Center for Immunology and Inflammatory Diseases
| | - Alex Sountoulidis
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute
| | - Maximilian Strunz
- Comprehensive Pneumology Center (CPC) and Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | | | - Dawei Sun
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Carlos Talavera-López
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Peng Tan
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jessica Tantivit
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
| | - Kyle J. Travaglini
- Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
| | - Nathan R. Tucker
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142; Masonic Medical Research Institute, Utica, NY, USA 13501
| | - Katherine A. Vernon
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marc H. Wadsworth
- Institute for Medical Engineering and Science, Department of Chemistry & Koch Institute for Integrative Cancer Research, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Xiuting Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA
| | - Ke Xu
- Boston University School of Medicine, Boston, MA 02118, USA
| | - Wenjun Yan
- Center for Brain Science, Harvard University, Cambridge, MA 02138; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - William Zhao
- Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA
| | - Carly G.K. Ziegler
- Harvard-MIT Health Sciences and Technology, Institute for Medical Engineering and Science, Koch Institute for Integrative Cancer Research, MIT; Broad Institute of MIT and Harvard; Ragon Institute of MGH, MIT and Harvard
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11
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Li Y, Schneider AM, Mehta A, Sade-Feldman M, Kays KR, Gentili M, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilly BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Parry BA, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Regan J, Flynn JP, Villani AC, Hacohen N, Goldberg MB, Filbin MR, Li JZ. SARS-CoV-2 Viremia is Associated with Distinct Proteomic Pathways and Predicts COVID-19 Outcomes. medRxiv 2021:2021.02.24.21252357. [PMID: 33655257 PMCID: PMC7924277 DOI: 10.1101/2021.02.24.21252357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
BACKGROUND Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) plasma viremia has been associated with severe disease and death in coronavirus disease 2019 (COVID-19) in small-scale cohort studies. The mechanisms behind this association remain elusive. METHODS We evaluated the relationship between SARS-CoV-2 viremia, disease outcome, inflammatory and proteomic profiles in a cohort of COVID-19 emergency department participants. SARS-CoV-2 viral load was measured using qRT-PCR based platform. Proteomic data were generated with Proximity Extension Assay (PEA) using the Olink platform. RESULTS Three hundred participants with nucleic acid test-confirmed COVID-19 were included in this study. Levels of plasma SARS-CoV-2 viremia at the time of presentation predicted adverse disease outcomes, with an adjusted odds ratio (aOR) of 10.6 (95% confidence interval [CI] 4.4, 25.5, P<0.001) for severe disease (mechanical ventilation and/or 28-day mortality) and aOR of 3.9 (95%CI 1.5, 10.1, P=0.006) for 28-day mortality. Proteomic analyses revealed prominent proteomic pathways associated with SARS-CoV-2 viremia, including upregulation of SARS-CoV-2 entry factors (ACE2, CTSL, FURIN), heightened markers of tissue damage to the lungs, gastrointestinal tract, endothelium/vasculature and alterations in coagulation pathways. CONCLUSIONS These results highlight the cascade of vascular and tissue damage associated with SARS-CoV-2 plasma viremia that underlies its ability to predict COVID-19 disease outcomes.
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12
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Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilly BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB. Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients. bioRxiv 2020:2020.11.02.365536. [PMID: 33173871 PMCID: PMC7654866 DOI: 10.1101/2020.11.02.365536] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
COVID-19 has caused over 1 million deaths globally, yet the cellular mechanisms underlying severe disease remain poorly understood. By analyzing several thousand plasma proteins in 306 COVID-19 patients and 78 symptomatic controls over serial timepoints using two complementary approaches, we uncover COVID-19 host immune and non-immune proteins not previously linked to this disease. Integration of plasma proteomics with nine published scRNAseq datasets shows that SARS-CoV-2 infection upregulates monocyte/macrophage, plasmablast, and T cell effector proteins. By comparing patients who died to severely ill patients who survived, we identify dynamic immunomodulatory and tissue-associated proteins associated with survival, providing insights into which host responses are beneficial and which are detrimental to survival. We identify intracellular death signatures from specific tissues and cell types, and by associating these with angiotensin converting enzyme 2 (ACE2) expression, we map tissue damage associated with severe disease and propose which damage results from direct viral infection rather than from indirect effects of illness. We find that disease severity in lung tissue is driven by myeloid cell phenotypes and cell-cell interactions with lung epithelial cells and T cells. Based on these results, we propose a model of immune and epithelial cell interactions that drive cell-type specific and tissue-specific damage in severe COVID-19.
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13
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Melnikov S, Kwok HS, Manakongtreecheep K, van den Elzen A, Thoreen CC, Söll D. Archaeal Ribosomal Proteins Possess Nuclear Localization Signal-Type Motifs: Implications for the Origin of the Cell Nucleus. Mol Biol Evol 2020; 37:124-133. [PMID: 31501901 DOI: 10.1093/molbev/msz207] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Eukaryotic cells are divided into the nucleus and the cytosol, and, to enter the nucleus, proteins typically possess short signal sequences, known as nuclear localization signals (NLSs). Although NLSs have long been considered as features unique to eukaryotic proteins, we show here that similar or identical protein segments are present in ribosomal proteins from the Archaea. Specifically, the ribosomal proteins uL3, uL15, uL18, and uS12 possess NLS-type motifs that are conserved across all major branches of the Archaea, including the most ancient groups Microarchaeota and Diapherotrites, pointing to the ancient origin of NLS-type motifs in the Archaea. Furthermore, by using fluorescence microscopy, we show that the archaeal NLS-type motifs can functionally substitute eukaryotic NLSs and direct the transport of ribosomal proteins into the nuclei of human cells. Collectively, these findings illustrate that the origin of NLSs preceded the origin of the cell nucleus, suggesting that the initial function of NLSs was not related to intracellular trafficking, but possibly was to improve recognition of nucleic acids by cellular proteins. Overall, our study reveals rare evolutionary intermediates among archaeal cells that can help elucidate the sequence of events that led to the origin of the eukaryotic cell.
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Affiliation(s)
- Sergey Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Hui-Si Kwok
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | | | | | - Carson C Thoreen
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
- Department of Chemistry, Yale University, New Haven, CT
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14
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Zhao C, Lyu Z, Long F, Akinyemi T, Manakongtreecheep K, Söll D, Whitman WB, Vinyard DJ, Liu Y. The Nbp35/ApbC homolog acts as a nonessential [4Fe-4S] transfer protein in methanogenic archaea. FEBS Lett 2019; 594:924-932. [PMID: 31709520 DOI: 10.1002/1873-3468.13673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 06/18/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 01/09/2023]
Abstract
The nucleotide binding protein 35 (Nbp35)/cytosolic Fe-S cluster deficient 1 (Cfd1)/alternative pyrimidine biosynthetic protein C (ApbC) protein homologs have been identified in all three domains of life. In eukaryotes, the Nbp35/Cfd1 heterocomplex is an essential Fe-S cluster assembly scaffold required for the maturation of Fe-S proteins in the cytosol and nucleus, whereas the bacterial ApbC is an Fe-S cluster transfer protein only involved in the maturation of a specific target protein. Here, we show that the Nbp35/ApbC homolog MMP0704 purified from its native archaeal host Methanococcus maripaludis contains a [4Fe-4S] cluster that can be transferred to a [4Fe-4S] apoprotein. Deletion of mmp0704 from M. maripaludis does not cause growth deficiency under our tested conditions. Our data indicate that Nbp35/ApbC is a nonessential [4Fe-4S] cluster transfer protein in methanogenic archaea.
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Affiliation(s)
- Cuiping Zhao
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Zhe Lyu
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Feng Long
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Taiwo Akinyemi
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | | | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Chemistry, Yale University, New Haven, CT, USA
| | | | - David J Vinyard
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Yuchen Liu
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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15
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Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT, Xu M, Gandal MJ, Lou S, Zhang J, Park JJ, Yan C, Rhie SK, Manakongtreecheep K, Zhou H, Nathan A, Peters M, Mattei E, Fitzgerald D, Brunetti T, Moore J, Jiang Y, Girdhar K, Hoffman GE, Kalayci S, Gümüş ZH, Crawford GE, Roussos P, Akbarian S, Jaffe AE, White KP, Weng Z, Sestan N, Geschwind DH, Knowles JA, Gerstein MB. Comprehensive functional genomic resource and integrative model for the human brain. Science 2019; 362:362/6420/eaat8464. [PMID: 30545857 DOI: 10.1126/science.aat8464] [Citation(s) in RCA: 462] [Impact Index Per Article: 92.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022]
Abstract
Despite progress in defining genetic risk for psychiatric disorders, their molecular mechanisms remain elusive. Addressing this, the PsychENCODE Consortium has generated a comprehensive online resource for the adult brain across 1866 individuals. The PsychENCODE resource contains ~79,000 brain-active enhancers, sets of Hi-C linkages, and topologically associating domains; single-cell expression profiles for many cell types; expression quantitative-trait loci (QTLs); and further QTLs associated with chromatin, splicing, and cell-type proportions. Integration shows that varying cell-type proportions largely account for the cross-population variation in expression (with >88% reconstruction accuracy). It also allows building of a gene regulatory network, linking genome-wide association study variants to genes (e.g., 321 for schizophrenia). We embed this network into an interpretable deep-learning model, which improves disease prediction by ~6-fold versus polygenic risk scores and identifies key genes and pathways in psychiatric disorders.
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16
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Melnikov SV, Manakongtreecheep K, Rivera KD, Makarenko A, Pappin DJ, Söll D. Muller's Ratchet and Ribosome Degeneration in the Obligate Intracellular Parasites Microsporidia. Int J Mol Sci 2018; 19:ijms19124125. [PMID: 30572624 PMCID: PMC6321566 DOI: 10.3390/ijms19124125] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 11/19/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 12/18/2022] Open
Abstract
Microsporidia are fungi-like parasites that have the smallest known eukaryotic genome, and for that reason they are used as a model to study the phenomenon of genome decay in parasitic forms of life. Similar to other intracellular parasites that reproduce asexually in an environment with alleviated natural selection, Microsporidia experience continuous genome decay that is driven by Muller's ratchet-an evolutionary process of irreversible accumulation of deleterious mutations that lead to gene loss and the miniaturization of cellular components. Particularly, Microsporidia have remarkably small ribosomes in which the rRNA is reduced to the minimal enzymatic core. In this study, we analyzed microsporidian ribosomes to study an apparent impact of Muller's ratchet on structure of RNA and protein molecules in parasitic forms of life. Through mass spectrometry of microsporidian proteome and analysis of microsporidian genomes, we found that massive rRNA reduction in microsporidian ribosomes appears to annihilate the binding sites for ribosomal proteins eL8, eL27, and eS31, suggesting that these proteins are no longer bound to the ribosome in microsporidian species. We then provided an evidence that protein eS31 is retained in Microsporidia due to its non-ribosomal function in ubiquitin biogenesis. Our study illustrates that, while Microsporidia carry the same set of ribosomal proteins as non-parasitic eukaryotes, some ribosomal proteins are no longer participating in protein synthesis in Microsporidia and they are preserved from genome decay by having extra-ribosomal functions. More generally, our study shows that many components of parasitic cells, which are identified by automated annotation of pathogenic genomes, may lack part of their biological functions due to continuous genome decay.
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Affiliation(s)
- Sergey V Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
| | | | - Keith D Rivera
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Arthur Makarenko
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Darryl J Pappin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
- Department of Molecular Biophysics and Biochemistry, Department of Chemistry, Yale University, New Haven, CT 06511, USA.
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17
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Abstract
Ribosomal proteins are indispensable components of a living cell, and yet their structures are remarkably diverse in different species. Here we use manually curated structural alignments to provide a comprehensive catalog of structural variations in homologous ribosomal proteins from bacteria, archaea, eukaryotes, and eukaryotic organelles. By resolving numerous ambiguities and errors of automated structural and sequence alignments, we uncover a whole new class of structural variations that reside within seemingly conserved segments of ribosomal proteins. We then illustrate that these variations reflect an apparent adaptation of ribosomal proteins to the specific environments and lifestyles of living species. Finally, we show that most of these structural variations reside within nonglobular extensions of ribosomal proteins-protein segments that are thought to promote ribosome biogenesis by stabilizing the proper folding of ribosomal RNA. We show that although the extensions are thought to be the most ancient peptides on our planet, they are in fact the most rapidly evolving and most structurally and functionally diverse segments of ribosomal proteins. Overall, our work illustrates that, despite being long considered as slowly evolving and highly conserved, ribosomal proteins are more complex and more specialized than is generally recognized.
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Affiliation(s)
- Sergey Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | | | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
- Department of Chemistry, Yale University, New Haven, CT
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Manakongtreecheep K. SMS-reminder for vaccination in Africa: research from published, unpublished and grey literature. Pan Afr Med J 2017; 27:23. [PMID: 29296158 PMCID: PMC5745941 DOI: 10.11604/pamj.supp.2017.27.3.12115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/01/2017] [Indexed: 11/17/2022] Open
Abstract
Immunization for children against vaccine-preventable diseases is one of the most important health intervention method in the world, both in terms of its health impact and cost-effectiveness. Through EPI and various other programs such as the Decades of Vaccines, immunization has been improving the health of children around the world. However, this progress falls short of global immunization targets of the Global Vaccine Action Plan (GVAP). Furthermore, the African region still lags behind in immunization, and suffers from a high proportion of vaccine preventable diseases as a result. Reminders and recall for vaccination have been shown to improve health care-seeking behaviours, and have been recommended for application in routine and supplemental measles immunization activities. With mobile phones becoming more accessible in Africa, SMS vaccine reminder system has been proposed as a convenient and easily scalable way to inform caregivers of the disease and the importance of immunization, to address any concerns related to immunization safety, and to remind them of vaccination schedules and campaigns. There have been 6 published articles and 1 unpublished article on the effect of SMS reminder system for immunization in Africa. The studies done has shown that SMS vaccination reminder has led to improvements in vaccination uptakes in various metrics, whether is through the increase in vaccination coverage, decrease in dropout rates, increase in completion rate, or decrease in delay for vaccination.
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Abstract
Despite the existence of a highly effective measles vaccine and the decrease in worldwide deaths from measles by more than 79% from the 2000 baseline levels, measles today remains one of the leading causes of vaccine-preventable deaths in the world. The African region is a key player in the global fight against measles. Africa has made tremendous progress in its effort to immunize children and to control the disease, increasing its regional measles vaccination coverage from 56% in 2001 to 85% in 2010. The Republic of Kenya has been a strong follower of the World Health Assembly and Measles Elimination 2020 resolutions, which aims to eliminate measles from the country. Since the beginning of the 21st century, Kenya has faced many challenges, but also aid, in the form of new innovations, in their fight against measles. In 2002, Kenya started its first SIA using A-D syringes, and from 2003-2005, GAVI funded injection safety support (INS) to Kenya, as an effort to scale-up safe injection in sub-Saharan Africa. In 2016, the Kenya introduced Measles-Rubella (MR) combined vaccine in its nationwide SIA campaign, after recognizing that rubella is a disease that must be controlled along with measles. In 2009 and 2012 SIAs, Red Cross volunteers conducted H2H visits to promote immunization as well as document information from the community with regards to immunization, including the current coverage, to campaign management levels. Case-based surveillance, using real-time PCR, measles-specific IgM detection and Epi-link were used to confirm and map measles infection during outbreaks. Alternative serosurveys such as Dried Blood Spot and Urine sample surveys were also tested in Kenya. In 2013 and 2016, two studies were also conducted in Kenya on the use of SMS reminder system for routine immunization. These studies, which showed SMS to significantly improve the vaccination coverage, paved way for use of SMS in a larger scale in Kenya.
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