1
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Nguyen LH, Okin D, Drew DA, Battista VM, Jesudasen SJ, Kuntz TM, Bhosle A, Thompson KN, Reinicke T, Lo CH, Woo JE, Caraballo A, Berra L, Vieira J, Huang CY, Das Adhikari U, Kim M, Sui HY, Magicheva-Gupta M, McIver L, Goldberg MB, Kwon DS, Huttenhower C, Chan AT, Lai PS. Metagenomic assessment of gut microbial communities and risk of severe COVID-19. Genome Med 2023; 15:49. [PMID: 37438797 DOI: 10.1186/s13073-023-01202-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/13/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. METHODS We profiled 127 hospitalized patients with COVID-19 (n = 79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. RESULTS Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID," suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with classifying whether stool was obtained from patients with severe vs. moderate COVID-19, a finding that was externally validated in an independent cohort. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease. CONCLUSIONS Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to expand upon these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.
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Affiliation(s)
- Long H Nguyen
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Daniel Okin
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David A Drew
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Vincent M Battista
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sirus J Jesudasen
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Thomas M Kuntz
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amrisha Bhosle
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Trenton Reinicke
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Chun-Han Lo
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jacqueline E Woo
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexander Caraballo
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lorenzo Berra
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jacob Vieira
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ching-Ying Huang
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Minsik Kim
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hui-Yu Sui
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Marina Magicheva-Gupta
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lauren McIver
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Marcia B Goldberg
- Division of Infectious Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Douglas S Kwon
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA, USA
- Division of Infectious Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Peggy S Lai
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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2
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Kumari R, Yadav Y, Misra R, Das U, Das Adhikari U, Malakar P, Dubey GP. Emerging frontiers of antibiotics use and their impacts on the human gut microbiome. Microbiol Res 2022; 263:127127. [PMID: 35914416 DOI: 10.1016/j.micres.2022.127127] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/17/2022] [Accepted: 07/11/2022] [Indexed: 02/07/2023]
Abstract
Antibiotics, the primary drugs used to cure bacterial diseases, are increasingly becoming ineffective due to the emergence of multiple drug resistance (MDR) leading to recurrence of previously sensitive pathogens. Human gut microbiome (GM), known to play an important role in various physiological processes, consists of pool of diverse microbes. Indiscriminate use of antibiotics during the life span of an individual may lead to development of resistant microbes e.g. Vibrio, Acinetobacter, Escherichia, Klebsiella, Clostridia, etc. in the human GM. Transmission of antibiotic resistant genes (ARGs) between pathogenic and commensal bacteria occurs more frequently in microbiome communities wherein bacteria communicate and exchange cellular constituents both among themselves and with the host. Additionally, co-factors like 'early vs. late' exposure, type of antibiotics and duration of treatment modulate the adverse effects of antibiotics on GM maturation. Furthermore, factors like mode of birth, ethnicity, malnutrition, demography, diet, lifestyle, etc., which influence GM composition, can also indirectly alter the host response to antibiotics. Currently, advanced 'omics' and culturomics approaches are revealing novel avenues to study the interplay between antibiotics and the microbiome and to identify resistant genes in these bacterial communities. Here, we discuss the recent developments that have given insights into the effects of antibiotics on the homeostatic balance of the gut microbiome and thus on human health.
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Affiliation(s)
- Rekha Kumari
- Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India.
| | - Yasha Yadav
- Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India
| | - Richa Misra
- Department of Zoology, Sri Venkateswara College, University of Delhi, Delhi 1100021, India
| | - Utpal Das
- Department of Neurosciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Upasana Das Adhikari
- The Ragon Institute of MGH, MIT and Harvard, 400 Technology Square Cambridge, MA 02139, USA
| | - Pushkar Malakar
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gyanendra P Dubey
- Molecular Microbial Pathogenesis Unit, Institut Pasteur, 28 rue du Docteur Roux, 75724 Cedex 15 Paris, France.
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3
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Lai P, Nguyen L, Okin D, Drew D, Battista V, Jesudasen S, Kuntz T, Bhosle A, Thompson K, Reinicke T, Lo CH, Woo J, Caraballo A, Berra L, Vieira J, Huang CY, Adhikari UD, Kim M, Sui HY, Magicheva-Gupta M, McIver L, Goldberg M, Kwon D, Huttenhower C, Chan A. Metagenomic assessment of gut microbial communities and risk of severe COVID-19. Res Sq 2022. [PMID: 35677075 PMCID: PMC9176657 DOI: 10.21203/rs.3.rs-1717624/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. We profiled 127 hospitalized patients with COVID-19 (n=79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. 48 species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or “long COVID”, suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with predicting whether stool was obtained from patients with severe vs. moderate COVID-19. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease. Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to validate these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.
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4
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Junqueira C, Crespo Â, Ranjbar S, de Lacerda LB, Lewandrowski M, Ingber J, Parry B, Ravid S, Clark S, Schrimpf MR, Ho F, Beakes C, Margolin J, Russell N, Kays K, Boucau J, Das Adhikari U, Vora SM, Leger V, Gehrke L, Henderson LA, Janssen E, Kwon D, Sander C, Abraham J, Goldberg MB, Wu H, Mehta G, Bell S, Goldfeld AE, Filbin MR, Lieberman J. FcγR-mediated SARS-CoV-2 infection of monocytes activates inflammation. Nature 2022; 606:576-584. [PMID: 35385861 PMCID: PMC10071495 DOI: 10.1038/s41586-022-04702-4] [Citation(s) in RCA: 256] [Impact Index Per Article: 128.0] [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: 01/22/2021] [Accepted: 03/29/2022] [Indexed: 12/26/2022]
Abstract
SARS-CoV-2 can cause acute respiratory distress and death in some patients1. Although severe COVID-19 is linked to substantial inflammation, how SARS-CoV-2 triggers inflammation is not clear2. Monocytes and macrophages are sentinel cells that sense invasive infection to form inflammasomes that activate caspase-1 and gasdermin D, leading to inflammatory death (pyroptosis) and the release of potent inflammatory mediators3. Here we show that about 6% of blood monocytes of patients with COVID-19 are infected with SARS-CoV-2. Monocyte infection depends on the uptake of antibody-opsonized virus by Fcγ receptors. The plasma of vaccine recipients does not promote antibody-dependent monocyte infection. SARS-CoV-2 begins to replicate in monocytes, but infection is aborted, and infectious virus is not detected in the supernatants of cultures of infected monocytes. Instead, infected cells undergo pyroptosis mediated by activation of NLRP3 and AIM2 inflammasomes, caspase-1 and gasdermin D. Moreover, tissue-resident macrophages, but not infected epithelial and endothelial cells, from lung autopsies from patients with COVID-19 have activated inflammasomes. Taken together, these findings suggest that antibody-mediated SARS-CoV-2 uptake by monocytes and macrophages triggers inflammatory cell death that aborts the production of infectious virus but causes systemic inflammation that contributes to COVID-19 pathogenesis.
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Affiliation(s)
- Caroline Junqueira
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil.
| | - Ângela Crespo
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Shahin Ranjbar
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Luna B de Lacerda
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Mercedes Lewandrowski
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Jacob Ingber
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Blair Parry
- Emergency Medicine, Institute for Patient Care, Massachusetts General Hospital, Boston, MA, USA
| | - Sagi Ravid
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Sarah Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Marie Rose Schrimpf
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Felicia Ho
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Caroline Beakes
- Emergency Medicine, Institute for Patient Care, Massachusetts General Hospital, Boston, MA, USA
| | - Justin Margolin
- Emergency Medicine, Institute for Patient Care, Massachusetts General Hospital, Boston, MA, USA
| | - Nicole Russell
- Emergency Medicine, Institute for Patient Care, Massachusetts General Hospital, Boston, MA, USA
| | - Kyle Kays
- Emergency Medicine, Institute for Patient Care, Massachusetts General Hospital, Boston, MA, USA
| | - Julie Boucau
- Ragon Institute, Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard Medical School, Cambridge, MA, USA
| | - Upasana Das Adhikari
- Ragon Institute, Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard Medical School, Cambridge, MA, USA
| | - Setu M Vora
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Valerie Leger
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lee Gehrke
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lauren A Henderson
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - Erin Janssen
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - Douglas Kwon
- Ragon Institute, Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard Medical School, Cambridge, MA, USA
| | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Marcia B Goldberg
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Center for Bacterial Pathogenesis, Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Hao Wu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gautam Mehta
- Institute for Liver and Digestive Health, University College London, London, UK
- Institute of Hepatology, Foundation for Liver Research, London, UK
| | - Steven Bell
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Anne E Goldfeld
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael R Filbin
- Emergency Medicine, Institute for Patient Care, Massachusetts General Hospital, Boston, MA, USA.
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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5
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Tieger M, Das Adhikari U, Mukai S, Farcasnu M, Stone JR, Eliott D, Kim LA, Kwon DS, Rossin EJ. SARS-CoV-2 RNA Detected in Vitreous Samples Obtained at Autopsy. Journal of VitreoRetinal Diseases 2022; 6:183-187. [PMID: 37008551 PMCID: PMC9976118 DOI: 10.1177/24741264221083408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Purpose: This work aims to examine the vitreous of autopsy patients with COVID-19 for the presence of SARS-CoV-2 RNA. Methods: Four deceased patients with COVID-19 had an autopsy at Massachusetts General Hospital. Two control specimens were obtained from patients undergoing retinal detachment repair with negative preoperative polymerase chain reaction (PCR) testing for SARS-CoV-2 RNA. Vitreous specimens were obtained from autopsy patients with COVID-19 after povidone was placed on the ocular surface to decrease the risk of contamination of the vitreous specimen. SARS-CoV-2 RNA for gene N (nucleocapsid) was tested using reverse transcription–PCR. Results: SARS-CoV-2 RNA was detected in the vitreous of 2 of 4 autopsy patients who died from complications of COVID-19. Conclusions: SARS-CoV-2 RNA can penetrate into the vitreous of systemically infected patients, which might present risks to operating room personnel during ophthalmic surgical procedures.
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Affiliation(s)
- Marisa Tieger
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Upasana Das Adhikari
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Shizuo Mukai
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Mara Farcasnu
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - James R. Stone
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Dean Eliott
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Leo A. Kim
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Douglas S. Kwon
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital. Boston, MA, USA
| | - Elizabeth J. Rossin
- Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
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6
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Roberts DJ, Edlow AG, Romero RJ, Coyne CB, Ting DT, Hornick JL, Zaki SR, Das Adhikari U, Serghides L, Gaw SL, Metz TD. A standardized definition of placental infection by SARS-CoV-2, a consensus statement from the National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health and Human Development SARS-CoV-2 Placental Infection Workshop. Am J Obstet Gynecol 2021; 225:593.e1-593.e9. [PMID: 34364845 PMCID: PMC8340595 DOI: 10.1016/j.ajog.2021.07.029] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 01/04/2023]
Abstract
Pregnant individuals infected with SARS-CoV-2 have higher rates of intensive care unit admission, oxygen requirement, need for mechanical ventilation, and death than nonpregnant individuals. Increased COVID-19 disease severity may be associated with an increased risk of viremia and placental infection. Maternal SARS-CoV-2 infection is also associated with pregnancy complications such as preeclampsia and preterm birth, which can be either placentally mediated or reflected in the placenta. Maternal viremia followed by placental infection may lead to maternal-fetal transmission (vertical), which affects 1% to 3% of exposed newborns. However, there is no agreed-upon or standard definition of placental infection. The National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health and Human Development convened a group of experts to propose a working definition of placental infection to inform ongoing studies of SARS-CoV-2 during pregnancy. Experts recommended that placental infection be defined using techniques that allow virus detection and localization in placental tissue by one or more of the following methods: in situ hybridization with antisense probe (detects replication) or a sense probe (detects viral messenger RNA) or immunohistochemistry to detect viral nucleocapsid or spike proteins. If the abovementioned methods are not possible, reverse transcription polymerase chain reaction detection or quantification of viral RNA in placental homogenates, or electron microscopy are alternative approaches. A graded classification for the likelihood of placental infection as definitive, probable, possible, and unlikely was proposed. Manuscripts reporting placental infection should describe the sampling method (location and number of samples collected), method of preservation of tissue, and detection technique. Recommendations were made for the handling of the placenta, examination, and sampling and the use of validated reagents and sample protocols (included as appendices).
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Affiliation(s)
| | - Andrea G Edlow
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA
| | - Roberto J Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD; Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI
| | - Carolyn B Coyne
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC
| | - David T Ting
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sherif R Zaki
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Lena Serghides
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Stephanie L Gaw
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, CA
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7
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Junqueira C, Crespo Â, Ranjbar S, Lewandrowski M, Ingber J, de Lacerda LB, Parry B, Ravid S, Clark S, Ho F, Vora SM, Leger V, Beakes C, Margolin J, Russell N, Kays K, Gehrke L, Adhikari UD, Henderson L, Janssen E, Kwon D, Sander C, Abraham J, Filbin M, Goldberg MB, Wu H, Mehta G, Bell S, Goldfeld AE, Lieberman J. SARS-CoV-2 infects blood monocytes to activate NLRP3 and AIM2 inflammasomes, pyroptosis and cytokine release. Res Sq 2021:rs.3.rs-153628. [PMID: 34401873 PMCID: PMC8366805 DOI: 10.21203/rs.3.rs-153628/v1] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 causes acute respiratory distress that can progress to multiorgan failure and death in a minority of patients. Although severe COVID-19 disease is linked to exuberant inflammation, how SARS-CoV-2 triggers inflammation is not understood. Monocytes and macrophages are sentinel immune cells in the blood and tissue, respectively, that sense invasive infection to form inflammasomes that activate caspase-1 and gasdermin D (GSDMD) pores, leading to inflammatory death (pyroptosis) and processing and release of IL-1 family cytokines, potent inflammatory mediators. Here we show that expression quantitative trait loci (eQTLs) linked to higher GSDMD expression increase the risk of severe COVID-19 disease (odds ratio, 1.3, p<0.005). We find that about 10% of blood monocytes in COVID-19 patients are infected with SARS-CoV-2. Monocyte infection depends on viral antibody opsonization and uptake of opsonized virus by the Fc receptor CD16. After uptake, SARS-CoV-2 begins to replicate in monocytes, as evidenced by detection of double-stranded RNA and subgenomic RNA and expression of a fluorescent reporter gene. However, infection is aborted, and infectious virus is not detected in infected monocyte supernatants or patient plasma. Instead, infected cells undergo inflammatory cell death (pyroptosis) mediated by activation of the NLRP3 and AIM2 inflammasomes, caspase-1 and GSDMD. Moreover, tissue-resident macrophages, but not infected epithelial cells, from COVID-19 lung autopsy specimens showed evidence of inflammasome activation. These findings taken together suggest that antibody-mediated SARS-CoV-2 infection of monocytes/macrophages triggers inflammatory cell death that aborts production of infectious virus but causes systemic inflammation that contributes to severe COVID-19 disease pathogenesis.
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Affiliation(s)
- Caroline Junqueira
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, USA
- Department of Pediatrics, Harvard Medical School, USA
- Instituto René Rachou, Fundação Oswaldo Cruz, Brazil
| | - Ângela Crespo
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, USA
- Department of Pediatrics, Harvard Medical School, USA
| | - Shahin Ranjbar
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, USA
- Department of Medicine, Harvard Medical School, USA
| | - Mercedes Lewandrowski
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, USA
- Department of Pediatrics, Harvard Medical School, USA
| | - Jacob Ingber
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, USA
- Department of Pediatrics, Harvard Medical School, USA
| | - Luna B. de Lacerda
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, USA
- Department of Pediatrics, Harvard Medical School, USA
- Instituto René Rachou, Fundação Oswaldo Cruz, Brazil
| | - Blair Parry
- Emergency Medicine, Massachusetts General Hospital Institute for Patient Care, USA
| | - Sagi Ravid
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, USA
- Department of Pediatrics, Harvard Medical School, USA
| | - Sarah Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, USA
| | - Felicia Ho
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, USA
- Department of Pediatrics, Harvard Medical School, USA
| | - Setu M. Vora
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, USA
| | - Valerie Leger
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, USA
| | - Caroline Beakes
- Emergency Medicine, Massachusetts General Hospital Institute for Patient Care, USA
| | - Justin Margolin
- Emergency Medicine, Massachusetts General Hospital Institute for Patient Care, USA
| | - Nicole Russell
- Emergency Medicine, Massachusetts General Hospital Institute for Patient Care, USA
| | - Kyle Kays
- Emergency Medicine, Massachusetts General Hospital Institute for Patient Care, USA
| | - Lee Gehrke
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, USA
| | - Upasana Das Adhikari
- Ragon Institute, Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard Medical School, USA
| | - Lauren Henderson
- Department of Pediatrics, Harvard Medical School, USA
- Division of Immunology, Boston Children’s Hospital, USA
| | - Erin Janssen
- Department of Pediatrics, Harvard Medical School, USA
- Division of Immunology, Boston Children’s Hospital, USA
| | - Douglas Kwon
- Ragon Institute, Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard Medical School, USA
| | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, USA
| | - Michael Filbin
- Emergency Medicine, Massachusetts General Hospital Institute for Patient Care, USA
| | - Marcia B. Goldberg
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, USA
- Center for Bacterial Pathogenesis, Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, USA
| | - Hao Wu
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, USA
- Department of Pediatrics, Harvard Medical School, USA
- Division of Immunology, Boston Children’s Hospital, USA
| | - Gautam Mehta
- Institute for Liver and Digestive Health, University College London, UK
- Institute of Hepatology, Foundation for Liver Research, London, UK
| | - Steven Bell
- Department of Clinical Neurosciences, University of Cambridge, UK
| | - Anne E. Goldfeld
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, USA
- Department of Medicine, Harvard Medical School, USA
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, USA
- Department of Pediatrics, Harvard Medical School, USA
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8
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Das Adhikari U, Eng G, Farcasanu M, Avena LE, Choudhary MC, Triant VA, Flagg M, Schiff AE, Gomez I, Froehle LM, Diefenbach TJ, Ronsard L, Lingwood D, Lee GC, Rabi SA, Erstad D, Velmahos G, Li JZ, Hodin R, Stone JR, Honko AN, Griffiths A, Yilmaz O, Kwon DS. Fecal SARS-CoV-2 RNA is associated with decreased COVID-19 survival. Clin Infect Dis 2021; 74:1081-1084. [PMID: 34245255 PMCID: PMC8406863 DOI: 10.1093/cid/ciab623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
The clinical significance of SARS CoV-2 RNA in stool remains uncertain. We found that extrapulmonary dissemination of infection to the gastrointestinal (GI) tract, assessed by the presence of SARS-CoV-2 RNA in stool, is associated with decreased COVID-19 survival. Measurement of SARS-CoV-2 RNA in stool may have utility for clinical risk assessment.
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Affiliation(s)
- Upasana Das Adhikari
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA.,Harvard Medical School, Boston, MA 02114 USA
| | - George Eng
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114 USA.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139 USA.,Harvard Medical School, Boston, MA 02114 USA
| | - Mara Farcasanu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA.,Harvard Medical School, Boston, MA 02114 USA
| | - Laura E Avena
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118 United States
| | - Manish C Choudhary
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115 USA
| | - Virginia A Triant
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Meaghan Flagg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA
| | - Abigail E Schiff
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA.,Harvard Medical School, Boston, MA 02114 USA
| | - Isabella Gomez
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA
| | - Leah M Froehle
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA
| | | | - Larance Ronsard
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA
| | - Grace C Lee
- Division of Surgery, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Seyed Alireza Rabi
- Division of Surgery, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Derek Erstad
- Division of Surgery, Massachusetts General Hospital, Boston, MA 02114 USA
| | - George Velmahos
- Division of Surgery, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Jonathan Z Li
- Harvard Medical School, Boston, MA 02114 USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115 USA
| | - Richard Hodin
- Division of Surgery, Massachusetts General Hospital, Boston, MA 02114 USA
| | - James R Stone
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114 USA.,Harvard Medical School, Boston, MA 02114 USA
| | - Anna N Honko
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118 United States
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118 United States
| | - Omer Yilmaz
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114 USA.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139 USA.,Harvard Medical School, Boston, MA 02114 USA
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA.,Harvard Medical School, Boston, MA 02114 USA.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114 USA
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9
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Junqueira C, Crespo Â, Ranjbar S, Ingber J, Parry B, Ravid S, de Lacerda LB, Lewandrowski M, Clark S, Ho F, Vora SM, Leger V, Beakes C, Margolin J, Russell N, Gehrke L, Adhikari UD, Henderson L, Janssen E, Kwon D, Sander C, Abraham J, Filbin M, Goldberg MB, Wu H, Mehta G, Bell S, Goldfeld AE, Lieberman J. SARS-CoV-2 infects blood monocytes to activate NLRP3 and AIM2 inflammasomes, pyroptosis and cytokine release. medRxiv 2021. [PMID: 33758872 DOI: 10.1101/2021.03.06.21252796] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2 causes acute respiratory distress that can progress to multiorgan failure and death in some patients. Although severe COVID-19 disease is linked to exuberant inflammation, how SARS-CoV-2 triggers inflammation is not understood. Monocytes are sentinel blood cells that sense invasive infection to form inflammasomes that activate caspase-1 and gasdermin D (GSDMD) pores, leading to inflammatory death (pyroptosis) and processing and release of IL-1 family cytokines, potent inflammatory mediators. Here we show that ~10% of blood monocytes in COVID-19 patients are dying and infected with SARS-CoV-2. Monocyte infection, which depends on antiviral antibodies, activates NLRP3 and AIM2 inflammasomes, caspase-1 and GSDMD cleavage and relocalization. Signs of pyroptosis (IL-1 family cytokines, LDH) in the plasma correlate with development of severe disease. Moreover, expression quantitative trait loci (eQTLs) linked to higher GSDMD expression increase the risk of severe COVID-19 disease (odds ratio, 1.3, p<0.005). These findings taken together suggest that antibody-mediated SARS-CoV-2 infection of monocytes triggers inflammation that contributes to severe COVID-19 disease pathogenesis. One sentence summary Antibody-mediated SARS-CoV-2 infection of monocytes activates inflammation and cytokine release.
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10
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Morgenstern Y, Das Adhikari U, Ayyash M, Elyada E, Tóth B, Moor A, Itzkovitz S, Ben-Neriah Y. Casein kinase 1-epsilon or 1-delta required for Wnt-mediated intestinal stem cell maintenance. EMBO J 2017; 36:3046-3061. [PMID: 28963394 DOI: 10.15252/embj.201696253] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 12/06/2016] [Revised: 08/09/2017] [Accepted: 08/11/2017] [Indexed: 01/01/2023] Open
Abstract
The intestinal epithelium holds an immense regenerative capacity mobilized by intestinal stem cells (ISCs), much of it supported by Wnt pathway activation. Several unique regulatory mechanisms ensuring optimal levels of Wnt signaling have been recognized in ISCs. Here, we identify another Wnt signaling amplifier, CKIε, which is specifically upregulated in ISCs and is essential for ISC maintenance, especially in the absence of its close isoform CKIδ. Co-ablation of CKIδ/ε in the mouse gut epithelium results in rapid ISC elimination, with subsequent growth arrest, crypt-villous shrinking, and rapid mouse death. Unexpectedly, Wnt activation is preserved in all CKIδ/ε-deficient enterocyte populations, with the exception of Lgr5+ ISCs, which exhibit Dvl2-dependent Wnt signaling attenuation. CKIδ/ε-depleted gut organoids cease proliferating and die rapidly, yet survive and resume self-renewal upon reconstitution of Dvl2 expression. Our study underscores a unique regulation mode of the Wnt pathway in ISCs, possibly providing new means of stem cell enrichment for regenerative medicine.
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Affiliation(s)
- Yael Morgenstern
- The Lautenberg Center for Immunology, Institute of Medical Research, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Upasana Das Adhikari
- The Lautenberg Center for Immunology, Institute of Medical Research, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Muneef Ayyash
- The Lautenberg Center for Immunology, Institute of Medical Research, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ela Elyada
- The Lautenberg Center for Immunology, Institute of Medical Research, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Beáta Tóth
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Andreas Moor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yinon Ben-Neriah
- The Lautenberg Center for Immunology, Institute of Medical Research, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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