1
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Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Soto Albrecht Y, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Zhang S, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Bram Y, Kidane Y, Priebe W, Emmett MR, Meller R, Demharter S, Stentoft-Hansen V, Salvatore M, Galeano D, Enguita FJ, Grabham P, Trovao NS, Singh U, Haltom J, Heise MT, Moorman NJ, Baxter VK, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, Wallace DC. Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts. Sci Transl Med 2023; 15:eabq1533. [PMID: 37556555 DOI: 10.1126/scitranslmed.abq1533] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/20/2023] [Indexed: 08/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins bind to host mitochondrial proteins, likely inhibiting oxidative phosphorylation (OXPHOS) and stimulating glycolysis. We analyzed mitochondrial gene expression in nasopharyngeal and autopsy tissues from patients with coronavirus disease 2019 (COVID-19). In nasopharyngeal samples with declining viral titers, the virus blocked the transcription of a subset of nuclear DNA (nDNA)-encoded mitochondrial OXPHOS genes, induced the expression of microRNA 2392, activated HIF-1α to induce glycolysis, and activated host immune defenses including the integrated stress response. In autopsy tissues from patients with COVID-19, SARS-CoV-2 was no longer present, and mitochondrial gene transcription had recovered in the lungs. However, nDNA mitochondrial gene expression remained suppressed in autopsy tissue from the heart and, to a lesser extent, kidney, and liver, whereas mitochondrial DNA transcription was induced and host-immune defense pathways were activated. During early SARS-CoV-2 infection of hamsters with peak lung viral load, mitochondrial gene expression in the lung was minimally perturbed but was down-regulated in the cerebellum and up-regulated in the striatum even though no SARS-CoV-2 was detected in the brain. During the mid-phase SARS-CoV-2 infection of mice, mitochondrial gene expression was starting to recover in mouse lungs. These data suggest that when the viral titer first peaks, there is a systemic host response followed by viral suppression of mitochondrial gene transcription and induction of glycolysis leading to the deployment of antiviral immune defenses. Even when the virus was cleared and lung mitochondrial function had recovered, mitochondrial function in the heart, kidney, liver, and lymph nodes remained impaired, potentially leading to severe COVID-19 pathology.
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Affiliation(s)
- Joseph W Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Joseph M Dybas
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Hossein Fazelinia
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Man S Kim
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | - Justin Frere
- Icahn School of Medicine at Mount Sinai, New York, NY 10023, USA
| | - Yuanchao Zhang
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Yentli Soto Albrecht
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Deborah G Murdock
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Scott L Weiss
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sonja M Best
- COVID-19 International Research Team, Medford, MA 02155, USA
- Rocky Mountain Laboratory, National Institute of Allergy and Infectious Disease, NIH, Hamilton, MT 59840, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Henry Cope
- University of Nottingham, Nottingham, UK
| | - Victoria Zaksas
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Chicago, Chicago, IL 60615, USA
- Clever Research Lab, Springfield, IL 62704, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team, Medford, MA 02155, USA
- Logyx, LLC, Mountain View, CA 94043, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | - Yaron Bram
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Yared Kidane
- COVID-19 International Research Team, Medford, MA 02155, USA
- Texas Scottish Rite Hospital for Children, Dallas, TX 75219, USA
| | - Waldemar Priebe
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark R Emmett
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Meller
- COVID-19 International Research Team, Medford, MA 02155, USA
- Morehouse School of Medicine, Atlanta, GA 30310, USA
| | | | | | | | - Diego Galeano
- COVID-19 International Research Team, Medford, MA 02155, USA
- Facultad de Ingeniería, Universidad Nacional de Asunción, San Lorenzo, Central, Paraguay
| | - Francisco J Enguita
- COVID-19 International Research Team, Medford, MA 02155, USA
- Faculdade de Medicina, Universidade de Lisboa, Instituto de Medicina Molecular João Lobo Antunes, 1649-028 Lisboa, Portugal
| | - Peter Grabham
- College of Physicians and Surgeons, Columbia University, New York, NY 19103, USA
| | - Nidia S Trovao
- COVID-19 International Research Team, Medford, MA 02155, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Urminder Singh
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Jeffrey Haltom
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Mark T Heise
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Victoria K Baxter
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emily A Madden
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Wes A Sanders
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Stephen B Baylin
- COVID-19 International Research Team, Medford, MA 02155, USA
- Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Pedro M Moraes-Vieira
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Campinas, Campinas, SP, Brazil
| | - Deanne Taylor
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Christopher E Mason
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
- New York Genome Center, New York, NY 10013, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert E Schwartz
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA 02155, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Division of Human Genetics, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
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2
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Ng AT, Moon JJ, Steidl OR, Bussan H, Tran JM, Luong G, Nihal A, Kenfield M, Frere J, TenOever BR, Costa da Silva AC, Mays JW, Cowen EW, Drolet BA, Singh AM, Arkin LM. Pernio and early SARS-CoV-2 variants: natural history of a prospective cohort and the role of interferon. Br J Dermatol 2022; 187:617-619. [PMID: 35653263 PMCID: PMC9347790 DOI: 10.1111/bjd.21693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/30/2022] [Revised: 05/18/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022]
Abstract
Cases of new-onset pernio and recurrences in our cohort align tightly with trends in mean 7-day COVID-19 positivity in Wisconsin and mean temperature in Madison, Wisconsin by month.
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Affiliation(s)
- Ashley T. Ng
- Department of Dermatology, School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - John J. Moon
- Department of Dermatology, School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Olivia R. Steidl
- Division of Allergy & Immunology, Department of Pediatrics, School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Hailey Bussan
- Department of Pathology and Laboratory Medicine, School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Jennifer M. Tran
- Department of Dermatology, School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - George Luong
- Department of Dermatology, School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Aman Nihal
- Department of Dermatology, School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Meaghan Kenfield
- Department of Dermatology, School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Justin Frere
- Department of MicrobiologyNew York University, Langone HealthNew YorkNY10016USA
| | | | | | | | | | - Beth A. Drolet
- Department of Dermatology, School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Anne Marie Singh
- Division of Allergy & Immunology, Department of Pediatrics, School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Lisa M. Arkin
- Department of Dermatology, School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWIUSA
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3
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Powell SK, Saali A, Frere J, Magill E, Krystal H, Serafini RA, Sultana S, Dale B, Ali M, Kumar V, Datta D, Hernandez-Antonio J, Aronson A, Meah YS, Gluhoski V, Katz CL. Design of and outcomes in a student-run free mental health clinic serving the uninsured in East Harlem. BMC Psychiatry 2022; 22:501. [PMID: 35883038 PMCID: PMC9321276 DOI: 10.1186/s12888-022-04112-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 07/05/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Safety-net clinics are an important source of low-cost or free mental healthcare to those with limited financial resources. Such clinics are often staffed by trainees in early stages of their career. Only limited data exist on best practices in treatment-implementation and on clinical outcomes attained in such clinics. The primary purpose of this article is to describe the design of an outpatient psychiatry student-run free clinic (SRFC) serving uninsured individuals in New York City's East Harlem neighborhood and to analyze the quality of services provided and the clinical outcomes attained. METHODS The authors conducted a retrospective chart review of n = 69 patients treated in the EHHOP Mental Health Clinic (E-MHC) to describe the demographic and clinical characteristics of the study population. Utilizing Health Effectiveness Data and Information Set metrics, they estimated the likelihoods of patients meeting metric quality criteria compared to those in other New York State (NYS) insurance groups. The authors derived linear mixed effect and logistic regression models to ascertain factors associated with clinical outcomes. Finally, the authors collected patient feedback on the clinical services received using a customized survey. RESULTS Almost all patients were of Hispanic ethnicity, and about half of patients had more than one psychiatric disorder. The clinical service performance of the E-MHC was non-inferior on most measures examined. Factors associated with symptom improvement were the number of treatment sessions and certain demographic and clinical variables. Patients provided highly positive feedback on the mental healthcare services they received. CONCLUSIONS SRFCs can provide quality care to vulnerable patients that leads to clinically meaningful reductions in psychiatric symptoms and is well-received by patients.
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Affiliation(s)
- Samuel K. Powell
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Alexandra Saali
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Justin Frere
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Elizabeth Magill
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Hannah Krystal
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Randal A. Serafini
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Syeda Sultana
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Brandon Dale
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Muhammad Ali
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Vedika Kumar
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Debjyoti Datta
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | | | - Anne Aronson
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Yasmin S. Meah
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Vicki Gluhoski
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Craig L. Katz
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
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4
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Oishi K, Horiuchi S, Frere J, Schwartz RE, tenOever BR. A diminished immune response underlies age-related SARS-CoV-2 pathologies. Cell Rep 2022; 39:111002. [PMID: 35714615 PMCID: PMC9181267 DOI: 10.1016/j.celrep.2022.111002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/27/2022] [Accepted: 06/03/2022] [Indexed: 12/02/2022] Open
Abstract
Morbidity and mortality in response to SARS-CoV-2 infection are significantly elevated in people of advanced age. To understand the underlying biology of this phenotype, we utilize the golden hamster model to compare how the innate and adaptive immune responses to SARS-CoV-2 infection differed between younger and older animals. We find that while both hamster cohorts showed similar virus kinetics in the lungs, the host response in older animals was dampened, with diminished tissue repair in the respiratory tract post-infection. Characterization of the adaptive immune response also revealed age-related differences, including fewer germinal center B cells in older hamsters, resulting in reduced potency of neutralizing antibodies. Moreover, older animals demonstrate elevated suppressor T cells and neutrophils in the respiratory tract, correlating with an increase in TGF-β and IL-17 induction. Together, these data support that diminished immunity is one of the underlying causes of age-related morbidity.
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Affiliation(s)
- Kohei Oishi
- Grossman School of Medicine, New York University, New York, NY 10016, USA
| | - Shu Horiuchi
- Grossman School of Medicine, New York University, New York, NY 10016, USA
| | - Justin Frere
- Grossman School of Medicine, New York University, New York, NY 10016, USA
| | - Robert E Schwartz
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
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5
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Victor J, Jordan T, Lamkin E, Ikeh K, March A, Frere J, Crompton A, Allen L, Fanning J, Lim WY, Muoio D, Fouquerel E, Martindale R, Dewitt J, deLance N, Taatjes D, Dragon J, Holcombe R, Greenblatt M, Kaminsky D, Hong J, Zhou P, tenOever B, Chatterjee N. SARS-CoV-2 hijacks host cell genome instability pathways. Res Sq 2022:rs.3.rs-1556634. [PMID: 35441168 PMCID: PMC9016650 DOI: 10.21203/rs.3.rs-1556634/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The repertoire of coronavirus disease 2019 (COVID-19)-mediated adverse health outcomes has continued to expand in infected patients, including the susceptibility to developing long-COVID; however, the molecular underpinnings at the cellular level are poorly defined. In this study, we report that SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection triggers host cell genome instability by modulating the expression of molecules of DNA repair and mutagenic translesion synthesis. Further, SARS-CoV-2 infection causes genetic alterations, such as increased mutagenesis, telomere dysregulation, and elevated microsatellite instability (MSI). The MSI phenotype was coupled to reduced MLH1, MSH6, and MSH2 in infected cells. Strikingly, pre-treatment of cells with the REV1-targeting translesion DNA synthesis inhibitor, JH-RE-06, suppresses SARS-CoV-2 proliferation and dramatically represses the SARS-CoV-2-dependent genome instability. Mechanistically, JH-RE-06 treatment induces autophagy, which we hypothesize limits SARS-CoV-2 proliferation and, therefore, the hijacking of host-cell genome instability pathways. These results have implications for understanding the pathobiological consequences of COVID-19.
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6
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Zazhytska M, Kodra A, Hoagland DA, Frere J, Fullard JF, Shayya H, McArthur NG, Moeller R, Uhl S, Omer AD, Gottesman ME, Firestein S, Gong Q, Canoll PD, Goldman JE, Roussos P, tenOever BR, Jonathan B Overdevest, Lomvardas S. Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia. Cell 2022; 185:1052-1064.e12. [PMID: 35180380 PMCID: PMC8808699 DOI: 10.1016/j.cell.2022.01.024] [Citation(s) in RCA: 127] [Impact Index Per Article: 63.5] [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: 08/04/2021] [Revised: 12/06/2021] [Accepted: 01/26/2022] [Indexed: 12/22/2022]
Abstract
SARS-CoV-2 infects less than 1% of cells in the human body, yet it can cause severe damage in a variety of organs. Thus, deciphering the non-cell-autonomous effects of SARS-CoV-2 infection is imperative for understanding the cellular and molecular disruption it elicits. Neurological and cognitive defects are among the least understood symptoms of COVID-19 patients, with olfactory dysfunction being their most common sensory deficit. Here, we show that both in humans and hamsters, SARS-CoV-2 infection causes widespread downregulation of olfactory receptors (ORs) and of their signaling components. This non-cell-autonomous effect is preceded by a dramatic reorganization of the neuronal nuclear architecture, which results in dissipation of genomic compartments harboring OR genes. Our data provide a potential mechanism by which SARS-CoV-2 infection alters the cellular morphology and the transcriptome of cells it cannot infect, offering insight to its systemic effects in olfaction and beyond.
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Affiliation(s)
- Marianna Zazhytska
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Albana Kodra
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Genetics and Development, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Daisy A Hoagland
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Justin Frere
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Hani Shayya
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Genetics and Development, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Natalie G McArthur
- Department of Biological Sciences, Columbia University New York, NY 10027, USA
| | - Rasmus Moeller
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Skyler Uhl
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Arina D Omer
- Baylor Genetics, 2450 Holcombe Blvd, Houston, TX 77021, USA
| | - Max E Gottesman
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Stuart Firestein
- Department of Biological Sciences, Columbia University New York, NY 10027, USA
| | - Qizhi Gong
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Peter D Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - James E Goldman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA.
| | - Jonathan B Overdevest
- Department of Otolaryngology, Head and Neck Surgery, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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7
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Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Albrecht YS, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Kidane YH, Priebe W, Emmett MR, Meller R, Singh U, Bram Y, tenOever BR, Heise MT, Moorman NJ, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baxter VK, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, Wallace DC. TARGETED DOWN REGULATION OF CORE MITOCHONDRIAL GENES DURING SARS-COV-2 INFECTION. bioRxiv 2022:2022.02.19.481089. [PMID: 35233572 PMCID: PMC8887073 DOI: 10.1101/2022.02.19.481089] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Defects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported in COVID-19 patients, but the timing and organs affected vary among reports. Here, we reveal the dynamics of COVID-19 through transcription profiles in nasopharyngeal and autopsy samples from patients and infected rodent models. While mitochondrial bioenergetics is repressed in the viral nasopharyngeal portal of entry, it is up regulated in autopsy lung tissues from deceased patients. In most disease stages and organs, discrete OXPHOS functions are blocked by the virus, and this is countered by the host broadly up regulating unblocked OXPHOS functions. No such rebound is seen in autopsy heart, results in severe repression of genes across all OXPHOS modules. Hence, targeted enhancement of mitochondrial gene expression may mitigate the pathogenesis of COVID-19.
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Affiliation(s)
- Joseph W. Guarnieri
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Joseph M. Dybas
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Hossein Fazelinia
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Man S. Kim
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
- Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | | | - Yuanchao Zhang
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Yentli Soto Albrecht
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | | | - Alessia Angelin
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Larry N. Singh
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Scott L. Weiss
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Sonja M. Best
- COVID-19 International Research Team
- Rocky Mountain Laboratories NIAID, Hamilton, MT 59840
| | - Marie T. Lott
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Henry Cope
- University of Nottingham, Nottingham, UK
| | - Viktorija Zaksas
- COVID-19 International Research Team
- University of Chicago, Chicago, IL, 60615, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team
- Logyx, LLC, Mountain View, CA 94043, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
| | | | | | - Yared H. Kidane
- COVID-19 International Research Team
- Scottish Rite for Children, Dallas, TX 75219, USA
| | - Waldemar Priebe
- COVID-19 International Research Team
- University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark R. Emmett
- COVID-19 International Research Team
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Meller
- COVID-19 International Research Team
- Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Urminder Singh
- COVID-19 International Research Team
- Iowa State University, Ames, IA 50011, USA
| | | | | | - Mark T. Heise
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | - Emily A. Madden
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Wes A. Sanders
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Stephen B. Baylin
- COVID-19 International Research Team
- Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team
- Iowa State University, Ames, IA 50011, USA
| | | | - Deanne Taylor
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Christopher E. Mason
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
- New York Genome Center, NY, USA
| | - Jonathan C. Schisler
- COVID-19 International Research Team
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Robert E. Schwartz
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
| | - Afshin Beheshti
- COVID-19 International Research Team
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- KBR, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Douglas C. Wallace
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
- University of Pennsylvania, Philadelphia, PA 19104 USA
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8
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Horiuchi S, Oishi K, Carrau L, Frere J, Møller R, Panis M, tenOever BR. Immune memory from SARS-CoV-2 infection in hamsters provides variant-independent protection but still allows virus transmission. Sci Immunol 2021; 6:eabm3131. [PMID: 34699266 DOI: 10.1126/sciimmunol.abm3131] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Shu Horiuchi
- Department of Microbiology, New York University, New York, NY 10016, USA
| | - Kohei Oishi
- Department of Microbiology, New York University, New York, NY 10016, USA
| | - Lucia Carrau
- Department of Microbiology, New York University, New York, NY 10016, USA
| | - Justin Frere
- Department of Microbiology, New York University, New York, NY 10016, USA
| | - Rasmus Møller
- Department of Microbiology, New York University, New York, NY 10016, USA
| | - Maryline Panis
- Department of Microbiology, New York University, New York, NY 10016, USA
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9
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Hernandez-Meza G, Vietti Violi N, Said D, Novogrodsky E, Villavisanis D, Maron SZ, Frere J, Schiano TD, Friedman S, Boffetta P, Branch A, Taouli B. MRI is the most commonly used imaging modality for HCC screening at a tertiary care transplant center. Abdom Radiol (NY) 2021; 46:5142-5151. [PMID: 34283266 DOI: 10.1007/s00261-021-03212-7] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/25/2021] [Accepted: 07/08/2021] [Indexed: 12/18/2022]
Abstract
PURPOSE In this study, we describe the patterns of hepatocellular carcinoma (HCC) screening with imaging and factors associated with imaging modality selection in a tertiary care transplant center. METHODS This was a retrospective study where all adult patients with cirrhosis and/or chronic hepatitis B virus infection referred for HCC screening with ultrasound (US), CT or MRI were identified during 2017. The association between imaging methods, demographic/clinical data were analyzed by uni- and multivariate analysis. RESULTS A total of 1437 patients were included (median age 61y, 59% male, median BMI 27.5 kg/m2, median AFP 3.4 ng/mL, 37% with HCV and 87% with cirrhosis). Index screening imaging method utilization included MRI (51%), US (33%) and CT (16%). Use of US as the index imaging modality for screening was significantly associated with race/ethnicity [Odds Ratio (OR) 1.71-2.01, all p < 0.05] in multivariate analysis. Presence of cirrhosis (OR 0.29, p < 0.001) and referral by a hepatologist (OR 0.23, p < 0.001) were associated with screening with MRI in the multivariate analysis; while gender, age, BMI, etiology and income at ZIP code of residence were not significantly associated with imaging modality selection. HCC was observed in 62 patients (prevalence 4.3%). Rate of HCC detection was significantly higher with MRI vs US (5.9% vs. 1.5%, p = 0.001). CONCLUSION MRI was the most frequently used modality (> 50%) for HCC screening in our tertiary care center, in contrast with the current practice guidelines. Race/ethnicity, cirrhosis and referral by a hepatologist were associated with the imaging method used for HCC screening.
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Affiliation(s)
- Gabriela Hernandez-Meza
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai (ISMMS), 1470 Madison Avenue, New York, NY, 10029, USA
- BioMedical Engineering and Imaging Institute, ISMMS, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Naik Vietti Violi
- BioMedical Engineering and Imaging Institute, ISMMS, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Radiology, Lausanne University Hospital, Lausanne, Switzerland
| | - Daniela Said
- BioMedical Engineering and Imaging Institute, ISMMS, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Radiology, Universidad de los Andes, Santiago, Chile
| | - Eitan Novogrodsky
- Department of Radiology, Albert Einstein College of Medicine, New York, NY, USA
| | - Dillan Villavisanis
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai (ISMMS), 1470 Madison Avenue, New York, NY, 10029, USA
- BioMedical Engineering and Imaging Institute, ISMMS, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Samuel Z Maron
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai (ISMMS), 1470 Madison Avenue, New York, NY, 10029, USA
- BioMedical Engineering and Imaging Institute, ISMMS, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Justin Frere
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai (ISMMS), 1470 Madison Avenue, New York, NY, 10029, USA
- BioMedical Engineering and Imaging Institute, ISMMS, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Thomas D Schiano
- Recanati/Miller Transplantation Institute, ISMMS, New York, NY, USA
| | | | - Paolo Boffetta
- Tisch Cancer Institute, ISMMS, New York, NY, USA
- Department of Family, Population & Preventive Medicine, Renaissance School of Medicine, Stony Brook, NY, USA
| | - Andrea Branch
- Division of Liver Diseases, ISMMS, New York, NY, USA
| | - Bachir Taouli
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai (ISMMS), 1470 Madison Avenue, New York, NY, 10029, USA.
- BioMedical Engineering and Imaging Institute, ISMMS, 1470 Madison Avenue, New York, NY, 10029, USA.
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10
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Si L, Bai H, Rodas M, Cao W, Oh CY, Jiang A, Moller R, Hoagland D, Oishi K, Horiuchi S, Uhl S, Blanco-Melo D, Albrecht RA, Liu WC, Jordan T, Nilsson-Payant BE, Golynker I, Frere J, Logue J, Haupt R, McGrath M, Weston S, Zhang T, Plebani R, Soong M, Nurani A, Kim SM, Zhu DY, Benam KH, Goyal G, Gilpin SE, Prantil-Baun R, Gygi SP, Powers RK, Carlson KE, Frieman M, tenOever BR, Ingber DE. A human-airway-on-a-chip for the rapid identification of candidate antiviral therapeutics and prophylactics. Nat Biomed Eng 2021; 5:815-829. [PMID: 33941899 PMCID: PMC8387338 DOI: 10.1038/s41551-021-00718-9] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [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: 12/31/2020] [Accepted: 03/19/2021] [Indexed: 02/05/2023]
Abstract
The rapid repurposing of antivirals is particularly pressing during pandemics. However, rapid assays for assessing candidate drugs typically involve in vitro screens and cell lines that do not recapitulate human physiology at the tissue and organ levels. Here we show that a microfluidic bronchial-airway-on-a-chip lined by highly differentiated human bronchial-airway epithelium and pulmonary endothelium can model viral infection, strain-dependent virulence, cytokine production and the recruitment of circulating immune cells. In airway chips infected with influenza A, the co-administration of nafamostat with oseltamivir doubled the treatment-time window for oseltamivir. In chips infected with pseudotyped severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), clinically relevant doses of the antimalarial drug amodiaquine inhibited infection but clinical doses of hydroxychloroquine and other antiviral drugs that inhibit the entry of pseudotyped SARS-CoV-2 in cell lines under static conditions did not. We also show that amodiaquine showed substantial prophylactic and therapeutic activities in hamsters challenged with native SARS-CoV-2. The human airway-on-a-chip may accelerate the identification of therapeutics and prophylactics with repurposing potential.
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Affiliation(s)
- Longlong Si
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Haiqing Bai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Melissa Rodas
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Wuji Cao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Crystal Yuri Oh
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Amanda Jiang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Rasmus Moller
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daisy Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kohei Oishi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shu Horiuchi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Skyler Uhl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Blanco-Melo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tristan Jordan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ilona Golynker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Justin Frere
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Logue
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robert Haupt
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marisa McGrath
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Roberto Plebani
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Center on Advanced Studies and Technology (CAST), Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Mercy Soong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Atiq Nurani
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Seong Min Kim
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Danni Y Zhu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Kambez H Benam
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Girija Goyal
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Sarah E Gilpin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Rachelle Prantil-Baun
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Rani K Powers
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Kenneth E Carlson
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, USA.
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11
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Hoagland DA, Møller R, Uhl SA, Oishi K, Frere J, Golynker I, Horiuchi S, Panis M, Blanco-Melo D, Sachs D, Arkun K, Lim JK, tenOever BR. Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity. Immunity 2021; 54:557-570.e5. [PMID: 33577760 PMCID: PMC7846242 DOI: 10.1016/j.immuni.2021.01.017] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/02/2020] [Accepted: 01/25/2021] [Indexed: 12/18/2022]
Abstract
The emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in significant global morbidity, mortality, and societal disruption. A better understanding of virus-host interactions may potentiate therapeutic insights toward limiting this infection. Here we investigated the dynamics of the systemic response to SARS-CoV-2 in hamsters by histological analysis and transcriptional profiling. Infection resulted in consistently high levels of virus in the upper and lower respiratory tracts and sporadic occurrence in other distal tissues. A longitudinal cohort revealed a wave of inflammation, including a type I interferon (IFN-I) response, that was evident in all tissues regardless of viral presence but was insufficient to prevent disease progression. Bolstering the antiviral response with intranasal administration of recombinant IFN-I reduced viral disease, prevented transmission, and lowered inflammation in vivo. This study defines the systemic host response to SARS-CoV-2 infection and supports use of intranasal IFN-I as an effective means of early treatment.
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Affiliation(s)
- Daisy A Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rasmus Møller
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Skyler A Uhl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kohei Oishi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Justin Frere
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ilona Golynker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shu Horiuchi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maryline Panis
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Blanco-Melo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Sachs
- Department of Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Knarik Arkun
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA 02111, USA
| | - Jean K Lim
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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12
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Oren E, Frere J, Yom-Tov E, Yom-Tov E. Respiratory syncytial virus tracking using internet search engine data. BMC Public Health 2018; 18:445. [PMID: 29615018 PMCID: PMC5883276 DOI: 10.1186/s12889-018-5367-z] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 03/22/2018] [Indexed: 01/25/2023] Open
Abstract
Background Respiratory Syncytial Virus (RSV) is the leading cause of hospitalization in children less than 1 year of age in the United States. Internet search engine queries may provide high resolution temporal and spatial data to estimate and predict disease activity. Methods After filtering an initial list of 613 symptoms using high-resolution Bing search logs, we used Google Trends data between 2004 and 2016 for a smaller list of 50 terms to build predictive models of RSV incidence for five states where long-term surveillance data was available. We then used domain adaptation to model RSV incidence for the 45 remaining US states. Results Surveillance data sources (hospitalization and laboratory reports) were highly correlated, as were laboratory reports with search engine data. The four terms which were most often statistically significantly correlated as time series with the surveillance data in the five state models were RSV, flu, pneumonia, and bronchiolitis. Using our models, we tracked the spread of RSV by observing the time of peak use of the search term in different states. In general, the RSV peak moved from south-east (Florida) to the north-west US. Conclusions Our study represents the first time that RSV has been tracked using Internet data results and highlights successful use of search filters and domain adaptation techniques, using data at multiple resolutions. Our approach may assist in identifying spread of both local and more widespread RSV transmission and may be applicable to other seasonal conditions where comprehensive epidemiological data is difficult to collect or obtain.
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Affiliation(s)
- Eyal Oren
- Division of Epidemiology & Biostatistics, Graduate School of Public Health, San Diego State University, San Diego, CA, USA. .,Department of Epidemiology & Biostatistics, University of Arizona College of Public Health, Tucson, AZ, USA.
| | - Justin Frere
- Department of Epidemiology & Biostatistics, University of Arizona College of Public Health, Tucson, AZ, USA
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13
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Souquette A, Frere J, Smithey M, Sauce D, Thomas PG. A constant companion: immune recognition and response to cytomegalovirus with aging and implications for immune fitness. GeroScience 2017. [PMID: 28647907 DOI: 10.1007/s11357-017-9982-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Approximately 50% of individuals aged 6-49 years in the United States are infected with cytomegalovirus (CMV), with seroprevalence increasing with age, reaching 85-90% by 75-80 years according to Bate et al. (Clin Infect Dis 50 (11): 1439-1447, 2010) and Pawelec et al. (Curr Opin Immunol 24:507-511, 2012). Following primary infection, CMV establishes lifelong latency with periodic reactivation. Immunocompetent hosts experience largely asymptomatic infection, but CMV can cause serious illness in immunocompromised populations, such as transplant patients and the elderly. Control of CMV requires constant immune surveillance, and recent discoveries suggest this demand alters general features of the immune system in infected individuals. Here, we review recent advances in the understanding of the immune response to CMV and the role of CMV in immune aging and fitness, while highlighting the importance of potential confounding factors that influence CMV studies. Understanding how CMV contributes to shaping "baseline" immunity has important implications for a host's ability to mount effective responses to diverse infections and vaccination.
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Affiliation(s)
- Aisha Souquette
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Justin Frere
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), INSERM U1135, Sorbonne Universités, UPMC DHU FAST, Paris, France.,Arizona Center on Aging, Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Megan Smithey
- Arizona Center on Aging, Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Delphine Sauce
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), INSERM U1135, Sorbonne Universités, UPMC DHU FAST, Paris, France
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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14
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Doyle A, Lesuer W, Pasha S, Lee N, Lee JJ, Shim K, Frere J, Kloeber J, Neely J. Eosinophils Promote Emphysematous Lesions in a Mouse Model of Chronic Type 2 Lung Inflammation. J Allergy Clin Immunol 2017. [DOI: 10.1016/j.jaci.2016.12.599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Thoraval C, Carreira RP, Barla C, Morvan H, Dubrulle A, Drazetic P, Delay JB, Frere J. Epidemiological study applied to the design of wrist guard. Comput Methods Biomech Biomed Engin 2012; 15 Suppl 1:272-3. [DOI: 10.1080/10255842.2012.713637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Frere J. [Not Available]. Cah Semin Philos 2001:49-67. [PMID: 11634782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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17
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Flahaut S, Frere J, Boutibonnes P, Auffray Y. Relationship between the thermotolerance and the increase of DnaK and GroEL synthesis in Enterococcus faecalis ATCC19433. J Basic Microbiol 1997; 37:251-8. [PMID: 9323866 DOI: 10.1002/jobm.3620370404] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Relationship between intrinsic thermal resistance, thermotolerance and heat shock proteins (hsp) synthesis is studied in Enterococcus faecalis. We showed that an impressive phenotypic heat resistance was induced by mild heat and a slight thermotolerance was developed by various sublethal pretreatments such as NaCl, SDS and bile salts. Hydrogen peroxide, acid and alkaline shifts or "thermomimetic" agent such as ethanol, did not enhance the survival of adapted cells against the lethal thermal shock (62 degrees C). The inhibition of protein synthesis by chloramphenicol or rifampin abolished thermotolerance. The immunological identification of the DnaK and GroEL proteins in E. faecalis allowed to study induction of these molecular chaperones under various conditions. Heat was the most efficient inductor of DnaK and GroEL synthesis. However, it was surprising that ethanol did not strongly induce these proteins. We also show that amplification of these hsp is not correlated to acquired thermotolerance with a linear relationship. A weak thermotolerance is not coupled from increased synthesis of DnaK and GroEL. So, we postulate that the high synthesis of the major hsp is not obligatory in the thermal cross-protection but that de novo protein synthesis is an absolute necessity in E. faecalis. Activation of preformed hsp or other factors depending or not on protein synthesis may be also necessary to enhance thermal resistance.
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Affiliation(s)
- S Flahaut
- Laboratoire de Microbiologie de l'Environnement, Université de Caen, France
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18
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Flahaut S, Frere J, Boutibonnes P, Auffray Y. Comparison of the bile salts and sodium dodecyl sulfate stress responses in Enterococcus faecalis. Appl Environ Microbiol 1996; 62:2416-20. [PMID: 8779581 PMCID: PMC168024 DOI: 10.1128/aem.62.7.2416-2420.1996] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The resistance to detergents and detergent-induced tolerance of a gastrointestinal organism, Enterococcus faecalis ATCC 19433, were examined. The most remarkable observation was the rapid response of cells in contact with bile salts and sodium dodecyl sulfate (SDS). The killing by high concentrations of detergents was nearly instantaneous. A 5-s adaptation with moderate sublethal concentrations of bile salts or SDS (0.08 or 0.01%, respectively) was sufficient to induce significant adaptation against homologous lethal conditions (0.3% bile salts or 0.017% SDS). However, resistance to a subsequent lethal challenge progressively increased further to a maximum reached after 30 min of adaptation. Furthermore, extremely strong cross-resistances were observed with bile salts- and SDS-adapted cells. However, no relationship seems to exist between levels of tolerance and de novo-synthesized proteins, since blockage of protein synthesis during adaptation had no effect on induction of resistance to bile salts and SDS. We conclude that this induced tolerance to detergent stress is independent of protein synthesis. Nevertheless, the stress-induced protein patterns of E. faecalis ATCC 19433 showed significant modifications. The rates of synthesis of 45 and 34 proteins were enhanced after treatments with bile salts and SDS, respectively. In spite of the overlap of 12 polypeptides, the protein profiles induced by the two detergents were different, suggesting that these detergents trigger different responses in E. faecalis. Therefore, bile salts cannot be substituted for SDS in biochemical detergent shock experiments with bacteria.
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Affiliation(s)
- S Flahaut
- Laboratoire de Microbiologie de l'Environnement, Institut de Recherche en Biologie Appliquée, Université de Caen, France.
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Frere J, Ghuysen J, Vanderhaeghe H, Adriaens P, Degelaen J, De Graeve J. Fate of thiazolidine ring during fragmentation of penicillin by exocellular DD-carboxypeptidase-transpeptidase of Streptomyces R61. Nature 1976; 260:451-4. [PMID: 815828 DOI: 10.1038/260451a0] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Frere J, Ghuysen J, Degelaen J, Loffet A, Perkins HR. Fragmentation of benzylpenicillin after interaction with the exocellular DD-carboxypeptidase-transpeptidases of Streptomyces R61 and R39. Nature 1975; 258:168-70. [PMID: 1186898 DOI: 10.1038/258168a0] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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