101
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Lee WS, Yousefi M, Yan B, Yong CL, Ooi YS. Know your enemy and know yourself - the case of SARS-CoV-2 host factors. Curr Opin Virol 2021; 50:159-170. [PMID: 34488003 PMCID: PMC8379091 DOI: 10.1016/j.coviro.2021.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/10/2021] [Accepted: 08/14/2021] [Indexed: 02/06/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiologic agent that causes Coronavirus Disease 2019 (COVID-19) pandemic, is a newly emerging respiratory RNA virus with exceptional transmissibility and pathogenicity. Numerous COVID-19 related studies have been fast-tracked, with the ultimate goal to end the pandemic. Here we review the major stages of SARS-CoV-2 infection cycle in cells, with specific emphasis on essential host factors. Insights into the cell biology of SARS-CoV-2 infection have accelerated the development of host-directed therapeutics, as shown by dozens of clinical trials evaluating COVID-19 treatments using host-targeting compounds.
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Affiliation(s)
- Wai Suet Lee
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Meisam Yousefi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Biaoguo Yan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Cythia Lingli Yong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Yaw Shin Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore.
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102
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Zhang C, Verma A, Feng Y, Melo MCR, McQuillan M, Hansen M, Lucas A, Park J, Ranciaro A, Thompson S, Rubel MA, Campbell MC, Beggs W, Hirbo J, Mpoloka SW, Mokone GG, Nyambo T, Meskel DW, Belay G, Fokunang C, Njamnshi AK, Omar SA, Williams SM, Rader D, Ritchie MD, de la Fuente Nunez C, Sirugo G, Tishkoff S. Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.06.28.21259529. [PMID: 34230933 PMCID: PMC8259910 DOI: 10.1101/2021.06.28.21259529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (ACE2, TMPRSS2, DPP4, and LY6E). We analyzed novel data from 2,012 ethnically diverse Africans and 15,997 individuals of European and African ancestry with electronic health records, and integrated with global data from the 1000GP. At ACE2, we identified 41 non-synonymous variants that were rare in most populations, several of which impact protein function. However, three non-synonymous variants were common among Central African hunter-gatherers from Cameroon and are on haplotypes that exhibit signatures of positive selection. We identify strong signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19.
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Affiliation(s)
- Chao Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuanqing Feng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcelo C. R. Melo
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael McQuillan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anastasia Lucas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simon Thompson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meghan A. Rubel
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - William Beggs
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | | | - Thomas Nyambo
- Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania
| | - Dawit Wolde Meskel
- Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia
| | - Gurja Belay
- Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Alfred K. Njamnshi
- Department of Neurology, Central Hospital Yaoundé; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Sabah A. Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Daniel Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marylyn D. Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cesar de la Fuente Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Giorgio Sirugo
- Division of Translational Medicine and Human Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Sarah Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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103
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Cheemarla NR, Watkins TA, Mihaylova VT, Wang B, Zhao D, Wang G, Landry ML, Foxman EF. Dynamic innate immune response determines susceptibility to SARS-CoV-2 infection and early replication kinetics. J Exp Med 2021; 218:e20210583. [PMID: 34128960 PMCID: PMC8210587 DOI: 10.1084/jem.20210583] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/21/2021] [Accepted: 06/01/2021] [Indexed: 12/25/2022] Open
Abstract
Initial replication of SARS-CoV-2 in the upper respiratory tract is required to establish infection, and the replication level correlates with the likelihood of viral transmission. Here, we examined the role of host innate immune defenses in restricting early SARS-CoV-2 infection using transcriptomics and biomarker-based tracking in serial patient nasopharyngeal samples and experiments with airway epithelial organoids. SARS-CoV-2 initially replicated exponentially, with a doubling time of ∼6 h, and induced interferon-stimulated genes (ISGs) in the upper respiratory tract, which rose with viral replication and peaked just as viral load began to decline. Rhinovirus infection before SARS-CoV-2 exposure accelerated ISG responses and prevented SARS-CoV-2 replication. Conversely, blocking ISG induction during SARS-CoV-2 infection enhanced viral replication from a low infectious dose. These results show that the activity of ISG-mediated defenses at the time of SARS-CoV-2 exposure impacts infection progression and that the heterologous antiviral response induced by a different virus can protect against SARS-CoV-2.
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Affiliation(s)
- Nagarjuna R. Cheemarla
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Timothy A. Watkins
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Valia T. Mihaylova
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Bao Wang
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Dejian Zhao
- Department of Genetics, Yale School of Medicine, New Haven, CT
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven, CT
| | - Guilin Wang
- Department of Genetics, Yale School of Medicine, New Haven, CT
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven, CT
| | - Marie L. Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Ellen F. Foxman
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
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104
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Boutin S, Hildebrand D, Boulant S, Kreuter M, Rüter J, Pallerla SR, Velavan TP, Nurjadi D. Host factors facilitating SARS-CoV-2 virus infection and replication in the lungs. Cell Mol Life Sci 2021; 78:5953-5976. [PMID: 34223911 PMCID: PMC8256233 DOI: 10.1007/s00018-021-03889-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 06/01/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 is the virus causing the major pandemic facing the world today. Although, SARS-CoV-2 primarily causes lung infection, a variety of symptoms have proven a systemic impact on the body. SARS-CoV-2 has spread in the community quickly infecting humans from all age, ethnicities and gender. However, fatal outcomes have been linked to specific host factors and co-morbidities such as age, hypertension, immuno-deficiencies, chronic lung diseases or metabolic disorders. A major shift in the microbiome of patients suffering of the coronavirus disease 2019 (COVID-19) have also been observed and is linked to a worst outcome of the disease. As many co-morbidities are already known to be associated with a dysbiosis of the microbiome such as hypertension, diabetes and metabolic disorders. Host factors and microbiome changes are believed to be involved as a network in the acquisition of the infection and the development of the diseases. We will review in detail in this manuscript, the immune response toward SARS-CoV-2 infection as well as the host factors involved in the facilitation and worsening of the infection. We will also address the impact of COVID-19 on the host's microbiome and secondary infection which also worsen the disease.
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Affiliation(s)
- Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany.
| | - Dagmar Hildebrand
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Steeve Boulant
- Division of Cellular Polarity and Viral Infection, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Kreuter
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
- Center for Interstitial and Rare Lung Diseases, Pneumology, Thoraxklinik, University of Heidelberg, Heidelberg, Germany
| | - Jule Rüter
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | | | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
| | - Dennis Nurjadi
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
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105
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Vilella F, Wang W, Moreno I, Roson B, Quake SR, Simon C. Single-cell RNA Sequencing of SARS-CoV-2 Cell Entry Factors in the Preconceptional Human Endometrium. Hum Reprod 2021; 36:2709-2719. [PMID: 34329437 PMCID: PMC8385818 DOI: 10.1093/humrep/deab183] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/17/2021] [Indexed: 12/26/2022] Open
Abstract
STUDY QUESTION Are SARS-CoV-2 canonical cell entry machinery, consisting of ACE2, TMPRSS2, NRP1 and LY6E, or alternative potential cell entry machinery, consisting of BSG, ANPEP, CD209, CLEC4G, TMPRSS4, TMPRSS11A, FURIN, CTSB, CTSL and IFITM1, expressed in the human endometrium across the menstrual cycle? SUMMARY ANSWER Analysis of cell entry factors for SARS-CoV-2 by single-cell RNA-sequencing (scRNAseq) in the preconceptional human endometrium reveals low risk of infection. WHAT IS KNOWN ALREADY Gene expression datasets from bulk endometrial tissue show no significant expression of the SARS-CoV-2 receptor ACE2 and TMPRSS2. This is in contrast to reported expression of ACE2 at the single-cell level in the decidua and trophoblast cells at the maternal–fetal interface in early pregnancy, as well as vertical transmission of SARS-CoV-2 during pregnancy. STUDY DESIGN, SIZE, DURATION This analysis of SARS-CoV-2 cell entry machinery gene expression was conducted by scRNAseq in 73 181 human endometrial cells isolated from endometrial biopsies obtained from 27 donors across the menstrual cycle. PARTICIPANTS/MATERIALS, SETTING, METHODS ScRNAseq examined the expression of genes encoding cell entry machinery for SARS-CoV-2. The raw data were from a previously published dataset. MAIN RESULTS AND THE ROLE OF CHANCE ScRNAseq analysis showed no significant expression of ACE2 in stromal or unciliated epithelial cells in any phase of the menstrual cycle. TMPRSS2 was expressed in epithelial cells during the early proliferative and mid-secretory phases. Interestingly, the expression of NRP1 was observed in both stromal and epithelial cells across all phases of the menstrual cycle, and LY6E was highly expressed in stromal cells. In the mid-secretory phase, coexpression of ACE2 and TMPRSS2 was detected in 0.07% of luminal epithelial cells. No cells simultaneously expressed ACE2, NRP1 and TMPRSS2 at the time of embryo implantation. Focusing on non-canonical cell entry machinery, BSG was highly expressed in all cell types across the menstrual cycle and may interact with CTSB or CTSL proteases, but viral infection using this machinery has not yet been confirmed. LARGE SCALE DATA All raw data in this study can be found at NCBI’s Gene Expression Omnibus (series accession code GSE111976) and Sequence Read Archive (accession code SRP135922). LIMITATIONS, REASONS FOR CAUTION Our findings at the single-cell level imply low efficiency of SARS-CoV-2 endometrial infection using canonical receptors in a cohort of healthy reproductive-age women; however, infection of endometrial cells can only be assessed in the presence of the virus. All samples were processed for scRNAseq, so no samples are remaining to analyze protein expression or spatial transcriptomics. WIDER IMPLICATIONS OF THE FINDINGS Our results offer a useful resource to guide reproductive decisions when assessing risk of endometrial infection by SARS-CoV-2 during the preconceptional period in asymptomatic COVID-19 carriers. STUDY FUNDING/COMPETING INTEREST(S) This study was jointly supported by the March of Dimes, Chan Zuckerberg Biohub and MINECO/FEDER (SAF-2015-67164-R, to C.S.) (Spanish Government), and the European Union’s Horizon 2020 Framework Programme for Research and Innovation (Grant agreement 874867). W.W. was supported by the Stanford Bio-X Graduate Bowes Fellowship and Chan Zuckerberg Biohub. F.V. was supported by the Miguel Servet Program Type II of ISCIII (CPII18/00020) and the FIS project (PI18/00957). A patent disclosure has been filed for the study with the title ‘Methods for assessing endometrial transformation’ and the global patent number ‘EP 3807648 A2’ under the inventors S.R.Q., C.S., W.W. and F.V. C.S. is the Founder and Head of the Scientific Advisory Board of Igenomix SL. S.R.Q is the Director of Mirvie. I.M. is partially employed by Igenomix SL. B.R. has no interests to declare.
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Affiliation(s)
- F Vilella
- Igenomix Foundation, INCLIVA Health Research Institute, C/Narcis de Monturiol Estarriol 11B, 46980, Valencia, Spain.,Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Harvard University, 330 Brookline Ave, Boston, MA 02215, United States
| | - W Wang
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, United States
| | - I Moreno
- Igenomix Foundation, INCLIVA Health Research Institute, C/Narcis de Monturiol Estarriol 11B, 46980, Valencia, Spain
| | - B Roson
- Igenomix Foundation, INCLIVA Health Research Institute, C/Narcis de Monturiol Estarriol 11B, 46980, Valencia, Spain
| | - S R Quake
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA 94305, United States.,Department of Applied Physics, Stanford University, 443 Via Ortega, Stanford, CA 94305, United States.,Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, United States
| | - C Simon
- Igenomix Foundation, INCLIVA Health Research Institute, C/Narcis de Monturiol Estarriol 11B, 46980, Valencia, Spain.,Department of Obstetrics & Gynecology, University of Valencia, Av. de Blasco Ibáñez, 15, 46010, Valencia, Spain.,Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Harvard University, 330 Brookline Ave, Boston, MA 02215, United States
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106
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Zhang C, Verma A, Feng Y, Dos Reis Melo MC, McQuillan M, Hansen M, Lucas A, Park J, Ranciaro A, Thompson S, Rubel M, Campbell M, Beggs W, Hirbo J, Mpoloka SW, Mokone GG, Jones M, Nyambo T, Meskel DW, Belay G, Fokunang C, Njamnshi A, Omar S, Williams S, Rader D, Ritchie M, de la Fuente C, Sirugo G, Tishkoff S. Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-CoV-2 infection. RESEARCH SQUARE 2021:rs.3.rs-673011. [PMID: 34341784 PMCID: PMC8328070 DOI: 10.21203/rs.3.rs-673011/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection ( ACE2, TMPRSS2, DPP4 , and LY6E ). We analyzed novel data from 2,012 ethnically diverse Africans and 15,997 individuals of European and African ancestry with electronic health records, and integrated with global data from the 1000GP. At ACE2 , we identified 41 non-synonymous variants that were rare in most populations, several of which impact protein function. However, three non-synonymous variants were common among Central African hunter-gatherers from Cameroon and are on haplotypes that exhibit signatures of positive selection. We identify strong signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2 , we identified 13 amino acid changes that are adaptive and specific to the human lineage. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19.
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Affiliation(s)
| | - Anurag Verma
- Perelman School of Medicine, University of Pennsylvania
| | | | | | | | | | | | - Joseph Park
- Perelman School of Medicine, University of Pennsylvania
| | | | | | | | | | | | | | | | | | | | | | - Dawit Wolde Meskel
- Addis Ababa University Department of Microbial Cellular and Molecular Biology
| | - Guija Belay
- Addis Ababa University Department of Microbial Cellular and Molecular Biology
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | | | | | | | - Daniel Rader
- Perelman School of Medicine at the University of Pennsylvania
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107
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Brezgin S, Kostyusheva A, Bayurova E, Volchkova E, Gegechkori V, Gordeychuk I, Glebe D, Kostyushev D, Chulanov V. Immunity and Viral Infections: Modulating Antiviral Response via CRISPR-Cas Systems. Viruses 2021; 13:1373. [PMID: 34372578 PMCID: PMC8310348 DOI: 10.3390/v13071373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022] Open
Abstract
Viral infections cause a variety of acute and chronic human diseases, sometimes resulting in small local outbreaks, or in some cases spreading across the globe and leading to global pandemics. Understanding and exploiting virus-host interactions is instrumental for identifying host factors involved in viral replication, developing effective antiviral agents, and mitigating the severity of virus-borne infectious diseases. The diversity of CRISPR systems and CRISPR-based tools enables the specific modulation of innate immune responses and has contributed impressively to the fields of virology and immunology in a very short time. In this review, we describe the most recent advances in the use of CRISPR systems for basic and translational studies of virus-host interactions.
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Affiliation(s)
- Sergey Brezgin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (S.B.); (A.K.); (V.C.)
- Institute of Immunology, Federal Medical Biological Agency, 115522 Moscow, Russia
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Anastasiya Kostyusheva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (S.B.); (A.K.); (V.C.)
| | - Ekaterina Bayurova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia; (E.B.); (I.G.)
| | - Elena Volchkova
- Department of Infectious Diseases, Sechenov University, 119991 Moscow, Russia;
| | - Vladimir Gegechkori
- Department of Pharmaceutical and Toxicological Chemistry, Sechenov University, 119991 Moscow, Russia;
| | - Ilya Gordeychuk
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia; (E.B.); (I.G.)
- Department of Organization and Technology of Immunobiological Drugs, Sechenov University, 119991 Moscow, Russia
| | - Dieter Glebe
- National Reference Center for Hepatitis B Viruses and Hepatitis D Viruses, Institute of Medical Virology, Justus Liebig University of Giessen, 35392 Giessen, Germany;
| | - Dmitry Kostyushev
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (S.B.); (A.K.); (V.C.)
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Vladimir Chulanov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (S.B.); (A.K.); (V.C.)
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Infectious Diseases, Sechenov University, 119991 Moscow, Russia;
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108
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Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE. Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity. Nat Commun 2021; 12:4314. [PMID: 34262047 PMCID: PMC8280215 DOI: 10.1038/s41467-021-24467-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/04/2021] [Indexed: 02/08/2023] Open
Abstract
Patients with chronic lung disease (CLD) have an increased risk for severe coronavirus disease-19 (COVID-19) and poor outcomes. Here, we analyze the transcriptomes of 611,398 single cells isolated from healthy and CLD lungs to identify molecular characteristics of lung cells that may account for worse COVID-19 outcomes in patients with chronic lung diseases. We observe a similar cellular distribution and relative expression of SARS-CoV-2 entry factors in control and CLD lungs. CLD AT2 cells express higher levels of genes linked directly to the efficiency of viral replication and the innate immune response. Additionally, we identify basal differences in inflammatory gene expression programs that highlight how CLD alters the inflammatory microenvironment encountered upon viral exposure to the peripheral lung. Our study indicates that CLD is accompanied by changes in cell-type-specific gene expression programs that prime the lung epithelium for and influence the innate and adaptive immune responses to SARS-CoV-2 infection.
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Affiliation(s)
- Linh T Bui
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Nichelle I Winters
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chitra Joseph
- Respiratory Medicine NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | | | - Arun C Habermann
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sergio Poli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lance M Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jessica B Blackburn
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bradley W Richmond
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
| | - Andrew G Nicholson
- National Heart and Lung Institute, Imperial College, London, UK
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Doris Rassl
- Pathology Research, Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - William A Wallace
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
- Division of Pathology, Edinburgh University Medical School, Edinburgh, UK
| | - Ivan O Rosas
- Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - R Gisli Jenkins
- Respiratory Medicine NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonathan A Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
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109
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Mourad M, Jacob T, Sadovsky E, Bejerano S, Simone GSD, Bagalkot TR, Zucker J, Yin MT, Chang JY, Liu L, Debelenko L, Shawber CJ, Firestein M, Ouyang Y, Gyamfi-Bannerman C, Penn A, Sorkin A, Wapner R, Sadovsky Y. Placental response to maternal SARS-CoV-2 infection. Sci Rep 2021; 11:14390. [PMID: 34257394 PMCID: PMC8277865 DOI: 10.1038/s41598-021-93931-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic affected people at all ages. Whereas pregnant women seemed to have a worse course of disease than age-matched non-pregnant women, the risk of feto-placental infection is low. Using a cohort of 66 COVID-19-positive women in late pregnancy, we correlated clinical parameters with disease severity, placental histopathology, and the expression of viral entry and Interferon-induced transmembrane (IFITM) antiviral transcripts. All newborns were negative for SARS-CoV-2. None of the demographic parameters or placental histopathological characteristics were associated with disease severity. The fetal-maternal transfer ratio for IgG against the N or S viral proteins was commonly less than one, as recently reported. We found that the expression level of placental ACE2, but not TMPRSS2 or Furin, was higher in women with severe COVID-19. Placental expression of IFITM1 and IFITM3, which have been implicated in antiviral response, was higher in participants with severe disease. We also showed that IFITM3 protein expression, which localized to early and late endosomes, was enhanced in severe COVID-19. Our data suggest an association between disease severity and placental SARS-CoV-2 processing and antiviral pathways, implying a role for these proteins in placental response to SARS-CoV-2.
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Affiliation(s)
- Mirella Mourad
- Department of Obstetrics, Gynecology and Reproductive Science, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Taylor Jacob
- Department of Obstetrics, Gynecology and Reproductive Science, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Elena Sadovsky
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Shai Bejerano
- Department of Obstetrics, Gynecology and Reproductive Science, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Glicella Salazar-De Simone
- Department of Obstetrics, Gynecology and Reproductive Science, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Jason Zucker
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael T Yin
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Jennifer Y Chang
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Lihong Liu
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Larisa Debelenko
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Carrie J Shawber
- Department of Obstetrics, Gynecology and Reproductive Science, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Surgery, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Morgan Firestein
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Yingshi Ouyang
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Cynthia Gyamfi-Bannerman
- Department of Obstetrics, Gynecology and Reproductive Science, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Anna Penn
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Alexander Sorkin
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ronald Wapner
- Department of Obstetrics, Gynecology and Reproductive Science, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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110
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Li X, Zhang L, Chen S, Ouyang H, Ren L. Possible Targets of Pan-Coronavirus Antiviral Strategies for Emerging or Re-Emerging Coronaviruses. Microorganisms 2021; 9:1479. [PMID: 34361915 PMCID: PMC8306356 DOI: 10.3390/microorganisms9071479] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 12/16/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which caused Coronaviruses Disease 2019 (COVID-19) and a worldwide pandemic, is the seventh human coronavirus that has been cross-transmitted from animals to humans. It can be predicted that with continuous contact between humans and animals, more viruses will spread from animals to humans. Therefore, it is imperative to develop universal coronavirus or pan-coronavirus vaccines or drugs against the next coronavirus pandemic. However, a suitable target is critical for developing pan-coronavirus antivirals against emerging or re-emerging coronaviruses. In this review, we discuss the latest progress of possible targets of pan-coronavirus antiviral strategies for emerging or re-emerging coronaviruses, including targets for pan-coronavirus inhibitors and vaccines, which will provide prospects for the current and future research and treatment of the disease.
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Affiliation(s)
| | | | | | | | - Linzhu Ren
- Key Laboratory for Zoonoses Research, College of Animal Sciences, Ministry of Education, Jilin University, 5333 Xi’An Road, Changchun 130062, China; (X.L.); (L.Z.); (S.C.); (H.O.)
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111
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Lin H, Ma X, Xiao F, Su H, Shi Y, Liu Y, Song L, Zhang Z, Zhang C, Peng H. Identification of a special cell type as a determinant of the kidney tropism of SARS-CoV-2. FEBS J 2021; 288:5163-5178. [PMID: 34228902 PMCID: PMC8420455 DOI: 10.1111/febs.16114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/09/2021] [Accepted: 07/06/2021] [Indexed: 12/01/2022]
Abstract
The kidney tropism of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been well‐validated clinically and often leads to various forms of renal damage in coronavirus disease‐2019 (COVID‐19) patients. However, the underlying mechanisms and diagnostic approaches remain to be determined. We interrogated the expression of virus‐related host factors in single‐cell RNA sequencing (scRNA‐seq) datasets of normal human kidneys and kidneys with pre‐existing diseases and validated the results with urinary proteomics of COVID‐19 patients and healthy individuals. We also assessed the effects of genetic variants on kidney susceptibility using expression quantitative trait loci (eQTLs) databases. We identified a subtype of tubular cells, which we named PT‐3 cells, as being vulnerable to SARS‐CoV‐2 infections in the kidneys. PT‐3 cells were enriched in viral entry factors and replication and assembly machinery but lacked antiviral restriction factors. Immunohistochemistry confirmed positive staining of PT‐3 cell marker SCL36A2 on kidney sections from COVID‐19 patients. Urinary proteomic analyses of COVID‐19 patients revealed that markers of PT‐3 cells were significantly increased, along with elevated viral receptor angiotensin‐converting enzyme 2. We further found that the proportion of PT‐3 cells increased in diabetic nephropathy but decreased in kidney allografts and lupus nephropathy, suggesting that kidney susceptibility varied among these diseases. We finally identified several eQTLs that regulate the expression of host factors in kidney cells. PT‐3 cells may represent a key determinant for the kidney tropism of SARS‐CoV‐2, and detection of PT‐3 cells may be used to assess the risk of renal infection during COVID‐19.
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Affiliation(s)
- Hongchun Lin
- Nephrology Division, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xinxin Ma
- Nephrology Division, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Fang Xiao
- Department of Cadres Medical Care and Geriatrics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hua Su
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaling Shi
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yuntao Liu
- Department of Emergency, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, China.,Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, China
| | - Lan Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeOmics, China
| | - Zhongde Zhang
- Department of Emergency, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, China.,Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, China
| | - Chun Zhang
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Peng
- Nephrology Division, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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112
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COVID-19 is a systemic vascular hemopathy: insight for mechanistic and clinical aspects. Angiogenesis 2021; 24:755-788. [PMID: 34184164 PMCID: PMC8238037 DOI: 10.1007/s10456-021-09805-6] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is presenting as a systemic disease associated with vascular inflammation and endothelial injury. Severe forms of SARS-CoV-2 infection induce acute respiratory distress syndrome (ARDS) and there is still an ongoing debate on whether COVID-19 ARDS and its perfusion defect differs from ARDS induced by other causes. Beside pro-inflammatory cytokines (such as interleukin-1 β [IL-1β] or IL-6), several main pathological phenomena have been seen because of endothelial cell (EC) dysfunction: hypercoagulation reflected by fibrin degradation products called D-dimers, micro- and macrothrombosis and pathological angiogenesis. Direct endothelial infection by SARS-CoV-2 is not likely to occur and ACE-2 expression by EC is a matter of debate. Indeed, endothelial damage reported in severely ill patients with COVID-19 could be more likely secondary to infection of neighboring cells and/or a consequence of inflammation. Endotheliopathy could give rise to hypercoagulation by alteration in the levels of different factors such as von Willebrand factor. Other than thrombotic events, pathological angiogenesis is among the recent findings. Overexpression of different proangiogenic factors such as vascular endothelial growth factor (VEGF), basic fibroblast growth factor (FGF-2) or placental growth factors (PlGF) have been found in plasma or lung biopsies of COVID-19 patients. Finally, SARS-CoV-2 infection induces an emergency myelopoiesis associated to deregulated immunity and mobilization of endothelial progenitor cells, leading to features of acquired hematological malignancies or cardiovascular disease, which are discussed in this review. Altogether, this review will try to elucidate the pathophysiology of thrombotic complications, pathological angiogenesis and EC dysfunction, allowing better insight in new targets and antithrombotic protocols to better address vascular system dysfunction. Since treating SARS-CoV-2 infection and its potential long-term effects involves targeting the vascular compartment and/or mobilization of immature immune cells, we propose to define COVID-19 and its complications as a systemic vascular acquired hemopathy.
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113
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Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Becker ME, Pratt D, Churas C, Rosenthal SB, Liu S, Weston S, De Jesus PD, O'Neill AM, Gounder AP, Nguyen C, Pu Y, Curry HM, Oom AL, Miorin L, Rodriguez-Frandsen A, Zheng F, Wu C, Xiong Y, Urbanowski M, Shaw ML, Chang MW, Benner C, Hope TJ, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK. Functional landscape of SARS-CoV-2 cellular restriction. Mol Cell 2021; 81:2656-2668.e8. [PMID: 33930332 PMCID: PMC8043580 DOI: 10.1016/j.molcel.2021.04.008] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/01/2021] [Accepted: 04/07/2021] [Indexed: 12/21/2022]
Abstract
A deficient interferon (IFN) response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been implicated as a determinant of severe coronavirus disease 2019 (COVID-19). To identify the molecular effectors that govern IFN control of SARS-CoV-2 infection, we conducted a large-scale gain-of-function analysis that evaluated the impact of human IFN-stimulated genes (ISGs) on viral replication. A limited subset of ISGs were found to control viral infection, including endosomal factors inhibiting viral entry, RNA binding proteins suppressing viral RNA synthesis, and a highly enriched cluster of endoplasmic reticulum (ER)/Golgi-resident ISGs inhibiting viral assembly/egress. These included broad-acting antiviral ISGs and eight ISGs that specifically inhibited SARS-CoV-2 and SARS-CoV-1 replication. Among the broad-acting ISGs was BST2/tetherin, which impeded viral release and is antagonized by SARS-CoV-2 Orf7a protein. Overall, these data illuminate a set of ISGs that underlie innate immune control of SARS-CoV-2/SARS-CoV-1 infection, which will facilitate the understanding of host determinants that impact disease severity and offer potential therapeutic strategies for COVID-19.
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Affiliation(s)
- Laura Martin-Sancho
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Mary K Lewinski
- Department of Medicine, University of California San Diego, and the VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Lars Pache
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Charlotte A Stoneham
- Department of Medicine, University of California San Diego, and the VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Xin Yin
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Mark E Becker
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Dexter Pratt
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Christopher Churas
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sara B Rosenthal
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sophie Liu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Paul D De Jesus
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Alan M O'Neill
- Department of Dermatology, University of California San Diego, La Jolla, CA 92093, USA
| | - Anshu P Gounder
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Courtney Nguyen
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Yuan Pu
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Heather M Curry
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Aaron L Oom
- Department of Medicine, University of California San Diego, and the VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA
| | - Ariel Rodriguez-Frandsen
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Fan Zheng
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Matthew Urbanowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA
| | - Megan L Shaw
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA; Department of Medical Biosciences, University of the Western Cape, Cape Town 7535, South Africa
| | - Max W Chang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Christopher Benner
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas J Hope
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA; The Tisch Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Judd F Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - John Guatelli
- Department of Medicine, University of California San Diego, and the VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
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114
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Zhou Y, Xu J, Hou Y, Leverenz JB, Kallianpur A, Mehra R, Liu Y, Yu H, Pieper AA, Jehi L, Cheng F. Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. Alzheimers Res Ther 2021; 13:110. [PMID: 34108016 PMCID: PMC8189279 DOI: 10.1186/s13195-021-00850-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Dementia-like cognitive impairment is an increasingly reported complication of SARS-CoV-2 infection. However, the underlying mechanisms responsible for this complication remain unclear. A better understanding of causative processes by which COVID-19 may lead to cognitive impairment is essential for developing preventive and therapeutic interventions. METHODS In this study, we conducted a network-based, multimodal omics comparison of COVID-19 and neurologic complications. We constructed the SARS-CoV-2 virus-host interactome from protein-protein interaction assay and CRISPR-Cas9-based genetic assay results and compared network-based relationships therein with those of known neurological manifestations using network proximity measures. We also investigated the transcriptomic profiles (including single-cell/nuclei RNA-sequencing) of Alzheimer's disease (AD) marker genes from patients infected with COVID-19, as well as the prevalence of SARS-CoV-2 entry factors in the brains of AD patients not infected with SARS-CoV-2. RESULTS We found significant network-based relationships between COVID-19 and neuroinflammation and brain microvascular injury pathways and processes which are implicated in AD. We also detected aberrant expression of AD biomarkers in the cerebrospinal fluid and blood of patients with COVID-19. While transcriptomic analyses showed relatively low expression of SARS-CoV-2 entry factors in human brain, neuroinflammatory changes were pronounced. In addition, single-nucleus transcriptomic analyses showed that expression of SARS-CoV-2 host factors (BSG and FURIN) and antiviral defense genes (LY6E, IFITM2, IFITM3, and IFNAR1) was elevated in brain endothelial cells of AD patients and healthy controls relative to neurons and other cell types, suggesting a possible role for brain microvascular injury in COVID-19-mediated cognitive impairment. Overall, individuals with the AD risk allele APOE E4/E4 displayed reduced expression of antiviral defense genes compared to APOE E3/E3 individuals. CONCLUSION Our results suggest significant mechanistic overlap between AD and COVID-19, centered on neuroinflammation and microvascular injury. These results help improve our understanding of COVID-19-associated neurological manifestations and provide guidance for future development of preventive or treatment interventions, although causal relationship and mechanistic pathways between COVID-19 and AD need future investigations.
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Affiliation(s)
- Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jielin Xu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - James B Leverenz
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Asha Kallianpur
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Reena Mehra
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14850, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, 14850, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Cornell University, Ithaca, NY, 14850, USA
| | - Andrew A Pieper
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106, USA
- Department of Psychiatry, Case Western Reserve University, Cleveland, OH, 44106, USA
- Geriatric Psychiatry, GRECC, Louis Stokes Cleveland VA Medical Center, Cleveland, OH, 44106, USA
- Institute for Transformative Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Weill Cornell Autism Research Program, Weill Cornell Medicine of Cornell University, New York, NY, 10065, USA
- Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Lara Jehi
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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115
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Galani IE, Andreakos E. Impaired innate antiviral defenses in COVID-19: Causes, consequences and therapeutic opportunities. Semin Immunol 2021; 55:101522. [PMID: 34815163 PMCID: PMC8576141 DOI: 10.1016/j.smim.2021.101522] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently emerged pathogen that has caused coronavirus disease 2019 (COVID-19), the worst pandemic of our times leading to tremendous loss of human life and unprecedented measures of social distancing. COVID-19 symptom manifestations range from asymptomatic disease to severe and lethal outcomes. Lack of previous exposure and immunity to SARS-CoV-2, and high infectivity of the virus have contributed to its broad spread across the globe. In the absence of specific adaptive immunity, innate immune mechanisms are crucial for efficient antiviral defenses and control of the infection. Accumulating evidence now suggests that the remarkable heterogeneity in COVID-19 disease manifestations is due to variable degrees of impairment of innate immune mechanisms. In this review, we summarize recent findings describing both viral and host intrinsic factors that have been linked to defective innate immune responses and account for severe COVID-19. We also discuss emerging therapeutic opportunities for targeting innate immunity for the treatment of COVID-19.
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Affiliation(s)
- Ioanna-Evdokia Galani
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece
| | - Evangelos Andreakos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Soranou Efesiou 4, 11527, Athens, Greece.
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116
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Role of host factors in SARS-CoV-2 entry. J Biol Chem 2021; 297:100847. [PMID: 34058196 PMCID: PMC8160279 DOI: 10.1016/j.jbc.2021.100847] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022] Open
Abstract
The zoonotic transmission of highly pathogenic coronaviruses into the human population is a pressing concern highlighted by the ongoing SARS-CoV-2 pandemic. Recent work has helped to illuminate much about the mechanisms of SARS-CoV-2 entry into the cell, which determines host- and tissue-specific tropism, pathogenicity, and zoonotic transmission. Here we discuss current findings on the factors governing SARS-CoV-2 entry. We first reviewed key features of the viral spike protein (S) mediating fusion of the viral envelope and host cell membrane through binding to the SARS-CoV-2 receptor, angiotensin-converting enzyme 2. We then examined the roles of host proteases including transmembrane protease serine 2 and cathepsins in processing S for virus entry and the impact of this processing on endosomal and plasma membrane virus entry routes. We further discussed recent work on several host cofactors that enhance SARS-CoV-2 entry including Neuropilin-1, CD147, phosphatidylserine receptors, heparan sulfate proteoglycans, sialic acids, and C-type lectins. Finally, we discussed two key host restriction factors, i.e., interferon-induced transmembrane proteins and lymphocyte antigen 6 complex locus E, which can disrupt SARS-CoV-2 entry. The features of SARS-CoV-2 are presented in the context of other human coronaviruses, highlighting unique aspects. In addition, we identify the gaps in understanding of SARS-CoV-2 entry that will need to be addressed by future studies.
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117
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Rebendenne A, Roy P, Bonaventure B, Chaves VAL, Desmarets L, Rouillé Y, Tauziet M, Arnaud-Arnould M, Giovannini D, Lee Y, DeWeirdt P, Hegde M, Garcia de GF, McKellar J, Wencker M, Dubuisson J, Belouzard S, Moncorgé O, Doench JG, Goujon C. Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs. RESEARCH SQUARE 2021:rs.3.rs-555275. [PMID: 34075371 PMCID: PMC8168385 DOI: 10.21203/rs.3.rs-555275/v1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor. Additionally, such screens have yet to identify the protease TMPRSS2, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity of additional models to uncover the full landscape of SARS-CoV-2 host factors. We performed genome-wide knockout and activation CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. In addition to identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Moreover, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins, IL6R, and CD44 were identified. We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A orthomyxovirus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.
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Affiliation(s)
| | - Priyanka Roy
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | | | - Lowiese Desmarets
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, France
| | - Yves Rouillé
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, France
| | | | | | | | - Yenarae Lee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Peter DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Mudra Hegde
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | | | | | - Jean Dubuisson
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, France
| | - Sandrine Belouzard
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, France
| | | | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
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Rebendenne A, Roy P, Bonaventure B, Chaves Valadão AL, Desmarets L, Rouillé Y, Tauziet M, Arnaud-Arnould M, Giovannini D, Lee Y, DeWeirdt P, Hegde M, Garcia de Gracia F, McKellar J, Wencker M, Dubuisson J, Belouzard S, Moncorgé O, Doench JG, Goujon C. Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34031654 DOI: 10.1101/2021.05.19.444823] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor. Additionally, such screens have yet to identify the protease TMPRSS2, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity of additional models to uncover the full landscape of SARS-CoV-2 host factors. We performed genome-wide knockout and activation CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. In addition to identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Moreover, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins, IL6R, and CD44 were identified. We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A orthomyxovirus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.
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119
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Taguchi YH, Turki T. Application of Tensor Decomposition to Gene Expression of Infection of Mouse Hepatitis Virus Can Identify Critical Human Genes and Efffective Drugs for SARS-CoV-2 Infection. IEEE JOURNAL OF SELECTED TOPICS IN SIGNAL PROCESSING 2021; 15:746-758. [PMID: 34812273 PMCID: PMC8545047 DOI: 10.1109/jstsp.2021.3061251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/06/2020] [Accepted: 02/18/2021] [Indexed: 01/19/2023]
Abstract
To better understand the genes with altered expression caused by infection with the novel coronavirus strain SARS-CoV-2 causing COVID-19 infectious disease, a tensor decomposition (TD)-based unsupervised feature extraction (FE) approach was applied to a gene expression profile dataset of the mouse liver and spleen with experimental infection of mouse hepatitis virus, which is regarded as a suitable model of human coronavirus infection. TD-based unsupervised FE selected 134 altered genes, which were enriched in protein-protein interactions with orf1ab, polyprotein, and 3C-like protease that are well known to play critical roles in coronavirus infection, suggesting that these 134 genes can represent the coronavirus infectious process. We then selected compounds targeting the expression of the 134 selected genes based on a public domain database. The identified drug compounds were mainly related to known antiviral drugs, several of which were also included in those previously screened with an in silico method to identify candidate drugs for treating COVID-19.
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Affiliation(s)
- Y-H. Taguchi
- Department of PhysicsChuo UniversityTokyo112-8551Japan
| | - Turki Turki
- Department of Computer ScienceKing Abdulaziz UniversityJeddah21589Saudi Arabia
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120
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Whittaker GR, Daniel S, Millet JK. Coronavirus entry: how we arrived at SARS-CoV-2. Curr Opin Virol 2021; 47:113-120. [PMID: 33744490 PMCID: PMC7942143 DOI: 10.1016/j.coviro.2021.02.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/08/2021] [Accepted: 02/25/2021] [Indexed: 01/12/2023]
Abstract
Because of the COVID-19 pandemic, the novel coronavirus SARS-CoV-2 has risen to shape scientific research during 2020, with its spike (S) protein being a predominant focus. The S protein is likely the most complicated of all viral glycoproteins and is a key factor in immunological responses and virus pathogenesis. It is also the driving force dictating virus entry mechanisms, which are highly 'plastic' for coronaviruses, allowing a plethora of options for different virus variants and strains in different cell types. Here we review coronavirus entry as a foundation for current work on SARS-CoV-2. We focus on the post-receptor binding events and cellular pathways that direct the membrane fusion events necessary for genome delivery, including S proteolytic priming and activation. We also address aspects of the entry process important for virus evolution and therapeutic development.
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Affiliation(s)
- Gary R Whittaker
- Department of Microbiology and Immunology and Master of Public Health Program, Cornell University, Ithaca, NY, USA.
| | - Susan Daniel
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
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121
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Yaron JR, Zhang L, Guo Q, Haydel SE, Lucas AR. Fibrinolytic Serine Proteases, Therapeutic Serpins and Inflammation: Fire Dancers and Firestorms. Front Cardiovasc Med 2021; 8:648947. [PMID: 33869309 PMCID: PMC8044766 DOI: 10.3389/fcvm.2021.648947] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
The making and breaking of clots orchestrated by the thrombotic and thrombolytic serine protease cascades are critical determinants of morbidity and mortality during infection and with vascular or tissue injury. Both the clot forming (thrombotic) and the clot dissolving (thrombolytic or fibrinolytic) cascades are composed of a highly sensitive and complex relationship of sequentially activated serine proteases and their regulatory inhibitors in the circulating blood. The proteases and inhibitors interact continuously throughout all branches of the cardiovascular system in the human body, representing one of the most abundant groups of proteins in the blood. There is an intricate interaction of the coagulation cascades with endothelial cell surface receptors lining the vascular tree, circulating immune cells, platelets and connective tissue encasing the arterial layers. Beyond their role in control of bleeding and clotting, the thrombotic and thrombolytic cascades initiate immune cell responses, representing a front line, "off-the-shelf" system for inducing inflammatory responses. These hemostatic pathways are one of the first response systems after injury with the fibrinolytic cascade being one of the earliest to evolve in primordial immune responses. An equally important contributor and parallel ancient component of these thrombotic and thrombolytic serine protease cascades are the serine protease inhibitors, termed serpins. Serpins are metastable suicide inhibitors with ubiquitous roles in coagulation and fibrinolysis as well as multiple central regulatory pathways throughout the body. Serpins are now known to also modulate the immune response, either via control of thrombotic and thrombolytic cascades or via direct effects on cellular phenotypes, among many other functions. Here we review the co-evolution of the thrombolytic cascade and the immune response in disease and in treatment. We will focus on the relevance of these recent advances in the context of the ongoing COVID-19 pandemic. SARS-CoV-2 is a "respiratory" coronavirus that causes extensive cardiovascular pathogenesis, with microthrombi throughout the vascular tree, resulting in severe and potentially fatal coagulopathies.
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Affiliation(s)
- Jordan R. Yaron
- Center for Personalized Diagnostics and Center for Immunotherapy, Vaccines and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School for Engineering of Matter, Transport and Energy, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, United States
| | - Liqiang Zhang
- Center for Personalized Diagnostics and Center for Immunotherapy, Vaccines and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Qiuyun Guo
- Center for Personalized Diagnostics and Center for Immunotherapy, Vaccines and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Shelley E. Haydel
- Center for Bioelectronics and Biosensors, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Alexandra R. Lucas
- Center for Personalized Diagnostics and Center for Immunotherapy, Vaccines and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
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122
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Zhou Y, Xu J, Hou Y, Leverenz JB, Kallianpur A, Mehra R, Liu Y, Yu H, Pieper AA, Jehi L, Cheng F. Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.15.435423. [PMID: 33791705 PMCID: PMC8010732 DOI: 10.1101/2021.03.15.435423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Dementia-like cognitive impairment is an increasingly reported complication of SARS-CoV-2 infection. However, the underlying mechanisms responsible for this complication remain unclear. A better understanding of causative processes by which COVID-19 may lead to cognitive impairment is essential for developing preventive interventions. METHODS In this study, we conducted a network-based, multimodal genomics comparison of COVID-19 and neurologic complications. We constructed the SARS-CoV-2 virus-host interactome from protein-protein interaction assay and CRISPR-Cas9 based genetic assay results, and compared network-based relationships therein with those of known neurological manifestations using network proximity measures. We also investigated the transcriptomic profiles (including single-cell/nuclei RNA-sequencing) of Alzheimer's disease (AD) marker genes from patients infected with COVID-19, as well as the prevalence of SARS-CoV-2 entry factors in the brains of AD patients not infected with SARS-CoV-2. RESULTS We found significant network-based relationships between COVID-19 and neuroinflammation and brain microvascular injury pathways and processes which are implicated in AD. We also detected aberrant expression of AD biomarkers in the cerebrospinal fluid and blood of patients with COVID-19. While transcriptomic analyses showed relatively low expression of SARS-CoV-2 entry factors in human brain, neuroinflammatory changes were pronounced. In addition, single-nucleus transcriptomic analyses showed that expression of SARS-CoV-2 host factors ( BSG and FURIN ) and antiviral defense genes ( LY6E , IFITM2 , IFITM3 , and IFNAR1 ) was significantly elevated in brain endothelial cells of AD patients and healthy controls relative to neurons and other cell types, suggesting a possible role for brain microvascular injury in COVID-19-mediated cognitive impairment. Notably, individuals with the AD risk allele APOE E4/E4 displayed reduced levels of antiviral defense genes compared to APOE E3/E3 individuals. CONCLUSION Our results suggest significant mechanistic overlap between AD and COVID-19, strongly centered on neuroinflammation and microvascular injury. These results help improve our understanding of COVID-19-associated neurological manifestations and provide guidance for future development of preventive or treatment interventions.
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Affiliation(s)
- Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jielin Xu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - James B. Leverenz
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Asha Kallianpur
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Reena Mehra
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850, USA
- Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Andrew A. Pieper
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
- Department of Psychiatry, Case Western Reserve University, Cleveland, OH 44106, USA
- Geriatric Psychiatry, GRECC, Louis Stokes Cleveland VA Medical Center; Cleveland, OH 44106, USA
- Institute for Transformative Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Weill Cornell Autism Research Program, Weill Cornell Medicine of Cornell University, New York, NY 10065, USA
- Department of Neuroscience, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
| | - Lara Jehi
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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123
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Cai L, Liu H, Huang F, Fujimoto J, Girard L, Chen J, Li Y, Zhang YA, Deb D, Stastny V, Pozo K, Kuo CS, Jia G, Yang C, Zou W, Alomar A, Huffman K, Papari-Zareei M, Yang L, Drapkin B, Akbay EA, Shames DS, Wistuba II, Wang T, Johnson JE, Xiao G, DeBerardinis RJ, Minna JD, Xie Y, Gazdar AF. Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer. Commun Biol 2021; 4:314. [PMID: 33750914 PMCID: PMC7943563 DOI: 10.1038/s42003-021-01842-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/09/2021] [Indexed: 12/17/2022] Open
Abstract
Small cell lung cancer (SCLC) is classified as a high-grade neuroendocrine (NE) tumor, but a subset of SCLC has been termed “variant” due to the loss of NE characteristics. In this study, we computed NE scores for patient-derived SCLC cell lines and xenografts, as well as human tumors. We aligned NE properties with transcription factor-defined molecular subtypes. Then we investigated the different immune phenotypes associated with high and low NE scores. We found repression of immune response genes as a shared feature between classic SCLC and pulmonary neuroendocrine cells of the healthy lung. With loss of NE fate, variant SCLC tumors regain cell-autonomous immune gene expression and exhibit higher tumor-immune interactions. Pan-cancer analysis revealed this NE lineage-specific immune phenotype in other cancers. Additionally, we observed MHC I re-expression in SCLC upon development of chemoresistance. These findings may help guide the design of treatment regimens in SCLC. Ling Cai et al. used transcriptomic profiling data of healthy lung, patient-derived small cell lung cancer cell lines, xenografts, and primary tumors to examine a link between neuroendocrine (NE) signatures and immune gene expression. Their findings suggest that cell-autonomous immune gene repression is a shared feature between healthy and tumor cells of NE lineage and may influence tumor-immune cell interaction and response to immunotherapy.
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Affiliation(s)
- Ling Cai
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA. .,Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA. .,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Hongyu Liu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Fang Huang
- Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luc Girard
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jun Chen
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China.,Department of Lung Cancer Surgery, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Yongwen Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Yu-An Zhang
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Dhruba Deb
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Victor Stastny
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Karine Pozo
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Christin S Kuo
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Gaoxiang Jia
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chendong Yang
- Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Wei Zou
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Adeeb Alomar
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kenneth Huffman
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Mahboubeh Papari-Zareei
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lin Yang
- Department of Pathology, National Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Benjamin Drapkin
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Esra A Akbay
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - David S Shames
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jane E Johnson
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ralph J DeBerardinis
- Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - John D Minna
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA. .,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA. .,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Adi F Gazdar
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
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V'kovski P, Kratzel A, Steiner S, Stalder H, Thiel V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol 2021; 19:155-170. [PMID: 33116300 PMCID: PMC7592455 DOI: 10.1038/s41579-020-00468-6] [Citation(s) in RCA: 1762] [Impact Index Per Article: 587.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
The SARS-CoV-2 pandemic and its unprecedented global societal and economic disruptive impact has marked the third zoonotic introduction of a highly pathogenic coronavirus into the human population. Although the previous coronavirus SARS-CoV and MERS-CoV epidemics raised awareness of the need for clinically available therapeutic or preventive interventions, to date, no treatments with proven efficacy are available. The development of effective intervention strategies relies on the knowledge of molecular and cellular mechanisms of coronavirus infections, which highlights the significance of studying virus-host interactions at the molecular level to identify targets for antiviral intervention and to elucidate critical viral and host determinants that are decisive for the development of severe disease. In this Review, we summarize the first discoveries that shape our current understanding of SARS-CoV-2 infection throughout the intracellular viral life cycle and relate that to our knowledge of coronavirus biology. The elucidation of similarities and differences between SARS-CoV-2 and other coronaviruses will support future preparedness and strategies to combat coronavirus infections.
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Affiliation(s)
- Philip V'kovski
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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125
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Triggle CR, Bansal D, Ding H, Islam MM, Farag EABA, Hadi HA, Sultan AA. A Comprehensive Review of Viral Characteristics, Transmission, Pathophysiology, Immune Response, and Management of SARS-CoV-2 and COVID-19 as a Basis for Controlling the Pandemic. Front Immunol 2021; 12:631139. [PMID: 33717166 PMCID: PMC7952616 DOI: 10.3389/fimmu.2021.631139] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/26/2021] [Indexed: 12/15/2022] Open
Abstract
COVID-19 emerged from China in December 2019 and during 2020 spread to every continent including Antarctica. The coronavirus, SARS-CoV-2, has been identified as the causative pathogen, and its spread has stretched the capacities of healthcare systems and negatively affected the global economy. This review provides an update on the virus, including the genome, the risks associated with the emergence of variants, mode of transmission, immune response, COVID-19 in children and the elderly, and advances made to contain, prevent and manage the disease. Although our knowledge of the mechanics of virus transmission and the immune response has been substantially demystified, concerns over reinfection, susceptibility of the elderly and whether asymptomatic children promote transmission remain unanswered. There are also uncertainties about the pathophysiology of COVID-19 and why there are variations in clinical presentations and why some patients suffer from long lasting symptoms-"the long haulers." To date, there are no significantly effective curative drugs for COVID-19, especially after failure of hydroxychloroquine trials to produce positive results. The RNA polymerase inhibitor, remdesivir, facilitates recovery of severely infected cases but, unlike the anti-inflammatory drug, dexamethasone, does not reduce mortality. However, vaccine development witnessed substantial progress with several being approved in countries around the globe.
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Affiliation(s)
- Chris R. Triggle
- Department of Pharmacology, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Devendra Bansal
- Department of Health Protection & Communicable Diseases Control, Ministry of Public Health, Doha, Qatar
| | - Hong Ding
- Department of Pharmacology, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Md Mazharul Islam
- Department of Animal Resources, Ministry of Municipality and Environment, Doha, Qatar
| | | | - Hamad Abdel Hadi
- Communicable Diseases Centre, Hamad Medical Corporations, Doha, Qatar
| | - Ali A. Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Doha, Qatar
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126
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Treveil A, Bohar B, Sudhakar P, Gul L, Csabai L, Olbei M, Poletti M, Madgwick M, Andrighetti T, Hautefort I, Modos D, Korcsmaros T. ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PLoS Comput Biol 2021; 17:e1008685. [PMID: 33534793 PMCID: PMC7886129 DOI: 10.1371/journal.pcbi.1008685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 02/16/2021] [Accepted: 01/10/2021] [Indexed: 12/21/2022] Open
Abstract
The SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects of the coronavirus virus and its infection. For fruitful and rapid investigation of viral pathomechanisms, a collaborative and interdisciplinary approach is required. Therefore, we have developed ViralLink: a systems biology workflow which reconstructs and analyses networks representing the effect of viruses on intracellular signalling. These networks trace the flow of signal from intracellular viral proteins through their human binding proteins and downstream signalling pathways, ending with transcription factors regulating genes differentially expressed upon viral exposure. In this way, the workflow provides a mechanistic insight from previously identified knowledge of virally infected cells. By default, the workflow is set up to analyse the intracellular effects of SARS-CoV-2, requiring only transcriptomics counts data as input from the user: thus, encouraging and enabling rapid multidisciplinary research. However, the wide-ranging applicability and modularity of the workflow facilitates customisation of viral context, a priori interactions and analysis methods. Through a case study of SARS-CoV-2 infected bronchial/tracheal epithelial cells, we evidence the functionality of the workflow and its ability to identify key pathways and proteins in the cellular response to infection. The application of ViralLink to different viral infections in a context specific manner using different available transcriptomics datasets will uncover key mechanisms in viral pathogenesis.
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Affiliation(s)
- Agatha Treveil
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Balazs Bohar
- Earlham Institute, Norwich, United Kingdom
- Department of Genetics, Eotvos Lorand University, Budapest, Hungary
| | - Padhmanand Sudhakar
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Lejla Gul
- Earlham Institute, Norwich, United Kingdom
| | - Luca Csabai
- Earlham Institute, Norwich, United Kingdom
- Department of Genetics, Eotvos Lorand University, Budapest, Hungary
| | - Marton Olbei
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Martina Poletti
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Matthew Madgwick
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Tahila Andrighetti
- Earlham Institute, Norwich, United Kingdom
- Institute of Biosciences, São Paulo University, Botucatu, Brazil
| | | | - Dezso Modos
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Tamas Korcsmaros
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
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127
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Cheemarla NR, Watkins TA, Mihaylova VT, Wang B, Zhao D, Wang G, Landry ML, Foxman EF. Magnitude and timing of the antiviral response determine SARS-CoV-2 replication early in infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.01.22.21249812. [PMID: 33532783 PMCID: PMC7852233 DOI: 10.1101/2021.01.22.21249812] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The interferon response is a potent antiviral defense mechanism, but its effectiveness depends on its timing relative to viral replication. Here, we report viral replication and host response kinetics in patients at the start of SARS-CoV-2 infection and explore the impact of these kinetics experimentally. In both longitudinal patient nasopharyngeal samples and airway epithelial organoids, we found that SARS-CoV-2 initially replicated exponentially with a doubling time of ~6hr, and induced interferon stimulated genes (ISGs) with delayed timing relative to viral replication. Prior exposure to rhinovirus increased ISG levels and blocked SARS-CoV-2 replication. Conversely, inhibiting ISG induction abrogated interference by rhinovirus and enhanced SARS-CoV-2 replication rate. These results demonstrate the importance of initial interferon-mediated defenses in determining the extent to which SARS-CoV-2 can replicate at the start of infection and indicate that biological variables that alter the airway interferon response, including heterologous induction of innate immunity by other viruses, could profoundly impact SARS-CoV-2 susceptibility and transmission.
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Affiliation(s)
| | - Timothy A. Watkins
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Department of Immunobiology, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Valia T. Mihaylova
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Bao Wang
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Department of Immunobiology, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Dejian Zhao
- Department of Genetics, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Guilin Wang
- Department of Genetics, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Marie L. Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Department of Internal Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Ellen F. Foxman
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Department of Immunobiology, Yale School of Medicine, New Haven CT, U.S.A. 06520
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128
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Mdkhana B, Saheb Sharif-Askari N, Ramakrishnan RK, Goel S, Hamid Q, Halwani R. Nucleic Acid-Sensing Pathways During SARS-CoV-2 Infection: Expectations versus Reality. J Inflamm Res 2021; 14:199-216. [PMID: 33531826 PMCID: PMC7847386 DOI: 10.2147/jir.s277716] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/16/2020] [Indexed: 12/22/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected millions of people and crippled economies worldwide. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for this pandemic has triggered avid research on its pathobiology to better understand the pathophysiology of COVID-19. In the absence of approved antiviral therapeutic strategies or vaccine platforms capable of effectively targeting this global threat, the hunt for effective therapeutics has led to many candidates being actively evaluated for their efficacy in controlling or preventing COVID-19. In this review, we gathered current evidence on the innate nucleic acid-sensing pathways expected to be elicited by SARS-CoV-2 and the immune evasion mechanisms they have developed to promote viral replication and infection. Within the nucleic acid-sensing pathways, SARS-CoV-2 infection and evasion mechanisms trigger the activation of NOD-signaling and NLRP3 pathways leading to the production of inflammatory cytokines, IL-1β and IL-6, while muting or blocking cGAS-STING and interferon type I and III pathways, resulting in decreased production of antiviral interferons and delayed innate response. Therefore, blocking the inflammatory arm and boosting the interferon production arm of nucleic acid-sensing pathways could facilitate early control of viral replication and dissemination, prevent disease progression, and cytokine storm development. We also discuss the rationale behind therapeutic modalities targeting these sensing pathways and their implications in the treatment of COVID-19.
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Affiliation(s)
- Bushra Mdkhana
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Narjes Saheb Sharif-Askari
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rakhee K Ramakrishnan
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Swati Goel
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Qutayba Hamid
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Rabih Halwani
- Sharjah Institute of Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
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129
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Wei J, Alfajaro MM, DeWeirdt PC, Hanna RE, Lu-Culligan WJ, Cai WL, Strine MS, Zhang SM, Graziano VR, Schmitz CO, Chen JS, Mankowski MC, Filler RB, Ravindra NG, Gasque V, de Miguel FJ, Patil A, Chen H, Oguntuyo KY, Abriola L, Surovtseva YV, Orchard RC, Lee B, Lindenbach BD, Politi K, van Dijk D, Kadoch C, Simon MD, Yan Q, Doench JG, Wilen CB. Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection. Cell 2021; 184:76-91.e13. [PMID: 33147444 PMCID: PMC7574718 DOI: 10.1016/j.cell.2020.10.028] [Citation(s) in RCA: 341] [Impact Index Per Article: 113.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/11/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022]
Abstract
Identification of host genes essential for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may reveal novel therapeutic targets and inform our understanding of coronavirus disease 2019 (COVID-19) pathogenesis. Here we performed genome-wide CRISPR screens in Vero-E6 cells with SARS-CoV-2, Middle East respiratory syndrome CoV (MERS-CoV), bat CoV HKU5 expressing the SARS-CoV-1 spike, and vesicular stomatitis virus (VSV) expressing the SARS-CoV-2 spike. We identified known SARS-CoV-2 host factors, including the receptor ACE2 and protease Cathepsin L. We additionally discovered pro-viral genes and pathways, including HMGB1 and the SWI/SNF chromatin remodeling complex, that are SARS lineage and pan-coronavirus specific, respectively. We show that HMGB1 regulates ACE2 expression and is critical for entry of SARS-CoV-2, SARS-CoV-1, and NL63. We also show that small-molecule antagonists of identified gene products inhibited SARS-CoV-2 infection in monkey and human cells, demonstrating the conserved role of these genetic hits across species. This identifies potential therapeutic targets for SARS-CoV-2 and reveals SARS lineage-specific and pan-CoV host factors that regulate susceptibility to highly pathogenic CoVs.
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Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruth E Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William J Lu-Culligan
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA; Department of Cell Biology, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Wesley L Cai
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shang-Min Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Vincent R Graziano
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Cameron O Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jennifer S Chen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Madeleine C Mankowski
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Neal G Ravindra
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Victor Gasque
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Fernando J de Miguel
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ajinkya Patil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Huacui Chen
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kasopefoluwa Y Oguntuyo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Robert C Orchard
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06520, USA
| | - Katerina Politi
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Department of Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - David van Dijk
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
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130
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Parkinson N, Rodgers N, Head Fourman M, Wang B, Zechner M, Swets MC, Millar JE, Law A, Russell CD, Baillie JK, Clohisey S. Dynamic data-driven meta-analysis for prioritisation of host genes implicated in COVID-19. Sci Rep 2020; 10:22303. [PMID: 33339864 PMCID: PMC7749145 DOI: 10.1038/s41598-020-79033-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
The increasing body of literature describing the role of host factors in COVID-19 pathogenesis demonstrates the need to combine diverse, multi-omic data to evaluate and substantiate the most robust evidence and inform development of therapies. Here we present a dynamic ranking of host genes implicated in human betacoronavirus infection (SARS-CoV-2, SARS-CoV, MERS-CoV, seasonal coronaviruses). We conducted an extensive systematic review of experiments identifying potential host factors. Gene lists from diverse sources were integrated using Meta-Analysis by Information Content (MAIC). This previously described algorithm uses data-driven gene list weightings to produce a comprehensive ranked list of implicated host genes. From 32 datasets, the top ranked gene was PPIA, encoding cyclophilin A, a druggable target using cyclosporine. Other highly-ranked genes included proposed prognostic factors (CXCL10, CD4, CD3E) and investigational therapeutic targets (IL1A) for COVID-19. Gene rankings also inform the interpretation of COVID-19 GWAS results, implicating FYCO1 over other nearby genes in a disease-associated locus on chromosome 3. Researchers can search and review the gene rankings and the contribution of different experimental methods to gene rank at https://baillielab.net/maic/covid19 . As new data are published we will regularly update the list of genes as a resource to inform and prioritise future studies.
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Affiliation(s)
- Nicholas Parkinson
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Natasha Rodgers
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Max Head Fourman
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Maaike C Swets
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Jonathan E Millar
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Andy Law
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Clark D Russell
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.
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131
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Zang R, Case JB, Yutuc E, Ma X, Shen S, Gomez Castro MF, Liu Z, Zeng Q, Zhao H, Son J, Rothlauf PW, Kreutzberger AJB, Hou G, Zhang H, Bose S, Wang X, Vahey MD, Mani K, Griffiths WJ, Kirchhausen T, Fremont DH, Guo H, Diwan A, Wang Y, Diamond MS, Whelan SPJ, Ding S. Cholesterol 25-hydroxylase suppresses SARS-CoV-2 replication by blocking membrane fusion. Proc Natl Acad Sci U S A 2020; 117:32105-32113. [PMID: 33239446 PMCID: PMC7749331 DOI: 10.1073/pnas.2012197117] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cholesterol 25-hydroxylase (CH25H) is an interferon (IFN)-stimulated gene that shows broad antiviral activities against a wide range of enveloped viruses. Here, using an IFN-stimulated gene screen against vesicular stomatitis virus (VSV)-SARS-CoV and VSV-SARS-CoV-2 chimeric viruses, we identified CH25H and its enzymatic product 25-hydroxycholesterol (25HC) as potent inhibitors of SARS-CoV-2 replication. Internalized 25HC accumulates in the late endosomes and potentially restricts SARS-CoV-2 spike protein catalyzed membrane fusion via blockade of cholesterol export. Our results highlight one of the possible antiviral mechanisms of 25HC and provide the molecular basis for its therapeutic development.
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Affiliation(s)
- Ruochen Zang
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, 266100 Qingdao, China
| | - James Brett Case
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Eylan Yutuc
- Swansea University Medical School, SA2 8PP Swansea, United Kingdom
| | - Xiucui Ma
- Center for Cardiovascular Research and Division of Cardiology, Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63111
- John Cochran VA Medical Center, St. Louis, MO 63106
| | - Sheng Shen
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Maria Florencia Gomez Castro
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Qiru Zeng
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Haiyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Juhee Son
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Program in Molecular Cell Biology, Washington University School of Medicine, St. Louis, MO 63110
| | - Paul W Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Program in Virology, Harvard Medical School, Boston, MA 02115
| | - Alex J B Kreutzberger
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Gaopeng Hou
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Hu Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
| | | | - Xin Wang
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, 266100 Qingdao, China
| | - Michael D Vahey
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63110
| | - Kartik Mani
- Center for Cardiovascular Research and Division of Cardiology, Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63111
- John Cochran VA Medical Center, St. Louis, MO 63106
| | | | - Tom Kirchhausen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Haitao Guo
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Abhinav Diwan
- Center for Cardiovascular Research and Division of Cardiology, Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63111
- John Cochran VA Medical Center, St. Louis, MO 63106
| | - Yuqin Wang
- Swansea University Medical School, SA2 8PP Swansea, United Kingdom
| | - Michael S Diamond
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110;
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132
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Buchrieser J, Dufloo J, Hubert M, Monel B, Planas D, Rajah MM, Planchais C, Porrot F, Guivel‐Benhassine F, Van der Werf S, Casartelli N, Mouquet H, Bruel T, Schwartz O. Syncytia formation by SARS-CoV-2-infected cells. EMBO J 2020; 39:e106267. [PMID: 33051876 PMCID: PMC7646020 DOI: 10.15252/embj.2020106267] [Citation(s) in RCA: 291] [Impact Index Per Article: 72.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 12/17/2022] Open
Abstract
Severe cases of COVID-19 are associated with extensive lung damage and the presence of infected multinucleated syncytial pneumocytes. The viral and cellular mechanisms regulating the formation of these syncytia are not well understood. Here, we show that SARS-CoV-2-infected cells express the Spike protein (S) at their surface and fuse with ACE2-positive neighboring cells. Expression of S without any other viral proteins triggers syncytia formation. Interferon-induced transmembrane proteins (IFITMs), a family of restriction factors that block the entry of many viruses, inhibit S-mediated fusion, with IFITM1 being more active than IFITM2 and IFITM3. On the contrary, the TMPRSS2 serine protease, which is known to enhance infectivity of cell-free virions, processes both S and ACE2 and increases syncytia formation by accelerating the fusion process. TMPRSS2 thwarts the antiviral effect of IFITMs. Our results show that SARS-CoV-2 pathological effects are modulated by cellular proteins that either inhibit or facilitate syncytia formation.
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Affiliation(s)
- Julian Buchrieser
- Virus and Immunity UnitDepartment of VirologyInstitut PasteurParisFrance
- CNRS‐UMR3569ParisFrance
| | - Jérémy Dufloo
- Virus and Immunity UnitDepartment of VirologyInstitut PasteurParisFrance
- CNRS‐UMR3569ParisFrance
- Bio Sorbonne Paris Cité (BioSPC)Université de ParisParisFrance
| | - Mathieu Hubert
- Virus and Immunity UnitDepartment of VirologyInstitut PasteurParisFrance
- CNRS‐UMR3569ParisFrance
| | - Blandine Monel
- Virus and Immunity UnitDepartment of VirologyInstitut PasteurParisFrance
- CNRS‐UMR3569ParisFrance
| | - Delphine Planas
- Virus and Immunity UnitDepartment of VirologyInstitut PasteurParisFrance
- CNRS‐UMR3569ParisFrance
- Vaccine Research InstituteCréteilFrance
| | - Maaran Michael Rajah
- Virus and Immunity UnitDepartment of VirologyInstitut PasteurParisFrance
- CNRS‐UMR3569ParisFrance
- Bio Sorbonne Paris Cité (BioSPC)Université de ParisParisFrance
| | - Cyril Planchais
- Laboratory of Humoral ImmunologyDepartment of ImmunologyInstitut PasteurINSERM U1222ParisFrance
| | - Françoise Porrot
- Virus and Immunity UnitDepartment of VirologyInstitut PasteurParisFrance
- CNRS‐UMR3569ParisFrance
| | | | - Sylvie Van der Werf
- Molecular Genetics of RNA VirusesDepartment of VirologyInstitut PasteurCNRS UMR 3569Université de ParisParisFrance
- National Reference Center for Respiratory VirusesInstitut PasteurParisFrance
| | - Nicoletta Casartelli
- Virus and Immunity UnitDepartment of VirologyInstitut PasteurParisFrance
- CNRS‐UMR3569ParisFrance
| | - Hugo Mouquet
- Laboratory of Humoral ImmunologyDepartment of ImmunologyInstitut PasteurINSERM U1222ParisFrance
| | - Timothée Bruel
- Virus and Immunity UnitDepartment of VirologyInstitut PasteurParisFrance
- CNRS‐UMR3569ParisFrance
| | - Olivier Schwartz
- Virus and Immunity UnitDepartment of VirologyInstitut PasteurParisFrance
- CNRS‐UMR3569ParisFrance
- Vaccine Research InstituteCréteilFrance
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133
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Ebrahimi N, Aslani S, Babaie F, Hemmatzadeh M, Hosseinzadeh R, Joneidi Z, Mehdizadeh Tourzani Z, Pakravan N, Mohammadi H. Recent findings on the Coronavirus disease 2019 (COVID-19); immunopathogenesis and immunotherapeutics. Int Immunopharmacol 2020; 89:107082. [PMID: 33068865 PMCID: PMC7547582 DOI: 10.1016/j.intimp.2020.107082] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) is responsible for recent ongoing public health emergency in the world. Sharing structural and behavioral similarities with its ancestors [SARS and Middle East Respiratory Syndrome (MERS)], SARS-CoV-2 has lower fatality but faster transmission. We have gone through a long path to recognize SARS and MERS, therefore our knowledge regarding SARS-CoV-2 is not raw. Various responses of the immune system account for the wide spectrum of clinical manifestations in Coronavirus disease-2019 (COVID-19). Given the innate immune response as the front line of defense, it is immediately activated after the virus entry. Consequently, adaptive immune response is activated to eradicate the virus. However, this does not occur in every case and immune response is the main culprit causing the pathological manifestations of COVID-19. Lethal forms of the disease are correlated with inefficient and/or insufficient immune responses associated with cytokine storm. Current therapeutic approach for COVID-19 is in favor of suppressing extreme inflammatory responses, while maintaining the immune system alert and responsive against the virus. This could be contributing along with administration of antiviral drugs in such patients. Furthermore, supplementation with different compounds, such as vitamin D, has been tested to modulate the immune system responses. A thorough understanding of chronological events in COVID-19 contributing to the development of a highly efficient treatment has not figured out yet. This review focuses on the virus-immune system interaction as well as currently available and potential therapeutic approaches targeting immune system in the treatment of COVID-19 patients.
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Affiliation(s)
- Negin Ebrahimi
- Department of International Medicine, Faculty of Medicine, Health Sciences University, Istanbul, Turkey
| | - Saeed Aslani
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farhad Babaie
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran; Department of Medical Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Maryam Hemmatzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ramin Hosseinzadeh
- Department of Medical Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | | | | | - Nafiseh Pakravan
- Department of Immunology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.
| | - Hamed Mohammadi
- Department of Immunology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran; Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.
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134
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Butowt R, Pyrc K, von Bartheld CS. Battle at the entrance gate: CIITA as a weapon to prevent the internalization of SARS-CoV-2 and Ebola viruses. Signal Transduct Target Ther 2020; 5:278. [PMID: 33235189 PMCID: PMC7683872 DOI: 10.1038/s41392-020-00405-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 11/09/2022] Open
Affiliation(s)
- Rafal Butowt
- L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland.
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland
| | - Christopher S von Bartheld
- Center of Biomedical Research Excellence in Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
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135
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Gulyaeva AA, Gorbalenya AE. A nidovirus perspective on SARS-CoV-2. Biochem Biophys Res Commun 2020; 538:24-34. [PMID: 33413979 PMCID: PMC7664520 DOI: 10.1016/j.bbrc.2020.11.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023]
Abstract
Two pandemics of respiratory distress diseases associated with zoonotic introductions of the species Severe acute respiratory syndrome-related coronavirus in the human population during 21st century raised unprecedented interest in coronavirus research and assigned it unseen urgency. The two viruses responsible for the outbreaks, SARS-CoV and SARS-CoV-2, respectively, are in the spotlight, and SARS-CoV-2 is the focus of the current fast-paced research. Its foundation was laid down by studies of many corona- and related viruses that collectively form the vast order Nidovirales. Comparative genomics of nidoviruses played a key role in this advancement over more than 30 years. It facilitated the transfer of knowledge from characterized to newly identified viruses, including SARS-CoV and SARS-CoV-2, as well as contributed to the dissection of the nidovirus proteome and identification of patterns of variations between different taxonomic groups, from species to families. This review revisits selected cases of protein conservation and variation that define nidoviruses, illustrates the remarkable plasticity of the proteome during nidovirus adaptation, and asks questions at the interface of the proteome and processes that are vital for nidovirus reproduction and could inform the ongoing research of SARS-CoV-2.
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Affiliation(s)
- Anastasia A Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, the Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, the Netherlands; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899, Moscow, Russia.
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136
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Abstract
Most severe cases with COVID-19, especially those with pulmonary failure, are not a consequence of viral burden and/or failure of the 'adaptive' immune response to subdue the pathogen by utilizing an adequate 'adaptive' immune defense. Rather it is a consequence of immunopathology, resulting from imbalanced innate immune response, which may not be linked to pathogen burden at all. In fact, it might be described as an autoinflammatory disease. The Kawasaki-like disease seen in children with SARS-CoV-2 exposure might be another example of similar mechanism.
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Affiliation(s)
- Chaim Oscar Jacob
- Department of Medicine, Division of Rheumatology and Immunology, Keck School of Medicine, University of Southern California, 2110 Zonal Ave, HMR 705 Los Angeles, CA, USA.
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137
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Iadecola C, Anrather J, Kamel H. Effects of COVID-19 on the Nervous System. Cell 2020; 183:16-27.e1. [PMID: 32882182 PMCID: PMC7437501 DOI: 10.1016/j.cell.2020.08.028] [Citation(s) in RCA: 413] [Impact Index Per Article: 103.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 02/06/2023]
Abstract
Neurological complications have emerged as a significant cause of morbidity and mortality in the ongoing COVID-19 pandemic. Beside respiratory insufficiency, many hospitalized patients exhibit neurological manifestations ranging from headache and loss of smell, to confusion and disabling strokes. COVID-19 is also anticipated to take a toll on the nervous system in the long term. Here, we will provide a critical appraisal of the potential for neurotropism and mechanisms of neuropathogenesis of SARS-CoV-2 as they relate to the acute and chronic neurological consequences of the infection. Finally, we will examine potential avenues for future research and therapeutic development.
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Affiliation(s)
- Costantino Iadecola
- Feil Family Brain and Mind Research Institute, Clinical Translational Neuroscience Unit, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Josef Anrather
- Feil Family Brain and Mind Research Institute, Clinical Translational Neuroscience Unit, Weill Cornell Medicine, New York, NY 10021, USA
| | - Hooman Kamel
- Feil Family Brain and Mind Research Institute, Clinical Translational Neuroscience Unit, Weill Cornell Medicine, New York, NY 10021, USA
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138
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Bansal R, Gubbi S, Muniyappa R. Metabolic Syndrome and COVID 19: Endocrine-Immune-Vascular Interactions Shapes Clinical Course. Endocrinology 2020; 161:bqaa112. [PMID: 32603424 PMCID: PMC7337756 DOI: 10.1210/endocr/bqaa112] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 06/26/2020] [Indexed: 02/06/2023]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic is caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Individuals with metabolic syndrome are at increased risk for poor disease outcomes and mortality from COVID-19. The pathophysiologic mechanisms for these observations have not been fully elucidated. A critical interaction between SARS-CoV-2 and the angiotensin-converting enzyme 2 (ACE2) facilitates viral entry into the host cell. ACE2 is expressed in pancreatic islets, vascular endothelium, and adipose tissue, and the SARS-CoV-2 -ACE2 interaction in these tissues, along with other factors, governs the spectrum and the severity of clinical manifestations among COVID-19 patients with metabolic syndrome. Moreover, the pro-inflammatory milieu observed in patients with metabolic syndrome may contribute toward COVID-19-mediated host immune dysregulation, including suboptimal immune responses, hyperinflammation, microvascular dysfunction, and thrombosis. This review describes the spectrum of clinical features, the likely pathophysiologic mechanisms, and potential implications for the management of metabolic syndrome in COVID-19 patients.
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Affiliation(s)
- Rashika Bansal
- Clinical Endocrine Section, Diabetes, Endocrinology, and
Obesity Branch, National Institute of Diabetes and Digestive and Kidney
Diseases, National Institutes of Health, Bethesda, MD
| | - Sriram Gubbi
- Clinical Endocrine Section, Diabetes, Endocrinology, and
Obesity Branch, National Institute of Diabetes and Digestive and Kidney
Diseases, National Institutes of Health, Bethesda, MD
| | - Ranganath Muniyappa
- Clinical Endocrine Section, Diabetes, Endocrinology, and
Obesity Branch, National Institute of Diabetes and Digestive and Kidney
Diseases, National Institutes of Health, Bethesda, MD
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139
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Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Pratt D, Churas C, Rosenthal SB, Liu S, De Jesus PD, O'Neill AM, Gounder AP, Nguyen C, Pu Y, Oom AL, Miorin L, Rodriguez-Frandsen A, Urbanowski M, Shaw ML, Chang MW, Benner C, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK. Functional Landscape of SARS-CoV-2 Cellular Restriction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.29.319566. [PMID: 33024967 PMCID: PMC7536870 DOI: 10.1101/2020.09.29.319566] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
A deficient interferon response to SARS-CoV-2 infection has been implicated as a determinant of severe COVID-19. To identify the molecular effectors that govern interferon control of SARS-CoV-2 infection, we conducted a large-scale gain-of-function analysis that evaluated the impact of human interferon stimulated genes (ISGs) on viral replication. A limited subset of ISGs were found to control viral infection, including endosomal factors that inhibited viral entry, nucleic acid binding proteins that suppressed viral RNA synthesis, and a highly enriched cluster of ER and Golgi-resident ISGs that inhibited viral translation and egress. These included the type II integral membrane protein BST2/tetherin, which was found to impede viral release, and is targeted for immune evasion by SARS-CoV-2 Orf7a protein. Overall, these data define the molecular basis of early innate immune control of viral infection, which will facilitate the understanding of host determinants that impact disease severity and offer potential therapeutic strategies for COVID-19.
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140
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Singh M, Bansal V, Feschotte C. A Single-Cell RNA Expression Map of Human Coronavirus Entry Factors. Cell Rep 2020; 32:108175. [PMID: 32946807 PMCID: PMC7470764 DOI: 10.1016/j.celrep.2020.108175] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/15/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
To predict the tropism of human coronaviruses, we profile 28 SARS-CoV-2 and coronavirus-associated receptors and factors (SCARFs) using single-cell transcriptomics across various healthy human tissues. SCARFs include cellular factors both facilitating and restricting viral entry. Intestinal goblet cells, enterocytes, and kidney proximal tubule cells appear highly permissive to SARS-CoV-2, consistent with clinical data. Our analysis also predicts non-canonical entry paths for lung and brain infections. Spermatogonial cells and prostate endocrine cells also appear to be permissive to SARS-CoV-2 infection, suggesting male-specific vulnerabilities. Both pro- and anti-viral factors are highly expressed within the nasal epithelium, with potential age-dependent variation, predicting an important battleground for coronavirus infection. Our analysis also suggests that early embryonic and placental development are at moderate risk of infection. Lastly, SCARF expression appears broadly conserved across a subset of primate organs examined. Our study establishes a resource for investigations of coronavirus biology and pathology.
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Affiliation(s)
- Manvendra Singh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Vikas Bansal
- Biomedical Data Science and Machine Learning Group, German Center for Neurodegenerative Diseases, Tübingen 72076, Germany; Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen 37075, Germany.
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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141
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Sanchez-David RY, Swann OC, Peacock TP, Barclay WS. ACE2: The Only Thing That Matters? Am J Respir Crit Care Med 2020; 202:161-163. [PMID: 32520592 PMCID: PMC7365380 DOI: 10.1164/rccm.202006-2151ed] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
| | - Olivia C Swann
- Section of Molecular VirologyImperial College LondonLondon, United Kingdom
| | - Thomas P Peacock
- Section of Molecular VirologyImperial College LondonLondon, United Kingdom
| | - Wendy S Barclay
- Section of Molecular VirologyImperial College LondonLondon, United Kingdom
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142
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Delgado-Chaves FM, Gómez-Vela F, Divina F, García-Torres M, Rodriguez-Baena DS. Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks. Genes (Basel) 2020; 11:E831. [PMID: 32708319 PMCID: PMC7397019 DOI: 10.3390/genes11070831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/26/2020] [Accepted: 07/13/2020] [Indexed: 12/21/2022] Open
Abstract
Gene networks have arisen as a promising tool in the comprehensive modeling and analysis of complex diseases. Particularly in viral infections, the understanding of the host-pathogen mechanisms, and the immune response to these, is considered a major goal for the rational design of appropriate therapies. For this reason, the use of gene networks may well encourage therapy-associated research in the context of the coronavirus pandemic, orchestrating experimental scrutiny and reducing costs. In this work, gene co-expression networks were reconstructed from RNA-Seq expression data with the aim of analyzing the time-resolved effects of gene Ly6E in the immune response against the coronavirus responsible for murine hepatitis (MHV). Through the integration of differential expression analyses and reconstructed networks exploration, significant differences in the immune response to virus were observed in Ly6E Δ H S C compared to wild type animals. Results show that Ly6E ablation at hematopoietic stem cells (HSCs) leads to a progressive impaired immune response in both liver and spleen. Specifically, depletion of the normal leukocyte mediated immunity and chemokine signaling is observed in the liver of Ly6E Δ H S C mice. On the other hand, the immune response in the spleen, which seemed to be mediated by an intense chromatin activity in the normal situation, is replaced by ECM remodeling in Ly6E Δ H S C mice. These findings, which require further experimental characterization, could be extrapolated to other coronaviruses and motivate the efforts towards novel antiviral approaches.
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143
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Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. An unbalanced immune response, characterized by a weak production of type I interferons (IFN-Is) and an exacerbated release of proinflammatory cytokines, contributes to the severe forms of the disease. SARS-CoV-2 is genetically related to SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV), which caused outbreaks in 2003 and 2013, respectively. Although IFN treatment gave some encouraging results against SARS-CoV and MERS-CoV in animal models, its potential as a therapeutic against COVID-19 awaits validation. Here, we describe our current knowledge of the complex interplay between SARS-CoV-2 infection and the IFN system, highlighting some of the gaps that need to be filled for a better understanding of the underlying molecular mechanisms. In addition to the conserved IFN evasion strategies that are likely shared with SARS-CoV and MERS-CoV, novel counteraction mechanisms are being discovered in SARS-CoV-2-infected cells. Since the last coronavirus epidemic, we have made considerable progress in understanding the IFN-I response, including its spatiotemporal regulation and the prominent role of plasmacytoid dendritic cells (pDCs), which are the main IFN-I-producing cells. While awaiting the results of the many clinical trials that are evaluating the efficacy of IFN-I alone or in combination with antiviral molecules, we discuss the potential benefits of a well-timed IFN-I treatment and propose strategies to boost pDC-mediated IFN responses during the early stages of viral infection.
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Affiliation(s)
- Margarida Sa Ribero
- CIRI, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, École Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | | | - Marlène Dreux
- CIRI, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, École Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Sébastien Nisole
- IRIM, CNRS UMR9004, Université de Montpellier, Montpellier, France
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144
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Vabret N, Britton GJ, Gruber C, Hegde S, Kim J, Kuksin M, Levantovsky R, Malle L, Moreira A, Park MD, Pia L, Risson E, Saffern M, Salomé B, Esai Selvan M, Spindler MP, Tan J, van der Heide V, Gregory JK, Alexandropoulos K, Bhardwaj N, Brown BD, Greenbaum B, Gümüş ZH, Homann D, Horowitz A, Kamphorst AO, Curotto de Lafaille MA, Mehandru S, Merad M, Samstein RM. Immunology of COVID-19: Current State of the Science. Immunity 2020; 52:910-941. [PMID: 32505227 PMCID: PMC7200337 DOI: 10.1016/j.immuni.2020.05.002] [Citation(s) in RCA: 1143] [Impact Index Per Article: 285.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions of people worldwide, igniting an unprecedented effort from the scientific community to understand the biological underpinning of COVID19 pathophysiology. In this Review, we summarize the current state of knowledge of innate and adaptive immune responses elicited by SARS-CoV-2 infection and the immunological pathways that likely contribute to disease severity and death. We also discuss the rationale and clinical outcome of current therapeutic strategies as well as prospective clinical trials to prevent or treat SARS-CoV-2 infection.
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Affiliation(s)
- Nicolas Vabret
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Graham J Britton
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Conor Gruber
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samarth Hegde
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joel Kim
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maria Kuksin
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Levantovsky
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Louise Malle
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alvaro Moreira
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D Park
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luisanna Pia
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma Risson
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Saffern
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bérengère Salomé
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Myvizhi Esai Selvan
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew P Spindler
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Tan
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Verena van der Heide
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jill K Gregory
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Nina Bhardwaj
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian D Brown
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Greenbaum
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zeynep H Gümüş
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dirk Homann
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amir Horowitz
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice O Kamphorst
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Saurabh Mehandru
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Robert M Samstein
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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145
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Singh M, Bansal V, Feschotte C. A Single-Cell RNA Expression Map of Human Coronavirus Entry Factors. SSRN 2020:3611279. [PMID: 32714119 PMCID: PMC7366802 DOI: 10.2139/ssrn.3611279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 05/27/2020] [Indexed: 02/06/2023]
Abstract
To predict the tropism of human coronaviruses, we profile 28 SCARFs using scRNA-seq data from a wide range of healthy human tissues. SCARFs include cellular factors both facilitating and restricting viral entry. Among adult organs, enterocytes and goblet cells of small intestine and colon, kidney proximal tubule cells, and gallbladder basal cells appear permissive to SARS-CoV-2, consistent with clinical data. Our analysis also suggests alternate entry paths for SARS-CoV-2 infection of the lung, CNS, and heart. We predict spermatogonial cells and prostate endocrine cells, but not ovarian cells, are highly permissive to SARS-CoV-2, suggesting male-specific vulnerabilities. Early embryonic and placental development show a moderate risk of infection. The nasal epithelium is characterized by high expression of both promoting and restricting factors and a potential age-dependent shift in SCARF expression. Lastly, SCARF expression appears broadly conserved across primate organs examined. Our study establishes an important resource for investigations of coronavirus pathology. Funding: M.S. is supported by a Presidential Postdoctoral Fellowship from Cornell University. V.B. is supported by a Career Development Fellowship at DZNE Tuebingen. Work on host-virus interactions in the Feschotte lab is funded by R35 GM122550 from the National Institutes of Health. Conflict of Interest: The authors declare that there is no conflict of interest.
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Affiliation(s)
- Manvendra Singh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Vikas Bansal
- Biomedical Data Science and Machine Learning Group, DZNE, Tübingen, Germany
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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146
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Zhou G, Chen S, Chen Z. Advances in COVID-19: the virus, the pathogenesis, and evidence-based control and therapeutic strategies. Front Med 2020; 14:117-125. [PMID: 32318975 PMCID: PMC7171433 DOI: 10.1007/s11684-020-0773-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 12/19/2022]
Abstract
Since the outbreak of the COVID-19 pandemic in early December 2019, 81 174 confirmed cases and 3242 deaths have been reported in China as of March 19, 2020. The Chinese people and government have contributed huge efforts to combat this disease, resulting in significant improvement of the situation, with 58 new cases (34 were imported cases) and 11 new deaths reported on March 19, 2020. However, as of March 19, 2020, the COVID-19 pandemic continues to develop in 167 countries/territories outside of China, and 128 665 confirmed cases and 5536 deaths have been reported, with 16 498 new cases and 817 new deaths occurring in last 24 hours. Therefore, the world should work together to fight against this pandemic. Here, we review the recent advances in COVID-19, including the insights in the virus, the responses of the host cells, the cytokine release syndrome, and the therapeutic approaches to inhibit the virus and alleviate the cytokine storm. By sharing knowledge and deepening our understanding of the virus and the disease pathogenesis, we believe that the community can efficiently develop effective vaccines and drugs, and the mankind will eventually win this battle against this pandemic.
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Affiliation(s)
- Guangbiao Zhou
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Saijuan Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhu Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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