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For: Cosgrove PR, Redhu NS, Tang Y, Monuteaux MC, Horwitz BH. Characterizing T cell subsets in the nasal mucosa of children with acute respiratory symptoms. Pediatr Res 2021;90:1023-1030. [PMID: 33504970 PMCID: PMC7838854 DOI: 10.1038/s41390-021-01364-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 11/21/2020] [Accepted: 01/05/2021] [Indexed: 01/30/2023]

For:	Cosgrove PR, Redhu NS, Tang Y, Monuteaux MC, Horwitz BH. Characterizing T cell subsets in the nasal mucosa of children with acute respiratory symptoms. Pediatr Res 2021;90:1023-1030. [PMID: 33504970 PMCID: PMC7838854 DOI: 10.1038/s41390-021-01364-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 11/21/2020] [Accepted: 01/05/2021] [Indexed: 01/30/2023]

Number

Cited by Other Article(s)

Ziegler CGK, Miao VN, Owings AH, Navia AW, Tang Y, Bromley JD, Lotfy P, Sloan M, Laird H, Williams HB, George M, Drake RS, Christian T, Parker A, Sindel CB, Burger MW, Pride Y, Hasan M, Abraham GE, Senitko M, Robinson TO, Shalek AK, Glover SC, Horwitz BH, Ordovas-Montanes J. Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19. Cell 2021;184:4713-4733.e22. [PMID: 34352228 PMCID: PMC8299217 DOI: 10.1016/j.cell.2021.07.023] [Citation(s) in RCA: 182] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/24/2021] [Accepted: 07/14/2021] [Indexed: 02/08/2023]

Affiliation(s)

Carly G K Ziegler Program in Health Sciences & Technology, Harvard Medical School & MIT, Boston, MA 02115, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Vincent N Miao Program in Health Sciences & Technology, Harvard Medical School & MIT, Boston, MA 02115, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Anna H Owings Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
Andrew W Navia Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Ying Tang Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA
Joshua D Bromley Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Microbiology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Peter Lotfy Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA
Meredith Sloan Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
Hannah Laird Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
Haley B Williams Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
Micayla George Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Riley S Drake Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Taylor Christian Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
Adam Parker Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
Campbell B Sindel Division of Pulmonary, Critical Care, and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
Molly W Burger Obstetrics and Gynecology, University of Mississippi Medical Center, Jackson, MS 39216, USA
Yilianys Pride Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
Mohammad Hasan Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
George E Abraham Division of Pulmonary, Critical Care, and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
Michal Senitko Division of Pulmonary, Critical Care, and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
Tanya O Robinson Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
Alex K Shalek Program in Health Sciences & Technology, Harvard Medical School & MIT, Boston, MA 02115, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
Sarah C Glover Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Bruce H Horwitz Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Division of Emergency Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA.
Jose Ordovas-Montanes Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.

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Ziegler CGK, Miao VN, Owings AH, Navia AW, Tang Y, Bromley JD, Lotfy P, Sloan M, Laird H, Williams HB, George M, Drake RS, Christian T, Parker A, Sindel CB, Burger MW, Pride Y, Hasan M, Abraham GE, Senitko M, Robinson TO, Shalek AK, Glover SC, Horwitz BH, Ordovas-Montanes J. Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.20.431155. [PMID: 33619488 PMCID: PMC7899452 DOI: 10.1101/2021.02.20.431155] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]

Abstract

Infection with SARS-CoV-2, the virus that causes COVID-19, can lead to severe lower respiratory illness including pneumonia and acute respiratory distress syndrome, which can result in profound morbidity and mortality. However, many infected individuals are either asymptomatic or have isolated upper respiratory symptoms, which suggests that the upper airways represent the initial site of viral infection, and that some individuals are able to largely constrain viral pathology to the nasal and oropharyngeal tissues. Which cell types in the human nasopharynx are the primary targets of SARS-CoV-2 infection, and how infection influences the cellular organization of the respiratory epithelium remains incompletely understood. Here, we present nasopharyngeal samples from a cohort of 35 individuals with COVID-19, representing a wide spectrum of disease states from ambulatory to critically ill, as well as 23 healthy and intubated patients without COVID-19. Using standard nasopharyngeal swabs, we collected viable cells and performed single-cell RNA-sequencing (scRNA-seq), simultaneously profiling both host and viral RNA. We find that following infection with SARS-CoV-2, the upper respiratory epithelium undergoes massive reorganization: secretory cells diversify and expand, and mature epithelial cells are preferentially lost. Further, we observe evidence for deuterosomal cell and immature ciliated cell expansion, potentially representing active repopulation of lost ciliated cells through coupled secretory cell differentiation. Epithelial cells from participants with mild/moderate COVID-19 show extensive induction of genes associated with anti-viral and type I interferon responses. In contrast, cells from participants with severe lower respiratory symptoms appear globally muted in their anti-viral capacity, despite substantially higher local inflammatory myeloid populations and equivalent nasal viral loads. This suggests an essential role for intrinsic, local epithelial immunity in curbing and constraining viral-induced pathology. Using a custom computational pipeline, we characterized cell-associated SARS-CoV-2 RNA and identified rare cells with RNA intermediates strongly suggestive of active replication. Both within and across individuals, we find remarkable diversity and heterogeneity among SARS-CoV-2 RNA+ host cells, including developing/immature and interferon-responsive ciliated cells, KRT13+ "hillock"-like cells, and unique subsets of secretory, goblet, and squamous cells. Finally, SARS-CoV-2 RNA+ cells, as compared to uninfected bystanders, are enriched for genes involved in susceptibility (e.g., CTSL, TMPRSS2) or response (e.g., MX1, IFITM3, EIF2AK2) to infection. Together, this work defines both protective and detrimental host responses to SARS-CoV-2, determines the direct viral targets of infection, and suggests that failed anti-viral epithelial immunity in the nasal mucosa may underlie the progression to severe COVID-19.

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Affiliation(s)

Carly G. K. Ziegler Program in Health Sciences & Technology, Harvard Medical School & MIT, Boston, MA 02115, USA Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Vincent N. Miao Program in Health Sciences & Technology, Harvard Medical School & MIT, Boston, MA 02115, USA Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Anna H. Owings Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
Andrew W. Navia Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Ying Tang Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA 02115, USA
Joshua D. Bromley Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Microbiology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Peter Lotfy Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA 02115, USA
Meredith Sloan Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
Hannah Laird Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
Haley B. Williams Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
Micayla George Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Riley S. Drake Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Taylor Christian Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
Adam Parker Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
Campbell B. Sindel Division of Pulmonary, Critical Care, and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
Molly W. Burger Obstetrics and Gynecology, University of Mississippi Medical Center, Jackson, MS 39216, USA
Yilianys Pride Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
Mohammad Hasan Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
George E. Abraham Division of Pulmonary, Critical Care, and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
Michal Senitko Division of Pulmonary, Critical Care, and Sleep Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
Tanya O. Robinson Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
Alex K. Shalek Program in Health Sciences & Technology, Harvard Medical School & MIT, Boston, MA 02115, USA Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Program in Immunology, Harvard Medical School, Boston, MA 02115, USA Harvard Stem Cell Institute, Cambridge, MA 02138, USA
Sarah C. Glover Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, MS 39216, USA
Bruce H. Horwitz Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA 02115, USA Division of Emergency Medicine, Boston Children’s Hospital, Boston, MA 02115, USA Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
Jose Ordovas-Montanes Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA 02115, USA Program in Immunology, Harvard Medical School, Boston, MA 02115, USA Harvard Stem Cell Institute, Cambridge, MA 02138, USA

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