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Weissert R. Nervous system-related tropism of SARS-CoV-2 and autoimmunity in COVID-19 infection. Eur J Immunol 2024; 54:e2250230. [PMID: 37733584 DOI: 10.1002/eji.202250230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 08/05/2023] [Accepted: 09/20/2023] [Indexed: 09/23/2023]
Abstract
The effects of SARS-CoV-2 in COVID-19 on the nervous system are incompletely understood. SARS-CoV-2 can infect endothelial cells, neurons, astrocytes, and oligodendrocytes with consequences for the host. There are indications that infection of these CNS-resident cells may result in long-term effects, including emergence of neurodegenerative diseases. Indirect effects of infection with SARS-CoV-2 relate to the induction of autoimmune disease involving molecular mimicry or/and bystander activation of T- and B cells and emergence of autoantibodies against various self-antigens. Data obtained in preclinical models of coronavirus-induced disease gives important clues for the understanding of nervous system-related assault of SARS-CoV-2. The pathophysiology of long-COVID syndrome and post-COVID syndrome in which autoimmunity and immune dysregulation might be the driving forces are still incompletely understood. A better understanding of nervous-system-related immunity in COVID-19 might support the development of therapeutic approaches. In this review, the current understanding of SARS-CoV-2 tropism for the nervous system, the associated immune responses, and diseases are summarized. The data indicates that there is viral tropism of SARS-CoV-2 in the nervous system resulting in various disease conditions. Prevention of SARS-CoV-2 infection by means of vaccination is currently the best strategy for the prevention of subsequent tissue damage involving the nervous system.
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Affiliation(s)
- Robert Weissert
- Department of Neurology, University of Regensburg Hospital, Regensburg, Germany
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2
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Bragazzi Cunha J, Leix K, Sherman EJ, Mirabelli C, Frum T, Zhang CJ, Kennedy AA, Lauring AS, Tai AW, Sexton JZ, Spence JR, Wobus CE, Emmer BT. Type I interferon signaling induces a delayed antiproliferative response in respiratory epithelial cells during SARS-CoV-2 infection. J Virol 2023; 97:e0127623. [PMID: 37975674 PMCID: PMC10734423 DOI: 10.1128/jvi.01276-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/22/2023] [Indexed: 11/19/2023] Open
Abstract
ABSTRACT Disease progression during SARS-CoV-2 infection is tightly linked to the fate of lung epithelial cells, with severe cases of COVID-19 characterized by direct injury of the alveolar epithelium and an impairment in its regeneration from progenitor cells. The molecular pathways that govern respiratory epithelial cell death and proliferation during SARS-CoV-2 infection, however, remain unclear. We now report a high-throughput CRISPR screen for host genetic modifiers of the survival and proliferation of SARS-CoV-2-infected Calu-3 respiratory epithelial cells. The top four genes identified in our screen encode components of the same type I interferon (IFN-I) signaling complex—IFNAR1, IFNAR2, JAK1, and TYK2. The fifth gene, ACE2, was an expected control encoding the SARS-CoV-2 viral receptor. Surprisingly, despite the antiviral properties of IFN-I signaling, its disruption in our screen was associated with an increase in Calu-3 cell fitness. We validated this effect and found that IFN-I signaling did not sensitize SARS-CoV-2-infected cultures to cell death but rather inhibited the proliferation of surviving cells after the early peak of viral replication and cytopathic effect. We also found that IFN-I signaling alone, in the absence of viral infection, was sufficient to induce this delayed antiproliferative response in both Calu-3 cells and iPSC-derived type 2 alveolar epithelial cells. Together, these findings highlight a cell autonomous antiproliferative response by respiratory epithelial cells to persistent IFN-I signaling during SARS-CoV-2 infection. This response may contribute to the deficient alveolar regeneration that has been associated with COVID-19 lung injury and represents a promising area for host-targeted therapeutic development.
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Affiliation(s)
- Juliana Bragazzi Cunha
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kyle Leix
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Emily J. Sherman
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Tristan Frum
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Charles J. Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew A. Kennedy
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Adam S. Lauring
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Andrew W. Tai
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- VA Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
| | - Jonathan Z. Sexton
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R. Spence
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Brian T. Emmer
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
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3
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Badla BA, Hanifa MS, Jain R, Naofal ME, Halabi N, Yaslam S, Ramaswamy S, Taylor A, Alfalasi R, Shenbagam S, Khansaheb H, Al Suwaidi H, Nowotny N, Popatia R, Al Khayat A, Alsheikh-Ali A, Loney T, AlDabal LM, Abou Tayoun A. Genetic determinants of severe COVID-19 in young Asian and Middle Eastern patients: a case series. Sci Rep 2023; 13:20294. [PMID: 37985737 PMCID: PMC10661561 DOI: 10.1038/s41598-023-47718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023] Open
Abstract
Studies of genetic factors associated with severe COVID-19 in young adults have been limited in non-Caucasian populations. Here, we clinically characterize a case series of patients with COVID-19, who were otherwise healthy, young adults (N = 55; mean age 34.1 ± SD 5.0 years) from 16 Asian, Middle Eastern, and North African countries. Using whole exome sequencing, we identify rare, likely deleterious variants affecting 16 immune-related genes in 17 out of 55 patients (31%), including 7 patients (41% of all carriers or 12.7% of all patients) who harbored multiple such variants mainly in interferon and toll-like receptor genes. Protein network analysis as well as transcriptomic analysis of nasopharyngeal swabs from an independent COVID-19 cohort (N = 50; 42% Asians and 22% Arabs) revealed that most of the altered genes, as identified by whole exome sequencing, and the associated molecular pathways were significantly altered in COVID-19 patients. Genetic variants tended to be associated with mortality, intensive care admission, and ventilation support. Our clinical cases series, genomic and transcriptomic findings suggest a possible role for interferon pathway genes in severe COVID-19 and highlight the importance of extending genetic studies to diverse populations to better understand the human genetics of disease.
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Affiliation(s)
- Beshr Abdulaziz Badla
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Mohamed Samer Hanifa
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Ruchi Jain
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Maha El Naofal
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Nour Halabi
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Sawsan Yaslam
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Sathishkumar Ramaswamy
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Alan Taylor
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Roudha Alfalasi
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Shruti Shenbagam
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Hamda Khansaheb
- Medical Education and Research Department, Dubai Health, Dubai, UAE
| | - Hanan Al Suwaidi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Norbert Nowotny
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Rizwana Popatia
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | | | - Alawi Alsheikh-Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
- Dubai Health, Dubai, UAE
| | - Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | | | - Ahmad Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE.
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE.
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4
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Isazadeh A, Heris JA, Shahabi P, Mohammadinasab R, Shomali N, Nasiri H, Valedkarimi Z, Khosroshahi AJ, Hajazimian S, Akbari M, Sadeghvand S. Pattern-recognition receptors (PRRs) in SARS-CoV-2. Life Sci 2023; 329:121940. [PMID: 37451397 DOI: 10.1016/j.lfs.2023.121940] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Pattern recognition receptors (PRRs) are specific sensors that directly recognize various molecules derived from viral or bacterial pathogens, senescent cells, damaged cells, and apoptotic cells. These sensors act as a bridge between nonspecific and specific immunity in humans. PRRs in human innate immunity were classified into six types: toll-like receptors (TLR), C-type lectin receptors (CLRs), nucleotide-binding and oligomerization domain (NOD)-like receptors (NLRs), absent in melanoma 2 (AIM2)-like receptors (ALRs), retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), and cyclic GMP-AMP (cGAMP) synthase (cGAS). Numerous types of PRRs are responsible for recognizing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which is immensely effective in prompting interferon responses. Detection of SARS-CoV-2 infection by PRRs causes the initiation of an intracellular signaling cascade and subsequently the activation of various transcription factors that stimulate the production of cytokines, chemokines, and other immune-related factors. Therefore, it seems that PRRs are a promising potential therapeutic approach for combating SARS-CoV-2 infection and other microbial infections. In this review, we have introduced the current knowledge of various PRRs and related signaling pathways in response to SARS-CoV-2.
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Affiliation(s)
- Alireza Isazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javad Ahmadian Heris
- Department of Allergy and Clinical Immunology, Pediatric Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parviz Shahabi
- Department of Physiology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Mohammadinasab
- Department of History of Medicine, School of Traditional Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Navid Shomali
- Department of Immunology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hadi Nasiri
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Valedkarimi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Saba Hajazimian
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Morteza Akbari
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Shahram Sadeghvand
- Department of Pediatrics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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5
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Ma W, Huang G, Wang Z, Wang L, Gao Q. IRF7: role and regulation in immunity and autoimmunity. Front Immunol 2023; 14:1236923. [PMID: 37638030 PMCID: PMC10449649 DOI: 10.3389/fimmu.2023.1236923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Interferon regulatory factor (IRF) 7 was originally identified as master transcriptional factor that produced IFN-I and regulated innate immune response, subsequent studies have revealed that IRF7 performs a multifaceted and versatile functions in multiple biological processes. In this review, we provide a comprehensive overview on the current knowledge of the role of IRF7 in immunity and autoimmunity. We focus on the latest regulatory mechanisms of IRF7 in IFN-I, including signaling pathways, transcription, translation, and post-translational levels, the dimerization and nuclear translocation, and the role of IRF7 in IFN-III and COVID-19. In addition to antiviral immunity, we also discuss the role and mechanism of IRF7 in autoimmunity, and the further research will expand our understanding of IRF7.
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Affiliation(s)
- Wei Ma
- Department of Cell Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Wound Infection and Drug, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Gang Huang
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Zhi Wang
- Department of Cell Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, China
| | - Li Wang
- Department of Cell Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, China
| | - Qiangguo Gao
- Department of Cell Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing, China
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6
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Cobat A, Zhang Q, Abel L, Casanova JL, Fellay J. Human Genomics of COVID-19 Pneumonia: Contributions of Rare and Common Variants. Annu Rev Biomed Data Sci 2023; 6:465-486. [PMID: 37196358 PMCID: PMC10879986 DOI: 10.1146/annurev-biodatasci-020222-021705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection is silent or benign in most infected individuals, but causes hypoxemic COVID-19 pneumonia in about 10% of cases. We review studies of the human genetics of life-threatening COVID-19 pneumonia, focusing on both rare and common variants. Large-scale genome-wide association studies have identified more than 20 common loci robustly associated with COVID-19 pneumonia with modest effect sizes, some implicating genes expressed in the lungs or leukocytes. The most robust association, on chromosome 3, concerns a haplotype inherited from Neanderthals. Sequencing studies focusing on rare variants with a strong effect have been particularly successful, identifying inborn errors of type I interferon (IFN) immunity in 1-5% of unvaccinated patients with critical pneumonia, and their autoimmune phenocopy, autoantibodies against type I IFN, in another 15-20% of cases. Our growing understanding of the impact of human genetic variation on immunity to SARS-CoV-2 is enabling health systems to improve protection for individuals and populations.
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Affiliation(s)
- Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
- Howard Hughes Medical Institute, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland;
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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Wang M, Yu F, Chang W, Zhang Y, Zhang L, Li P. Inflammasomes: a rising star on the horizon of COVID-19 pathophysiology. Front Immunol 2023; 14:1185233. [PMID: 37251383 PMCID: PMC10213254 DOI: 10.3389/fimmu.2023.1185233] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/02/2023] [Indexed: 05/31/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a contagious respiratory virus that is the cause of the coronavirus disease 2019 (COVID-19) pandemic which has posed a serious threat to public health. COVID-19 is characterized by a wide spectrum of clinical manifestations, ranging from asymptomatic infection to mild cold-like symptoms, severe pneumonia or even death. Inflammasomes are supramolecular signaling platforms that assemble in response to danger or microbial signals. Upon activation, inflammasomes mediate innate immune defense by favoring the release of proinflammatory cytokines and triggering pyroptotic cell death. Nevertheless, abnormalities in inflammasome functioning can result in a variety of human diseases such as autoimmune disorders and cancer. A growing body of evidence has showed that SARS-CoV-2 infection can induce inflammasome assembly. Dysregulated inflammasome activation and consequent cytokine burst have been associated with COVID-19 severity, alluding to the implication of inflammasomes in COVID-19 pathophysiology. Accordingly, an improved understanding of inflammasome-mediated inflammatory cascades in COVID-19 is essential to uncover the immunological mechanisms of COVID-19 pathology and identify effective therapeutic approaches for this devastating disease. In this review, we summarize the most recent findings on the interplay between SARS-CoV-2 and inflammasomes and the contribution of activated inflammasomes to COVID-19 progression. We dissect the mechanisms involving the inflammasome machinery in COVID-19 immunopathogenesis. In addition, we provide an overview of inflammasome-targeted therapies or antagonists that have potential clinical utility in COVID-19 treatment.
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Affiliation(s)
- Man Wang
- *Correspondence: Man Wang, ; Peifeng Li,
| | | | | | | | | | - Peifeng Li
- *Correspondence: Man Wang, ; Peifeng Li,
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8
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Mantovani S, Oliviero B, Varchetta S, Renieri A, Mondelli MU. TLRs: Innate Immune Sentries against SARS-CoV-2 Infection. Int J Mol Sci 2023; 24:ijms24098065. [PMID: 37175768 PMCID: PMC10178469 DOI: 10.3390/ijms24098065] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been responsible for a devastating pandemic since March 2020. Toll-like receptors (TLRs), crucial components in the initiation of innate immune responses to different pathogens, trigger the downstream production of pro-inflammatory cytokines, interferons, and other mediators. It has been demonstrated that they contribute to the dysregulated immune response observed in patients with severe COVID-19. TLR2, TLR3, TLR4 and TLR7 have been associated with COVID-19 severity. Here, we review the role of TLRs in the etiology and pathogenesis of COVID-19, including TLR7 and TLR3 rare variants, the L412F polymorphism in TLR3 that negatively regulates anti-SARS-CoV-2 immune responses, the TLR3-related cellular senescence, the interaction of TLR2 and TLR4 with SARS-CoV-2 proteins and implication of TLR2 in NET formation by SARS-CoV-2. The activation of TLRs contributes to viral clearance and disease resolution. However, TLRs may represent a double-edged sword which may elicit dysregulated immune signaling, leading to the production of proinflammatory mediators, resulting in severe disease. TLR-dependent excessive inflammation and TLR-dependent antiviral response may tip the balance towards the former or the latter, altering the equilibrium that drives the severity of disease.
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Affiliation(s)
- Stefania Mantovani
- Department of Research, Division of Clinical Immunology-Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Barbara Oliviero
- Department of Research, Division of Clinical Immunology-Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Stefania Varchetta
- Department of Research, Division of Clinical Immunology-Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy
| | - Mario U Mondelli
- Department of Research, Division of Clinical Immunology-Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
- Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, Italy
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Cappadona C, Rimoldi V, Paraboschi EM, Asselta R. Genetic susceptibility to severe COVID-19. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 110:105426. [PMID: 36934789 PMCID: PMC10022467 DOI: 10.1016/j.meegid.2023.105426] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the coronavirus disease 2019 (COVID-19) pandemic. Clinical manifestations of the disease range from an asymptomatic condition to life-threatening events and death, with more severe courses being associated with age, male sex, and comorbidities. Besides these risk factors, intrinsic characteristics of the virus as well as genetic factors of the host are expected to account for COVID-19 clinical heterogeneity. Genetic studies have long been recognized as fundamental to identify biological mechanisms underlying congenital diseases, to pinpoint genes/proteins responsible for the susceptibility to different inherited conditions, to highlight targets of therapeutic relevance, to suggest drug repurposing, and even to clarify causal relationships that make modifiable some environmental risk factors. Though these studies usually take long time to be concluded and, above all, to translate their discoveries to patients' bedside, the scientific community moved really fast to deliver genetic signals underlying different COVID-19 phenotypes. In this Review, besides a concise description of COVID-19 symptomatology and of SARS-CoV-2 mechanism of infection, we aimed to recapitulate the current literature in terms of host genetic factors that specifically associate with an increased severity of the disease.
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Affiliation(s)
- Claudio Cappadona
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele - Milan 20090, Italy
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele - Milan 20090, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele - Milan 20090, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele - Milan 20090, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy.
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10
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Cunha JB, Leix K, Sherman EJ, Mirabelli C, Kennedy AA, Lauring AS, Tai AW, Wobus CE, Emmer BT. Type I interferon signaling induces a delayed antiproliferative response in Calu-3 cells during SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530557. [PMID: 36909579 PMCID: PMC10002732 DOI: 10.1101/2023.02.28.530557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Disease progression during SARS-CoV-2 infection is tightly linked to the fate of lung epithelial cells, with severe cases of COVID-19 characterized by direct injury of the alveolar epithelium and an impairment in its regeneration from progenitor cells. The molecular pathways that govern respiratory epithelial cell death and proliferation during SARS-CoV-2 infection, however, remain poorly understood. We now report a high-throughput CRISPR screen for host genetic modifiers of the survival and proliferation of SARS-CoV-2-infected Calu-3 respiratory epithelial cells. The top 4 genes identified in our screen encode components of the same type I interferon signaling complex - IFNAR1, IFNAR2, JAK1, and TYK2. The 5th gene, ACE2, was an expected control encoding the SARS-CoV-2 viral receptor. Surprisingly, despite the antiviral properties of IFN-I signaling, its disruption in our screen was associated with an increase in Calu-3 cell fitness. We validated this effect and found that IFN-I signaling did not sensitize SARS-CoV-2-infected cultures to cell death but rather inhibited the proliferation of surviving cells after the early peak of viral replication and cytopathic effect. We also found that IFN-I signaling alone, in the absence of viral infection, was sufficient to induce this delayed antiproliferative response. Together, these findings highlight a cell autonomous antiproliferative response by respiratory epithelial cells to persistent IFN-I signaling during SARS-CoV-2 infection. This response may contribute to the deficient alveolar regeneration that has been associated with COVID-19 lung injury and represents a promising area for host-targeted therapeutic development.
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Affiliation(s)
| | - Kyle Leix
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI
| | - Emily J. Sherman
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor MI
| | - Andrew A. Kennedy
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI
| | - Adam S. Lauring
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor MI
| | - Andrew W. Tai
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor MI
- VA Ann Arbor Healthcare System, Ann Arbor MI
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor MI
| | - Brian T. Emmer
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI
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11
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Enichen E, Harvey C, Demmig-Adams B. COVID-19 Spotlights Connections between Disease and Multiple Lifestyle Factors. Am J Lifestyle Med 2023; 17:231-257. [PMID: 36883129 PMCID: PMC9445631 DOI: 10.1177/15598276221123005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The SARS-CoV-2 virus (severe acute respiratory syndrome coronavirus 2), and the disease it causes (COVID-19), have had a profound impact on global human society and threaten to continue to have such an impact with newly emerging variants. Because of the widespread effects of SARS-CoV-2, understanding how lifestyle choices impact the severity of disease is imperative. This review summarizes evidence for an involvement of chronic, non-resolving inflammation, gut microbiome disruption (dysbiosis with loss of beneficial microorganisms), and impaired viral defenses, all of which are associated with an imbalanced lifestyle, in severe disease manifestations and post-acute sequelae of SARS-CoV-2 (PASC). Humans' physiological propensity for uncontrolled inflammation and severe COVID-19 are briefly contrasted with bats' low propensity for inflammation and their resistance to viral disease. This insight is used to identify positive lifestyle factors with the potential to act in synergy for restoring balance to the immune response and gut microbiome, and thereby protect individuals against severe COVID-19 and PASC. It is proposed that clinicians should consider recommending lifestyle factors, such as stress management, balanced nutrition and physical activity, as preventative measures against severe viral disease and PASC.
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Affiliation(s)
- Elizabeth Enichen
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA (EE, CH, BDA)
| | - Caitlyn Harvey
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA (EE, CH, BDA)
| | - Barbara Demmig-Adams
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA (EE, CH, BDA)
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12
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Yamada T, Takaoka A. Innate immune recognition against SARS-CoV-2. Inflamm Regen 2023; 43:7. [PMID: 36703213 PMCID: PMC9879261 DOI: 10.1186/s41232-023-00259-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative virus of pandemic acute respiratory disease called coronavirus disease 2019 (COVID-19). Most of the infected individuals have asymptomatic or mild symptoms, but some patients show severe and critical systemic inflammation including tissue damage and multi-organ failures. Immune responses to the pathogen determine clinical course. In general, the activation of innate immune responses is mediated by host pattern-recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs) as well as host damage-associated molecular patterns (DAMPs), which results in the activation of the downstream gene induction programs of types I and III interferons (IFNs) and proinflammatory cytokines for inducing antiviral activity. However, the excessive activation of these responses may lead to deleterious inflammation. Here, we review the recent advances in our understanding of innate immune responses to SARS-CoV-2 infection, particularly in terms of innate recognition and the subsequent inflammation underlying COVID-19 immunopathology.
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Affiliation(s)
- Taisho Yamada
- grid.39158.360000 0001 2173 7691Division of Signaling in Cancer and Immunology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido Japan ,grid.39158.360000 0001 2173 7691Molecular Medical Biochemistry Unit, Graduate School of Chemical Sciences and Engineering Hokkaido University, Sapporo, Hokkaido Japan
| | - Akinori Takaoka
- grid.39158.360000 0001 2173 7691Division of Signaling in Cancer and Immunology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido Japan ,grid.39158.360000 0001 2173 7691Molecular Medical Biochemistry Unit, Graduate School of Chemical Sciences and Engineering Hokkaido University, Sapporo, Hokkaido Japan
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13
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Zsichla L, Müller V. Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors. Viruses 2023; 15:175. [PMID: 36680215 PMCID: PMC9863423 DOI: 10.3390/v15010175] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease and death. Understanding the risk factors of severe COVID-19 is relevant both in the clinical setting and at the epidemiological level. Here, we provide an overview of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes. The factors considered in detail include the age and frailty, genetic polymorphisms, biological sex (and pregnancy), co- and superinfections, non-communicable comorbidities, immunological history, microbiota, and lifestyle of the patient; viral genetic variation and infecting dose; socioeconomic factors; and air pollution. For each category, we compile (sometimes conflicting) evidence for the association of the factor with COVID-19 outcomes (including the strength of the effect) and outline possible action mechanisms. We also discuss the complex interactions between the various risk factors.
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Affiliation(s)
- Levente Zsichla
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
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14
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Mbarek H, Ismail SI. Mapping the Arab genome. Nat Genet 2022; 54:1761-1763. [PMID: 36446885 DOI: 10.1038/s41588-022-01239-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Doha, Qatar. .,Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, and Amsterdam Reproduction and Development Institute, Amsterdam, The Netherlands.
| | - Said I Ismail
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Doha, Qatar. .,Medical School, The Univeristy of Jordan, Amman, Jordan. .,Biomedical Research Center, Qatar University, Doha, Qatar. .,College of Health and Life Sciences, Hamad Bin Khalifa Univeristy, Doha, Qatar.
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15
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Abstract
Since the identification of sickle cell trait as a heritable form of resistance to malaria, candidate gene studies, linkage analysis paired with sequencing, and genome-wide association (GWA) studies have revealed many examples of genetic resistance and susceptibility to infectious diseases. GWA studies enabled the identification of many common variants associated with small shifts in susceptibility to infectious diseases. This is exemplified by multiple loci associated with leprosy, malaria, HIV, tuberculosis, and coronavirus disease 2019 (COVID-19), which illuminate genetic architecture and implicate pathways underlying pathophysiology. Despite these successes, most of the heritability of infectious diseases remains to be explained. As the field advances, current limitations may be overcome by applying methodological innovations such as cellular GWA studies and phenome-wide association (PheWA) studies as well as by improving methodological rigor with more precise case definitions, deeper phenotyping, increased cohort diversity, and functional validation of candidate loci in the laboratory or human challenge studies.
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Affiliation(s)
- Kyle D Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA;
| | - Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA; .,Duke University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA; .,Duke University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, North Carolina, USA
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16
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Karki R, Kanneganti TD. Innate immunity, cytokine storm, and inflammatory cell death in COVID-19. J Transl Med 2022; 20:542. [PMID: 36419185 PMCID: PMC9682745 DOI: 10.1186/s12967-022-03767-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022] Open
Abstract
The innate immune system serves as the first line of defense against invading pathogens; however, dysregulated innate immune responses can induce aberrant inflammation that is detrimental to the host. Therefore, careful innate immune regulation is critical during infections. The coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has resulted in global morbidity and mortality as well as socio-economic stresses. Innate immune sensing of SARS-CoV-2 by multiple host cell pattern recognition receptors leads to the production of various pro-inflammatory cytokines and the induction of inflammatory cell death. These processes can contribute to cytokine storm, tissue damage, and acute respiratory distress syndrome. Here, we discuss the sensing of SARS-CoV-2 to induce innate immune activation and the contribution of this innate immune signaling in the development and severity of COVID-19. In addition, we provide a conceptual framework for innate immunity driving cytokine storm and organ damage in patients with severe COVID-19. A better understanding of the molecular mechanisms regulated by innate immunity is needed for the development of targeted modalities that can improve patient outcomes by mitigating severe disease.
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Affiliation(s)
- Rajendra Karki
- Department of Immunology, St. Jude Children's Research Hospital, MS #351, 262 Danny Thomas Place, Memphis, TN, 38105-3678, USA
| | - Thirumala-Devi Kanneganti
- Department of Immunology, St. Jude Children's Research Hospital, MS #351, 262 Danny Thomas Place, Memphis, TN, 38105-3678, USA.
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17
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Hoang TN, Viox EG, Upadhyay AA, Strongin Z, Tharp GK, Pino M, Nchioua R, Hirschenberger M, Gagne M, Nguyen K, Harper JL, Marciano S, Boddapati AK, Pellegrini KL, Tisoncik-Go J, Whitmore LS, Karunakaran KA, Roy M, Kirejczyk S, Curran EH, Wallace C, Wood JS, Connor-Stroud F, Kasturi SP, Levit RD, Gale M, Vanderford TH, Silvestri G, Busman-Sahay K, Estes JD, Vaccari M, Douek DC, Sparrer KM, Kirchhoff F, Johnson RP, Schreiber G, Bosinger SE, Paiardini M. Modulation of type I interferon responses potently inhibits SARS-CoV-2 replication and inflammation in rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.21.512606. [PMID: 36324810 PMCID: PMC9628196 DOI: 10.1101/2022.10.21.512606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Type-I interferons (IFN-I) are critical mediators of innate control of viral infections, but also drive recruitment of inflammatory cells to sites of infection, a key feature of severe COVID-19. Here, and for the first time, IFN-I signaling was modulated in rhesus macaques (RMs) prior to and during acute SARS-CoV-2 infection using a mutated IFNα2 (IFN-modulator; IFNmod), which has previously been shown to reduce the binding and signaling of endogenous IFN-I. In SARS-CoV-2-infected RMs, IFNmod reduced both antiviral and inflammatory ISGs. Notably, IFNmod treatment resulted in a potent reduction in (i) SARS-CoV-2 viral load in Bronchoalveolar lavage (BAL), upper airways, lung, and hilar lymph nodes; (ii) inflammatory cytokines, chemokines, and CD163+MRC1-inflammatory macrophages in BAL; and (iii) expression of Siglec-1, which enhances SARS-CoV-2 infection and predicts disease severity, on circulating monocytes. In the lung, IFNmod also reduced pathogenesis and attenuated pathways of inflammasome activation and stress response during acute SARS-CoV-2 infection. This study, using an intervention targeting both IFN-α and IFN-β pathways, shows that excessive inflammation driven by type 1 IFN critically contributes to SARS-CoV-2 pathogenesis in RMs, and demonstrates the potential of IFNmod to limit viral replication, SARS-CoV-2 induced inflammation, and COVID-19 severity.
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Affiliation(s)
- Timothy N. Hoang
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,These authors contributed equally
| | - Elise G. Viox
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,These authors contributed equally
| | - Amit A. Upadhyay
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,These authors contributed equally
| | - Zachary Strongin
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Gregory K. Tharp
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Maria Pino
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | | | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Nguyen
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Justin L. Harper
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Shir Marciano
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Arun K. Boddapati
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Kathryn L. Pellegrini
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jennifer Tisoncik-Go
- Department of Immunology, University of Washington School of Medicine, and the Washington National Primate Research Center, Seattle, WA, 98109, USA
| | - Leanne S. Whitmore
- Department of Immunology, University of Washington School of Medicine, and the Washington National Primate Research Center, Seattle, WA, 98109, USA
| | - Kirti A. Karunakaran
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Melissa Roy
- Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Shannon Kirejczyk
- Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Elizabeth H. Curran
- Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Chelsea Wallace
- Division of Animal Resources, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jennifer S. Wood
- Division of Animal Resources, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Fawn Connor-Stroud
- Division of Animal Resources, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Sudhir P. Kasturi
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Rebecca D. Levit
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Michael Gale
- Department of Immunology, University of Washington School of Medicine, and the Washington National Primate Research Center, Seattle, WA, 98109, USA
| | - Thomas H. Vanderford
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Monica Vaccari
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA,Department of Microbiology and Immunology, Tulane School of Medicine, New Orleans, LA 70112, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - R. Paul Johnson
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Infectious Disease Division, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA,Correspondence to: (M.P; Lead Contact); (S.E.B.)
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Correspondence to: (M.P; Lead Contact); (S.E.B.)
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18
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Tziastoudi M, Cholevas C, Stefanidis I, Theoharides TC. Genetics of COVID-19 and myalgic encephalomyelitis/chronic fatigue syndrome: a systematic review. Ann Clin Transl Neurol 2022; 9:1838-1857. [PMID: 36204816 PMCID: PMC9639636 DOI: 10.1002/acn3.51631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 01/08/2023] Open
Abstract
COVID‐19 and ME/CFS present with some similar symptoms, especially physical and mental fatigue. In order to understand the basis of these similarities and the possibility of underlying common genetic components, we performed a systematic review of all published genetic association and cohort studies regarding COVID‐19 and ME/CFS and extracted the genes along with the genetic variants investigated. We then performed gene ontology and pathway analysis of those genes that gave significant results in the individual studies to yield functional annotations of the studied genes using protein analysis through evolutionary relationships (PANTHER) VERSION 17.0 software. Finally, we identified the common genetic components of these two conditions. Seventy‐one studies for COVID‐19 and 26 studies for ME/CFS were included in the systematic review in which the expression of 97 genes for COVID‐19 and 429 genes for ME/CFS were significantly affected. We found that ACE, HLA‐A, HLA‐C, HLA‐DQA1, HLA‐DRB1, and TYK2 are the common genes that gave significant results. The findings of the pathway analysis highlight the contribution of inflammation mediated by chemokine and cytokine signaling pathways, and the T cell activation and Toll receptor signaling pathways. Protein class analysis revealed the contribution of defense/immunity proteins, as well as protein‐modifying enzymes. Our results suggest that the pathogenesis of both syndromes could involve some immune dysfunction.
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Affiliation(s)
- Maria Tziastoudi
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Christos Cholevas
- First Department of Ophthalmology, Faculty of Health Sciences, Aristotle University, AHEPA Hospital, Thessaloniki, Greece
| | - Ioannis Stefanidis
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Theoharis C Theoharides
- Institute of Neuro-Immune Medicine, Nova Southeastern University, Clearwater, FL, USA.,Laboratory of Molecular Immunopharmacology and Drug Discovery, Department of Immunology, Tufts University School of Medicine, Boston, Massachusetts, USA.,School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA.,Departments of Internal Medicine and Psychiatry, Tufts University School of Medicine and Tufts Medical Center, Boston, Massachusetts, USA
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19
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Motelow JE, Lippa NC, Hostyk J, Feldman E, Nelligan M, Ren Z, Alkelai A, Milner JD, Gharavi AG, Tang Y, Goldstein DB, Kernie SG. Risk Variants in the Exomes of Children With Critical Illness. JAMA Netw Open 2022; 5:e2239122. [PMID: 36306130 PMCID: PMC9617179 DOI: 10.1001/jamanetworkopen.2022.39122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE Diagnostic genetic testing can lead to changes in management in the pediatric intensive care unit. Genetic risk in children with critical illness but nondiagnostic exome sequencing (ES) has not been explored. OBJECTIVE To assess the association between loss-of-function (LOF) variants and pediatric critical illness. DESIGN, SETTING, AND PARTICIPANTS This genetic association study examined ES first screened for causative variants among 267 children at the Morgan Stanley Children's Hospital of NewYork-Presbyterian, of whom 22 were otherwise healthy with viral respiratory failure; 18 deceased children with bronchiolitis from the Office of the Chief Medical Examiner of New York City, of whom 14 were previously healthy; and 9990 controls from the Institute for Genomic Medicine at Columbia University Irving Medical Center. The ES data were generated between January 1, 2015, and December 31, 2020, and analyzed between January 1, 2017, and September 2, 2022. EXPOSURE Critical illness. MAIN OUTCOMES AND MEASURES Odds ratios and P values for genes and gene-sets enriched for rare LOF variants and the loss-of-function observed/expected upper bound fraction (LOEUF) score at which cases have a significant enrichment. RESULTS This study included 285 children with critical illness (median [range] age, 4.1 [0-18.9] years; 148 [52%] male) and 9990 controls. A total of 228 children (80%) did not receive a genetic diagnosis. After quality control (QC), 231 children harbored excess rare LOF variants in genes with a LOEUF score of 0.680 or less (intolerant genes) (P = 1.0 × 10-5). After QC, 176 children without a diagnosis harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 1.8; 95% CI, 1.3-2.5). After QC, 25 children with viral respiratory failure harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 2.8; 95% CI, 1.1-6.6). A total of 114 undiagnosed children were enriched for de novo LOF variants in genes without a known disease association (observed, 14; expected, 6.8; enrichment, 2.05). CONCLUSIONS AND RELEVANCE In this genetic association study, excess LOF variants were observed among critically ill children despite nondiagnostic ES. Variants lay in genes without a known disease association, suggesting future investigation may connect phenotypes to causative genes.
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Affiliation(s)
- Joshua E. Motelow
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Natalie C. Lippa
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Joseph Hostyk
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Evin Feldman
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Matthew Nelligan
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York
| | | | - Ali G. Gharavi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, NewYork-Presbyterian, New York, New York
| | - Yingying Tang
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, New York, New York
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Steven G. Kernie
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
- NewYork-Presbyterian Hospital, New York, New York
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20
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Zhang Z. Genomic Biomarker Heterogeneities between SARS-CoV-2 and COVID-19. Vaccines (Basel) 2022; 10:vaccines10101657. [PMID: 36298522 PMCID: PMC9608907 DOI: 10.3390/vaccines10101657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
Abstract
Genes functionally associated with SARS-CoV-2 infection and genes functionally related to the COVID-19 disease can be different, whose distinction will become the first essential step for successfully fighting against the COVID-19 pandemic. Unfortunately, this first step has not been completed in all biological and medical research. Using a newly developed max-competing logistic classifier, two genes, ATP6V1B2 and IFI27, stand out to be critical in the transcriptional response to SARS-CoV-2 infection with differential expressions derived from NP/OP swab PCR. This finding is evidenced by combining these two genes with another gene in predicting disease status to achieve better-indicating accuracy than existing classifiers with the same number of genes. In addition, combining these two genes with three other genes to form a five-gene classifier outperforms existing classifiers with ten or more genes. These two genes can be critical in fighting against the COVID-19 pandemic as a new focus and direction with their exceptional predicting accuracy. Comparing the functional effects of these genes with a five-gene classifier with 100% accuracy identified and tested from blood samples in our earlier work, the genes and their transcriptional response and functional effects on SARS-CoV-2 infection, and the genes and their functional signature patterns on COVID-19 antibodies, are significantly different. We will use a total of fourteen cohort studies (including breakthrough infections and omicron variants) with 1481 samples to justify our results. Such significant findings can help explore the causal and pathological links between SARS-CoV-2 infection and the COVID-19 disease, and fight against the disease with more targeted genes, vaccines, antiviral drugs, and therapies.
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Affiliation(s)
- Zhengjun Zhang
- Department of Statistics, School of Computer, Data & Information Sciences, University of Wisconsin, Madison, WI 53706, USA
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21
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Abstract
Human genetics can inform the biology and epidemiology of coronavirus disease 2019 (COVID-19) by pinpointing causal mechanisms that explain why some individuals become more severely affected by the disease upon infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Large-scale genetic association studies, encompassing both rare and common genetic variants, have used different study designs and multiple disease phenotype definitions to identify several genomic regions associated with COVID-19. Along with a multitude of follow-up studies, these findings have increased our understanding of disease aetiology and provided routes for management of COVID-19. Important emergent opportunities include the clinical translatability of genetic risk prediction, the repurposing of existing drugs, exploration of variable host effects of different viral strains, study of inter-individual variability in vaccination response and understanding the long-term consequences of SARS-CoV-2 infection. Beyond the current pandemic, these transferrable opportunities are likely to affect the study of many infectious diseases.
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Affiliation(s)
- Mari E K Niemi
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark J Daly
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Broad Institute, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
- Broad Institute, Cambridge, MA, USA.
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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22
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Upadhyai P, Shenoy PU, Banjan B, Albeshr MF, Mahboob S, Manzoor I, Das R. Exome-Wide Association Study Reveals Host Genetic Variants Likely Associated with the Severity of COVID-19 in Patients of European Ancestry. Life (Basel) 2022; 12:1300. [PMID: 36143338 PMCID: PMC9504138 DOI: 10.3390/life12091300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 12/03/2022] Open
Abstract
Host genetic variability plays a pivotal role in modulating COVID-19 clinical outcomes. Despite the functional relevance of protein-coding regions, rare variants located here are less likely to completely explain the considerable numbers of acutely affected COVID-19 patients worldwide. Using an exome-wide association approach, with individuals of European descent, we sought to identify common coding variants linked with variation in COVID-19 severity. Herein, cohort 1 compared non-hospitalized (controls) and hospitalized (cases) individuals, and in cohort 2, hospitalized subjects requiring respiratory support (cases) were compared to those not requiring it (controls). 229 and 111 variants differed significantly between cases and controls in cohorts 1 and 2, respectively. This included FBXO34, CNTN2, and TMCC2 previously linked with COVID-19 severity using association studies. Overall, we report SNPs in 26 known and 12 novel candidate genes with strong molecular evidence implicating them in the pathophysiology of life-threatening COVID-19 and post-recovery sequelae. Of these few notable known genes include, HLA-DQB1, AHSG, ALOX5AP, MUC5AC, SMPD1, SPG7, SPEG,GAS6, and SERPINA12. These results enhance our understanding of the pathomechanisms underlying the COVID-19 clinical spectrum and may be exploited to prioritize biomarkers for predicting disease severity, as well as to improve treatment strategies in individuals of European ancestry.
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Affiliation(s)
- Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Pooja U. Shenoy
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Bhavya Banjan
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Mohammed F. Albeshr
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Irfan Manzoor
- Department of Biology, The College of Arts and Sciences, Indiana University, Bloomington, IN 47405, USA
| | - Ranajit Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
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23
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van der Made CI, Netea MG, van der Veerdonk FL, Hoischen A. Clinical implications of host genetic variation and susceptibility to severe or critical COVID-19. Genome Med 2022; 14:96. [PMID: 35986347 PMCID: PMC9390103 DOI: 10.1186/s13073-022-01100-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/03/2022] [Indexed: 01/08/2023] Open
Abstract
Since the start of the coronavirus disease 2019 (COVID-19) pandemic, important insights have been gained into virus biology and the host factors that modulate the human immune response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 displays a highly variable clinical picture that ranges from asymptomatic disease to lethal pneumonia. Apart from well-established general risk factors such as advanced age, male sex and chronic comorbidities, differences in host genetics have been shown to influence the individual predisposition to develop severe manifestations of COVID-19. These differences range from common susceptibility loci to rare genetic variants with strongly predisposing effects, or proven pathogenic variants that lead to known or novel inborn errors of immunity (IEI), which constitute a growing group of heterogeneous Mendelian disorders with increased susceptibility to infectious disease, auto-inflammation, auto-immunity, allergy or malignancies. The current genetic findings point towards a convergence of common and rare genetic variants that impact the interferon signalling pathways in patients with severe or critical COVID-19. Monogenic risk factors that impact IFN-I signalling have an expected prevalence between 1 and 5% in young, previously healthy individuals (<60 years of age) with critical COVID-19. The identification of these IEI such as X-linked TLR7 deficiency indicates a possibility for targeted genetic screening and personalized clinical management. This review aims to provide an overview of our current understanding of the host genetic factors that predispose to severe manifestations of COVID-19 and focuses on rare variants in IFN-I signalling genes and their potential clinical implications.
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24
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Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK. Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature 2022; 607:97-103. [PMID: 35255492 PMCID: PMC9259496 DOI: 10.1038/s41586-022-04576-6] [Citation(s) in RCA: 158] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2-4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.
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Affiliation(s)
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Clark D Russell
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Xia Shen
- Biostatistics Group, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | | | | | | | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine and Institute in the Park, Alder Hey Children's Hospital and University of Liverpool, Liverpool, UK
| | | | | | | | | | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tom A Fowler
- Genomics England, London, UK
- Test and Trace, the Health Security Agency, Department of Health and Social Care, London, UK
| | - Manu Shankar-Hari
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Charles Hinds
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust: London, London, UK
| | | | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit and Research Centre, London, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Richard H Scott
- Genomics England, London, UK
- Great Ormond Street Hospital, London, UK
| | | | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Mark J Caulfield
- Genomics England, London, UK.
- William Harvey Research Institute, Queen Mary University of London, London, UK.
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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25
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Dhaliwal M, Tyagi R, Malhotra P, Barman P, Loganathan SK, Sharma J, Sharma K, Mondal S, Rawat A, Singh S. Mechanisms of Immune Dysregulation in COVID-19 Are Different From SARS and MERS: A Perspective in Context of Kawasaki Disease and MIS-C. Front Pediatr 2022; 10:790273. [PMID: 35601440 PMCID: PMC9119432 DOI: 10.3389/fped.2022.790273] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/04/2022] [Indexed: 12/15/2022] Open
Abstract
Coronaviruses have led to three major outbreaks to date-Severe Acute Respiratory Syndrome (SARS; 2002), Middle East Respiratory Syndrome (MERS; 2012) and the ongoing pandemic, Coronavirus Disease (COVID-19; 2019). Coronavirus infections are usually mild in children. However, a few children with MERS had presented with a severe phenotype in the acute phase resulting in progressive pneumonic changes with increasing oxygen dependency and acute respiratory distress requiring ventilatory support. A subset of children with a history of SARS-CoV-2 infection develops a multisystem hyper-inflammatory phenotype known as Multisystem Inflammatory Syndrome in Children (MIS-C). This syndrome occurs 4-6 weeks after infection with SARS-CoV-2 and has been reported more often from areas with high community transmission. Children with MIS-C present with high fever and often have involvement of cardiovascular, gastrointestinal and hematologic systems leading to multiorgan failure. This is accompanied by elevation of pro-inflammatory cytokines such as IL-6 and IL-10. MIS-C has several similarities with Kawasaki disease (KD) considering children with both conditions present with fever, rash, conjunctival injection, mucosal symptoms and swelling of hands and feet. For reasons that are still not clear, both KD and MIS-C were not reported during the SARS-CoV and MERS-CoV outbreaks. As SARS-CoV-2 differs from SARS-CoV by 19.5% and MERS by 50% in terms of sequence identity, differences in genomic and proteomic profiles may explain the varied disease immunopathology and host responses. Left untreated, MIS-C may lead to severe abdominal pain, ventricular dysfunction and shock. Immunological investigations reveal reduced numbers of follicular B cells, increased numbers of terminally differentiated CD4+T lymphocytes, and decreased IL-17A. There is still ambiguity about the clinical and immunologic risk factors that predispose some children to development of MIS-C while sparing others. Host-pathogen interactions in SARS, MERS and COVID-19 are likely to play a crucial role in the clinical phenotypes that manifest. This narrative review focuses on the immunological basis for development of MIS-C syndrome in the ongoing SARS-CoV-2 pandemic. To the best of our knowledge, these aspects have not been reviewed before.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Surjit Singh
- Allergy and Immunology Unit, Department of Pediatrics, Advanced Pediatrics Center, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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26
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Gray PE, Bartlett AW, Tangye SG. Severe COVID-19 represents an undiagnosed primary immunodeficiency in a high proportion of infected individuals. Clin Transl Immunology 2022; 11:e1365. [PMID: 35444807 PMCID: PMC9013505 DOI: 10.1002/cti2.1365] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 01/08/2023] Open
Abstract
Since the emergence of the COVID-19 pandemic in early 2020, a key challenge has been to define risk factors, other than age and pre-existing comorbidities, that predispose some people to severe disease, while many other SARS-CoV-2-infected individuals experience mild, if any, consequences. One explanation for intra-individual differences in susceptibility to severe COVID-19 may be that a growing percentage of otherwise healthy people have a pre-existing asymptomatic primary immunodeficiency (PID) that is unmasked by SARS-CoV-2 infection. Germline genetic defects have been identified in individuals with life-threatening COVID-19 that compromise local type I interferon (IFN)-mediated innate immune responses to SARS-CoV-2. Remarkably, these variants - which impact responses initiated through TLR3 and TLR7, as well as the response to type I IFN cytokines - may account for between 3% and 5% of severe COVID-19 in people under 70 years of age. Similarly, autoantibodies against type I IFN cytokines (IFN-α, IFN-ω) have been detected in patients' serum prior to infection with SARS-CoV-2 and were found to cause c. 20% of severe COVID-19 in the above 70s and 20% of total COVID-19 deaths. These autoantibodies, which are more common in the elderly, neutralise type I IFNs, thereby impeding innate antiviral immunity and phenocopying an inborn error of immunity. The discovery of PIDs underlying a significant percentage of severe COVID-19 may go some way to explain disease susceptibility, may allow for the application of targeted therapies such as plasma exchange, IFN-α or IFN-β, and may facilitate better management of social distancing, vaccination and early post-exposure prophylaxis.
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Affiliation(s)
- Paul E Gray
- Department of Immunology and Infectious Diseases Sydney Children's Hospital Randwick NSW Australia.,School of Women's and Children's Health University of New South Wales Randwick NSW Australia
| | - Adam W Bartlett
- Department of Immunology and Infectious Diseases Sydney Children's Hospital Randwick NSW Australia.,School of Women's and Children's Health University of New South Wales Randwick NSW Australia
| | - Stuart G Tangye
- Garvan Institute of Medical Research Darlinghurst NSW Australia.,St Vincent's Clinical School UNSW Sydney Randwick NSW Australia
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27
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Identification of Genetic Risk Factors of Severe COVID-19 Using Extensive Phenotypic Data: A Proof-of-Concept Study in a Cohort of Russian Patients. Genes (Basel) 2022; 13:genes13030534. [PMID: 35328087 PMCID: PMC8949130 DOI: 10.3390/genes13030534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
The COVID-19 pandemic has drawn the attention of many researchers to the interaction between pathogen and host genomes. Over the last two years, numerous studies have been conducted to identify the genetic risk factors that predict COVID-19 severity and outcome. However, such an analysis might be complicated in cohorts of limited size and/or in case of limited breadth of genome coverage. In this work, we tried to circumvent these challenges by searching for candidate genes and genetic variants associated with a variety of quantitative and binary traits in a cohort of 840 COVID-19 patients from Russia. While we found no gene- or pathway-level associations with the disease severity and outcome, we discovered eleven independent candidate loci associated with quantitative traits in COVID-19 patients. Out of these, the most significant associations correspond to rs1651553 in MYH14p = 1.4 × 10-7), rs11243705 in SETX (p = 8.2 × 10-6), and rs16885 in ATXN1 (p = 1.3 × 10-5). One of the identified variants, rs33985936 in SCN11A, was successfully replicated in an independent study, and three of the variants were found to be associated with blood-related quantitative traits according to the UK Biobank data (rs33985936 in SCN11A, rs16885 in ATXN1, and rs4747194 in CDH23). Moreover, we show that a risk score based on these variants can predict the severity and outcome of hospitalization in our cohort of patients. Given these findings, we believe that our work may serve as proof-of-concept study demonstrating the utility of quantitative traits and extensive phenotyping for identification of genetic risk factors of severe COVID-19.
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28
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Ferreira de Araújo JL, Menezes D, Saraiva‐Duarte JM, de Lima Ferreira L, Santana de Aguiar R, Pedra de Souza R. Systematic review of host genetic association with Covid-19 prognosis and susceptibility: What have we learned in 2020? Rev Med Virol 2022; 32:e2283. [PMID: 34338380 PMCID: PMC8420453 DOI: 10.1002/rmv.2283] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/18/2021] [Accepted: 07/22/2021] [Indexed: 02/06/2023]
Abstract
Biomarker identification may provide strategic opportunities to understand disease pathophysiology, predict outcomes, improve human health, and reduce healthcare costs. The highly heterogeneous Covid-19 clinical manifestation suggests a complex interaction of several different human, viral and environmental factors. Here, we systematically reviewed genetic association studies evaluating Covid-19 severity or susceptibility to SARS-CoV-2 infection following PRISMA recommendations. Our research comprised papers published until December 31st , 2020, in PubMed and BioRXiv databases focusing on genetic association studies with Covid-19 prognosis or susceptibility. We found 20 eligible genetic association studies, of which 11 assessed Covid-19 outcome and 14 evaluated infection susceptibility (five analyzed both effects). Q-genie assessment indicated moderate quality. Five large-scale association studies (GWAS, whole-genome, or exome sequencing) were reported with no consistent replication to date. Promising hits were found on the 3p21.31 region and ABO locus. Candidate gene studies examined ACE1, ACE2, TMPRSS2, IFITM3, APOE, Furin, IFNL3, IFNL4, HLA, TNF-ɑ genes, and ABO system. The most evaluated single locus was the ABO, and the most sampled region was the HLA with three and five candidate gene studies, respectively. Meta-analysis could not be performed. Available data showed the need for further reports to replicate claimed associations.
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Affiliation(s)
- João Locke Ferreira de Araújo
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
- Grupo de Pesquisa em Bioestatística e Epidemiologia molecular, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
- Programa de Pós‐graduação em Genética, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Diego Menezes
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
- Grupo de Pesquisa em Bioestatística e Epidemiologia molecular, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
- Programa de Pós‐graduação em Genética, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Julia Maria Saraiva‐Duarte
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
- Programa de Pós‐graduação em Genética, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Luciana de Lima Ferreira
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
- Grupo de Pesquisa em Bioestatística e Epidemiologia molecular, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
- Programa de Pós‐graduação em Genética, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Renato Santana de Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
- Grupo de Pesquisa em Bioestatística e Epidemiologia molecular, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
- Programa de Pós‐graduação em Genética, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Renan Pedra de Souza
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
- Grupo de Pesquisa em Bioestatística e Epidemiologia molecular, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
- Programa de Pós‐graduação em Genética, Departamento de Genética, Ecologia e EvoluçãoInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
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29
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Human genetic and immunological determinants of critical COVID-19 pneumonia. Nature 2022; 603:587-598. [PMID: 35090163 DOI: 10.1038/s41586-022-04447-0] [Citation(s) in RCA: 200] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/19/2022] [Indexed: 11/08/2022]
Abstract
SARS-CoV-2 infection is benign in most individuals but, in ˜10% of cases, it triggers hypoxemic COVID-19 pneumonia, which becomes critical in ˜3% of cases. The ensuing risk of death (˜1%) doubles every five years from childhood onward and is ˜1.5 times greater in men than in women. What are the molecular and cellular determinants of critical COVID-19 pneumonia? Inborn errors of type I IFNs, including autosomal TLR3 and X-linked TLR7 deficiencies, are found in ˜1-5% of patients with critical pneumonia under 60 years old, and a lower proportion in older patients. Pre-existing autoantibodies neutralizing IFN-α, -β, and/or -ω, which are more common in men than in women, are found in ˜15-20% of patients with critical pneumonia over 70 years old, and a lower proportion in younger patients. Thus, at least 15% of cases of critical COVID-19 pneumonia can apparently be explained. The TLR3- and TLR7-dependent production of type I IFNs by respiratory epithelial cells and plasmacytoid dendritic cells, respectively, is essential for host defense against SARS-CoV-2. In ways that can depend on age and sex, insufficient type I IFN immunity in the respiratory tract during the first few days of infection may account for the spread of the virus, leading to pulmonary and systemic inflammation.
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30
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Zepeda-Cervantes J, Martínez-Flores D, Ramírez-Jarquín JO, Tecalco-Cruz ÁC, Alavez-Pérez NS, Vaca L, Sarmiento-Silva RE. Implications of the Immune Polymorphisms of the Host and the Genetic Variability of SARS-CoV-2 in the Development of COVID-19. Viruses 2022; 14:94. [PMID: 35062298 PMCID: PMC8778858 DOI: 10.3390/v14010094] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current pandemic affecting almost all countries in the world. SARS-CoV-2 is the agent responsible for coronavirus disease 19 (COVID-19), which has claimed millions of lives around the world. In most patients, SARS-CoV-2 infection does not cause clinical signs. However, some infected people develop symptoms, which include loss of smell or taste, fever, dry cough, headache, severe pneumonia, as well as coagulation disorders. The aim of this work is to report genetic factors of SARS-CoV-2 and host-associated to severe COVID-19, placing special emphasis on the viral entry and molecules of the immune system involved with viral infection. Besides this, we analyze SARS-CoV-2 variants and their structural characteristics related to the binding to polymorphic angiotensin-converting enzyme type 2 (ACE2). Additionally, we also review other polymorphisms as well as some epigenetic factors involved in the immunopathogenesis of COVID-19. These factors and viral variability could explain the increment of infection rate and/or in the development of severe COVID-19.
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Affiliation(s)
- Jesús Zepeda-Cervantes
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Daniel Martínez-Flores
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Josué Orlando Ramírez-Jarquín
- Departamento de Neuropatología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Ángeles C. Tecalco-Cruz
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), Mexico City 06720, Mexico;
| | - Noé Santiago Alavez-Pérez
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07340, Mexico;
| | - Luis Vaca
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Rosa Elena Sarmiento-Silva
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
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Brodin P. SARS-CoV-2 infections in children: understanding diverse outcomes. Immunity 2022; 55:201-209. [PMID: 35093190 PMCID: PMC8769938 DOI: 10.1016/j.immuni.2022.01.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/20/2021] [Accepted: 01/14/2022] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2 infections mostly lead to mild or even asymptomatic infections in children, but the reasons for this are not fully understood. More efficient local tissue responses, better thymic function, and cross-reactive immunity have all been proposed to explain this. In rare cases of children and young people, but very rarely in adults, post-infectious hyperinflammatory syndromes can develop and be serious. Here, I will discuss our current understanding of SARS-CoV-2 infections in children and hypothesize that a life history and energy allocation perspective might offer an additional explanation to mild infections, viral dynamics, and the higher incidence of rare multisystem inflammatory syndromes in children and young people.
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Casadevall A, Jackson S, Semenza GL, Tomaselli GF, Ahima RS. The Journal of Clinical Investigation in the time of COVID-19. J Clin Invest 2021; 131:156409. [PMID: 34907915 DOI: 10.1172/jci156409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In this editorial, we describe the experience of the JCI editors during the COVID-19 pandemic. Our goal is to share how we operated during the pandemic, recount how the JCI contributed to the response, highlight some of the major papers we published on SARS-CoV-2 and COVID-19, and impart our insights in the hope that these are helpful to journal editors that may need to deal with similar types of crises in the future.
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Abstract
PURPOSE OF REVIEW This review is meant to describe the genetic associations with pediatric severe COVID-19 pneumonia and the postinfectious complication of the multisystem inflammatory syndrome in children (MIS-C). Multiple genetic approaches have been carried out, primarily in adults with extrapolation to children, including genome-wide association studies (GWAS), whole exome and whole genome sequencing (WES/WGS), and target gene analyses. RECENT FINDINGS Data from adults with severe COVID-19 have identified genomic regions (human leukocyte antigen locus and 3p21.31) as potential risk factors. Genes related to viral entry into cells (ABO blood group locus, ACE2, TMPRS22) have been linked to severe COVID-19 patients by GWAS and target gene approaches. Type I interferon (e.g. IFNAR2) and antiviral gene (e.g. TLR7) associations have been identified by several genetic approaches in severe COVID-19. WES has noted associations with several immune regulatory genes (e.g. SOCS1). Target gene approaches have identified mutations in perforin-mediated cytolytic pathway genes in children and adults with severe COVID-19 and children with MIS-C. SUMMARY Several genetic associations have been identified in individuals with severe COVID-19 and MIS-C via various genetic approaches. Broadly speaking, COVID-19 genetic associations include genes involved with antiviral functions, viral cell entry, immune regulation, chemotaxis of white blood cells, and lymphocyte cytolytic function.
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Affiliation(s)
- Grant S. Schulert
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Sydney A. Blum
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center
| | - Randy Q. Cron
- Division of Rheumatology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Cappadona C, Paraboschi EM, Ziliotto N, Bottaro S, Rimoldi V, Gerussi A, Azimonti A, Brenna D, Brunati A, Cameroni C, Campanaro G, Carloni F, Cavadini G, Ciravegna M, Composto A, Converso G, Corbella P, D’Eugenio D, Dal Rì G, Di Giorgio SM, Grondelli MC, Guerrera L, Laffoucriere G, Lando B, Lopedote L, Maizza B, Marconi E, Mariola C, Matronola GM, Menga LM, Montorsi G, Papatolo A, Patti R, Profeta L, Rebasti V, Smidili A, Tarchi SM, Tartaglia FC, Tettamanzi G, Tinelli E, Stuani R, Bolchini C, Pattini L, Invernizzi P, Degenhardt F, Franke A, Duga S, Asselta R. MEDTEC Students against Coronavirus: Investigating the Role of Hemostatic Genes in the Predisposition to COVID-19 Severity. J Pers Med 2021; 11:jpm11111166. [PMID: 34834519 PMCID: PMC8622845 DOI: 10.3390/jpm11111166] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the coronavirus disease 2019 (COVID-19) pandemic. Besides virus intrinsic characteristics, the host genetic makeup is predicted to account for the extreme clinical heterogeneity of the disease, which is characterized, among other manifestations, by a derangement of hemostasis associated with thromboembolic events. To date, large-scale studies confirmed that genetic predisposition plays a role in COVID-19 severity, pinpointing several susceptibility genes, often characterized by immunologic functions. With these premises, we performed an association study of common variants in 32 hemostatic genes with COVID-19 severity. We investigated 49,845 single-nucleotide polymorphism in a cohort of 332 Italian severe COVID-19 patients and 1668 controls from the general population. The study was conducted engaging a class of students attending the second year of the MEDTEC school (a six-year program, held in collaboration between Humanitas University and the Politecnico of Milan, allowing students to gain an MD in Medicine and a Bachelor’s Degree in Biomedical Engineering). Thanks to their willingness to participate in the fight against the pandemic, we evidenced several suggestive hits (p < 0.001), involving the PROC, MTHFR, MTR, ADAMTS13, and THBS2 genes (top signal in PROC: chr2:127192625:G:A, OR = 2.23, 95%CI = 1.50–3.34, p = 8.77 × 10−5). The top signals in PROC, MTHFR, MTR, ADAMTS13 were instrumental for the construction of a polygenic risk score, whose distribution was significantly different between cases and controls (p = 1.62 × 10−8 for difference in median levels). Finally, a meta-analysis performed using data from the Regeneron database confirmed the contribution of the MTHFR variant chr1:11753033:G:A to the predisposition to severe COVID-19 (pooled OR = 1.21, 95%CI = 1.09–1.33, p = 4.34 × 10−14 in the weighted analysis).
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Affiliation(s)
- Claudio Cappadona
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
- Humanitas Clinical and Research Center, IRCCS, Via Manzoni 56, 20089 Rozzano, Italy
| | - Nicole Ziliotto
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Sandro Bottaro
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
- Humanitas Clinical and Research Center, IRCCS, Via Manzoni 56, 20089 Rozzano, Italy
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Alessio Gerussi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (A.G.); (P.I.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
| | - Andrea Azimonti
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Daniele Brenna
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Andrea Brunati
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Charlotte Cameroni
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Giovanni Campanaro
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Francesca Carloni
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Giacomo Cavadini
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Martina Ciravegna
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Antonio Composto
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Giuseppe Converso
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Pierluigi Corbella
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Davide D’Eugenio
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Giovanna Dal Rì
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Sofia Maria Di Giorgio
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Maria Chiara Grondelli
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Lorenza Guerrera
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Georges Laffoucriere
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Beatrice Lando
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Leandro Lopedote
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Benedetta Maizza
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Elettra Marconi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Carlotta Mariola
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Guia Margherita Matronola
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Luca Maria Menga
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Giulia Montorsi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Antonio Papatolo
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Riccardo Patti
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Lorenzo Profeta
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Vera Rebasti
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Alice Smidili
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Sofia Maria Tarchi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Francesco Carlo Tartaglia
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Gaia Tettamanzi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Elena Tinelli
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Riccardo Stuani
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Cristiana Bolchini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy; (C.B.); (L.P.)
| | - Linda Pattini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy; (C.B.); (L.P.)
| | - Pietro Invernizzi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (A.G.); (P.I.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, 24105 Kiel, Germany; (F.D.); (A.F.)
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, 24105 Kiel, Germany; (F.D.); (A.F.)
- University Hospital Schleswig-Holstein (UKSH), 24105 Kiel, Germany
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
- Humanitas Clinical and Research Center, IRCCS, Via Manzoni 56, 20089 Rozzano, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
- Humanitas Clinical and Research Center, IRCCS, Via Manzoni 56, 20089 Rozzano, Italy
- Correspondence:
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Ferré EMN, Schmitt MM, Lionakis MS. Autoimmune Polyendocrinopathy-Candidiasis-Ectodermal Dystrophy. Front Pediatr 2021; 9:723532. [PMID: 34790633 PMCID: PMC8591095 DOI: 10.3389/fped.2021.723532] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/07/2021] [Indexed: 12/12/2022] Open
Abstract
Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), also known as autoimmune polyglandular syndrome type-1 (APS-1), is a rare monogenic autoimmune disease caused by loss-of-function mutations in the autoimmune regulator (AIRE) gene. AIRE deficiency impairs immune tolerance in the thymus and results in the peripheral escape of self-reactive T lymphocytes and the generation of several cytokine- and tissue antigen-targeted autoantibodies. APECED features a classic triad of characteristic clinical manifestations consisting of chronic mucocutaneous candidiasis (CMC), hypoparathyroidism, and primary adrenal insufficiency (Addison's disease). In addition, APECED patients develop several non-endocrine autoimmune manifestations with variable frequencies, whose recognition by pediatricians should facilitate an earlier diagnosis and allow for the prompt implementation of targeted screening, preventive, and therapeutic strategies. This review summarizes our current understanding of the genetic, immunological, clinical, diagnostic, and treatment features of APECED.
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Affiliation(s)
| | | | - Michail S. Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
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Zhuang X, Tsukuda S, Wrensch F, Wing PA, Schilling M, Harris JM, Borrmann H, Morgan SB, Cane JL, Mailly L, Thakur N, Conceicao C, Sanghani H, Heydmann L, Bach C, Ashton A, Walsh S, Tan TK, Schimanski L, Huang KYA, Schuster C, Watashi K, Hinks TS, Jagannath A, Vausdevan SR, Bailey D, Baumert TF, McKeating JA. The circadian clock component BMAL1 regulates SARS-CoV-2 entry and replication in lung epithelial cells. iScience 2021; 24:103144. [PMID: 34545347 PMCID: PMC8443536 DOI: 10.1016/j.isci.2021.103144] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
The coronavirus disease 2019 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus, is a global health issue with unprecedented challenges for public health. SARS-CoV-2 primarily infects cells of the respiratory tract via spike glycoprotein binding to angiotensin-converting enzyme (ACE2). Circadian rhythms coordinate an organism's response to its environment and can regulate host susceptibility to virus infection. We demonstrate that silencing the circadian regulator Bmal1 or treating lung epithelial cells with the REV-ERB agonist SR9009 reduces ACE2 expression and inhibits SARS-CoV-2 entry and replication. Importantly, treating infected cells with SR9009 limits SARS-CoV-2 replication and secretion of infectious particles, showing that post-entry steps in the viral life cycle are influenced by the circadian system. Transcriptome analysis revealed that Bmal1 silencing induced interferon-stimulated gene transcripts in Calu-3 lung epithelial cells, providing a mechanism for the circadian pathway to limit SARS-CoV-2 infection. Our study highlights alternative approaches to understand and improve therapeutic targeting of SARS-CoV-2.
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Affiliation(s)
- Xiaodong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Senko Tsukuda
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Florian Wrensch
- Université de Strasbourg, Strasbourg, France and INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
| | - Peter A.C. Wing
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Mirjam Schilling
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James M. Harris
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Helene Borrmann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie B. Morgan
- Respiratory Medicine Unit and National Institute for Health Research Oxford Biomedical Research Centre, Nuffield Department of Medicine, Experimental Medicine, University of Oxford, UK
| | - Jennifer L. Cane
- Respiratory Medicine Unit and National Institute for Health Research Oxford Biomedical Research Centre, Nuffield Department of Medicine, Experimental Medicine, University of Oxford, UK
| | - Laurent Mailly
- Université de Strasbourg, Strasbourg, France and INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
| | - Nazia Thakur
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, UK
| | - Carina Conceicao
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, UK
| | - Harshmeena Sanghani
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Laura Heydmann
- Université de Strasbourg, Strasbourg, France and INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
| | - Charlotte Bach
- Université de Strasbourg, Strasbourg, France and INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
| | - Anna Ashton
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Steven Walsh
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute, John Radcliffe Hospital, Oxford 17 OX3 9DS, UK
| | - Lisa Schimanski
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute, John Radcliffe Hospital, Oxford 17 OX3 9DS, UK
| | - Kuan-Ying A. Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University and Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Catherine Schuster
- Université de Strasbourg, Strasbourg, France and INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan
| | - Timothy S.C. Hinks
- Respiratory Medicine Unit and National Institute for Health Research Oxford Biomedical Research Centre, Nuffield Department of Medicine, Experimental Medicine, University of Oxford, UK
| | - Aarti Jagannath
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | | | - Dalan Bailey
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, UK
| | - Thomas F. Baumert
- Université de Strasbourg, Strasbourg, France and INSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Pole Hépato-digestif, IHU, Hopitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jane A. McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
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37
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Velavan TP, Pallerla SR, Rüter J, Augustin Y, Kremsner PG, Krishna S, Meyer CG. Host genetic factors determining COVID-19 susceptibility and severity. EBioMedicine 2021; 72:103629. [PMID: 34655949 PMCID: PMC8512556 DOI: 10.1016/j.ebiom.2021.103629] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) poses an unprecedented challenge to humanity. SARS-CoV-2 infections range from asymptomatic to severe courses of COVID-19 with acute respiratory distress syndrome (ARDS), multiorgan involvement and death. Risk factors for disease severity include older age, male sex, increased BMI and pre-existing comorbidities. Ethnicity is also relevant to COVID-19 susceptibility and severity. Host genetic predisposition to COVID-19 is now increasingly recognized and whole genome and candidate gene association studies regarding COVID-19 susceptibility have been performed. Several common and rare variants in genes related to inflammation or immune responses have been identified. We summarize research on COVID-19 host genetics and compile genetic variants associated with susceptibility to COVID-19 and disease severity. We discuss candidate genes that should be investigated further to understand such associations and provide insights relevant to pathogenesis, risk classification, therapy response, precision medicine, and drug repurposing.
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Affiliation(s)
- Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.
| | - Srinivas Reddy Pallerla
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Jule Rüter
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany
| | - Yolanda Augustin
- Institute of Infection and Immunity, St George's University of London, United Kingdom
| | - Peter G Kremsner
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Centre de Recherches Médicales de Lambaréné (CERMEL), Gabon
| | - Sanjeev Krishna
- Institute of Infection and Immunity, St George's University of London, United Kingdom; Centre de Recherches Médicales de Lambaréné (CERMEL), Gabon
| | - Christian G Meyer
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam; Duy Tan University, Da Nang, Vietnam
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38
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Hargadon KM. A call for discovery: Re-envisioning The Cancer Genome Atlas as a blueprint for a TCGA2.0-The COVID-19 Genome Atlas. CLINICAL AND TRANSLATIONAL DISCOVERY 2021; 1:e7. [PMID: 34901953 PMCID: PMC8653019 DOI: 10.1002/ctd2.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/25/2022]
Abstract
The COVID‐19 pandemic has impacted the health of millions and had a myriad of devastating consequences for global societies since its emergence in 2019. Noting parallels between the impact of COVID‐19 and cancer as diseases of global health significance, and as a way of building off the successes of The Cancer Genome Atlas (TCGA) as a comprehensive, multiomics approach to understand and combat cancer, this Call For Discovery provides a vision for creating a new TCGA2.0 (The COVID‐19 Genome Atlas) as a tool that will benefit researchers, clinicians, and patients alike as the scientific community works to better understand not only the various determinants of COVID‐19 disease outcome but also the most effective ways to manage and treat COVID‐19 disease complications.
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Affiliation(s)
- Kristian M Hargadon
- Hargadon Laboratory Department of Biology Hampden-Sydney College Hampden-Sydney Virginia USA
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39
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Interfering with SARS-CoV-2: are interferons friends or foes in COVID-19? Curr Opin Virol 2021; 50:119-127. [PMID: 34454352 PMCID: PMC8367741 DOI: 10.1016/j.coviro.2021.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 01/06/2023]
Abstract
Type I and type III interferons are among the most potent anti-viral cytokines produced by the immune system. The recent outbreak of SARS-CoV-2, which causes COVID-19, underscores the vital role of these cytokines in controlling the virus and dictating disease severity. Here we delineate the pathways that lead to interferon production in response to SARS-CoV-2 encounter, and elucidate how this virus hinders the production and action of these cytokines; we also highlight that these interferon families serve protective as well as detrimental roles in patients with COVID-19, and conclude that a better understanding of the time, dose, localization, and activity of specific members of the interferon families is imperative for designing more efficient therapeutic interventions against this disease.
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40
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Palermo E, Di Carlo D, Sgarbanti M, Hiscott J. Type I Interferons in COVID-19 Pathogenesis. BIOLOGY 2021; 10:829. [PMID: 34571706 PMCID: PMC8468334 DOI: 10.3390/biology10090829] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
Among the many activities attributed to the type I interferon (IFN) multigene family, their roles as mediators of the antiviral immune response have emerged as important components of the host response to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. Viruses likewise have evolved multiple immune evasion strategies to circumvent the host immune response and promote virus propagation and dissemination. Therefore, a thorough characterization of host-virus interactions is essential to understand SARS-CoV-2 pathogenesis. Here, we summarize the virus-mediated evasion of the IFN responses and the viral functions involved, the genetic basis of IFN production in SARS-CoV-2 infection and the progress of clinical trials designed to utilize type I IFN as a potential therapeutic tool.
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Affiliation(s)
- Enrico Palermo
- Istituto Pasteur Italia—Cenci Bolognetti Foundation, Viale Regina Elena 291, 00161 Rome, Italy;
| | - Daniele Di Carlo
- Istituto Pasteur Italia—Cenci Bolognetti Foundation, Viale Regina Elena 291, 00161 Rome, Italy;
| | - Marco Sgarbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - John Hiscott
- Istituto Pasteur Italia—Cenci Bolognetti Foundation, Viale Regina Elena 291, 00161 Rome, Italy;
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41
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Povysil G, Butler-Laporte G, Gharavi AG, Richards JB, Goldstein DB, Kiryluk K. Association of rare predicted loss-of-function variants of influenza-related type I IFN genes with critical COVID-19 pneumonia. Reply. J Clin Invest 2021; 131:e152475. [PMID: 34156980 DOI: 10.1172/jci152475] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Montreal, Quebec, Canada.,Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada
| | - Ali G Gharavi
- Department of Medicine and.,Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Montreal, Quebec, Canada.,Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada.,Department of Twin Research, King's College London, London, United Kingdom
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, New York, USA.,Department of Genetics and Development, Columbia University, New York, New York, USA
| | - Krzysztof Kiryluk
- Department of Medicine and.,Institute for Genomic Medicine, Columbia University, New York, New York, USA
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42
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Zhang Q, Cobat A, Bastard P, Notarangelo LD, Su HC, Abel L, Casanova JL. Association of rare predicted loss-of-function variants of influenza-related type I IFN genes with critical COVID-19 pneumonia. J Clin Invest 2021; 131:e152474. [PMID: 34166232 DOI: 10.1172/jci152474] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Aurélie Cobat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID) and.,NIAID Clinical Genomics Program, NIH, Bethesda, Maryland, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID) and.,NIAID Clinical Genomics Program, NIH, Bethesda, Maryland, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,University of Paris, Imagine Institute, Paris, France.,Howard Hughes Medical Institute, New York, New York, USA.,Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
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43
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Cotsapas C, Saarela J, Farmer JR, Scaria V, Abraham RS. Do monogenic inborn errors of immunity cause susceptibility to severe COVID-19? J Clin Invest 2021; 131:e149459. [PMID: 34061775 DOI: 10.1172/jci149459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The SARS-CoV-2 virus, which causes COVID-19, has been associated globally with substantial morbidity and mortality. Numerous reports over the past year have described the clinical and immunological profiles of COVID-19 patients, and while some trends have emerged for risk stratification, they do not provide a complete picture. Therefore, efforts are ongoing to identify genetic susceptibility factors of severe disease. In this issue of the JCI, Povysil et al. performed a large, multiple-country study, sequencing genomes from patients with mild and severe COVID-19, along with population controls. Contrary to previous reports, the authors observed no enrichment of predicted loss-of-function variants in genes in the type I interferon pathway, which might predispose to severe disease. These studies suggest that more evidence is needed to substantiate the hypothesis for a genetic immune predisposition to severe COVID-19, and highlights the importance of considering experimental design when implicating a monogenic basis for severe disease.
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Affiliation(s)
- Chris Cotsapas
- Yale University School of Medicine, New Haven, Connecticut, USA.,The Broad Institute, Cambridge, Massachusetts, USA
| | - Janna Saarela
- Center for Molecular Medicine, University of Oslo, Oslo, Norway
| | | | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,The Ohio State University Wexner College of Medicine, Columbus, Ohio, USA
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44
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Kosmicki JA, Horowitz JE, Banerjee N, Lanche R, Marcketta A, Maxwell E, Bai X, Sun D, Backman JD, Sharma D, Kury FSP, Kang HM, O'Dushlaine C, Yadav A, Mansfield AJ, Li AH, Watanabe K, Gurski L, McCarthy SE, Locke AE, Khalid S, O'Keeffe S, Mbatchou J, Chazara O, Huang Y, Kvikstad E, O'Neill A, Nioi P, Parker MM, Petrovski S, Runz H, Szustakowski JD, Wang Q, Wong E, Cordova-Palomera A, Smith EN, Szalma S, Zheng X, Esmaeeli S, Davis JW, Lai YP, Chen X, Justice AE, Leader JB, Mirshahi T, Carey DJ, Verma A, Sirugo G, Ritchie MD, Rader DJ, Povysil G, Goldstein DB, Kiryluk K, Pairo-Castineira E, Rawlik K, Pasko D, Walker S, Meynert A, Kousathanas A, Moutsianas L, Tenesa A, Caulfield M, Scott R, Wilson JF, Baillie JK, Butler-Laporte G, Nakanishi T, Lathrop M, Richards JB, Jones M, Balasubramanian S, Salerno W, Shuldiner AR, Marchini J, Overton JD, Habegger L, Cantor MN, Reid JG, Baras A, Abecasis GR, Ferreira MAR. Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals. Am J Hum Genet 2021; 108:1350-1355. [PMID: 34115965 PMCID: PMC8173480 DOI: 10.1016/j.ajhg.2021.05.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/24/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a respiratory illness that can result in hospitalization or death. We used exome sequence data to investigate associations between rare genetic variants and seven COVID-19 outcomes in 586,157 individuals, including 20,952 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome wide or when specifically focusing on (1) 13 interferon pathway genes in which rare deleterious variants have been reported in individuals with severe COVID-19, (2) 281 genes located in susceptibility loci identified by the COVID-19 Host Genetics Initiative, or (3) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, and results are publicly available through the Regeneron Genetics Center COVID-19 Results Browser.
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Affiliation(s)
- Jack A Kosmicki
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Julie E Horowitz
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Nilanjana Banerjee
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Rouel Lanche
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Anthony Marcketta
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Evan Maxwell
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Xiaodong Bai
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Dylan Sun
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Joshua D Backman
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Deepika Sharma
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Fabricio S P Kury
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Hyun M Kang
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Colm O'Dushlaine
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Ashish Yadav
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Adam J Mansfield
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Alexander H Li
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Kyoko Watanabe
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Lauren Gurski
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Shane E McCarthy
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Adam E Locke
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Shareef Khalid
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Sean O'Keeffe
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Joelle Mbatchou
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Olympe Chazara
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | | | - Erika Kvikstad
- Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, NJ 08543, USA
| | - Amanda O'Neill
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Paul Nioi
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Meg M Parker
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, MA 02142, USA
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Heiko Runz
- Biogen, 300 Binney Street, Cambridge, MA 02142, USA
| | | | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Emily Wong
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, CA 92121, USA
| | | | - Erin N Smith
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, CA 92121, USA
| | - Sandor Szalma
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, CA 92121, USA
| | - Xiuwen Zheng
- AbbVie, Inc., 1 N. Waukegan Road, North Chicago, IL 60064, USA
| | - Sahar Esmaeeli
- AbbVie, Inc., 1 N. Waukegan Road, North Chicago, IL 60064, USA
| | - Justin W Davis
- AbbVie, Inc., 1 N. Waukegan Road, North Chicago, IL 60064, USA
| | - Yi-Pin Lai
- Pfizer, Inc., 1 Portland Street, Cambridge, MA 02139, USA
| | - Xing Chen
- Pfizer, Inc., 1 Portland Street, Cambridge, MA 02139, USA
| | | | | | | | | | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Giorgio Sirugo
- 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
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Krzysztof Kiryluk
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | | | | | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | | | | | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - Mark Caulfield
- Genomics England, London EC1M 6BQ, UK; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Richard Scott
- Genomics England, London EC1M 6BQ, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh EH16 5SA, UK
| | - Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 0G4, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A 0G4, Canada; Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montréal, QC H3A 0G4, Canada; Canadian Centre for Computational Genomics, McGill University, Montréal, QC H3A 0G4, Canada
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 0G4, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A 0G4, Canada; Department of Twins Research, King's College London, London WC2R 2LS, UK
| | - Marcus Jones
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | | | - William Salerno
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Alan R Shuldiner
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jonathan Marchini
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - John D Overton
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Lukas Habegger
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Michael N Cantor
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jeffrey G Reid
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Aris Baras
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Goncalo R Abecasis
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
| | - Manuel A R Ferreira
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
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45
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Schmidt A, Peters S, Knaus A, Sabir H, Hamsen F, Maj C, Fazaal J, Sivalingam S, Savchenko O, Mantri A, Holzinger D, Neudorf U, Müller A, Ludwig KU, Krawitz PM, Engels H, Nöthen MM, Bagci S. TBK1 and TNFRSF13B mutations and an autoinflammatory disease in a child with lethal COVID-19. NPJ Genom Med 2021; 6:55. [PMID: 34210994 PMCID: PMC8249618 DOI: 10.1038/s41525-021-00220-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/09/2021] [Indexed: 12/16/2022] Open
Abstract
Among children, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are typically mild. Here, we describe the case of a 3.5-year-old girl with an unusually severe presentation of coronavirus disease (COVID-19). The child had an autoinflammatory disorder of unknown etiology, which had been treated using prednisolone and methotrexate, and her parents were half cousins of Turkish descent. After 5 days of nonspecific viral infection symptoms, tonic-clonic seizures occurred followed by acute cardiac insufficiency, multi-organ insufficiency, and ultimate death. Trio exome sequencing identified a homozygous splice-variant in the gene TBK1, and a homozygous missense variant in the gene TNFRSF13B. Heterozygous deleterious variants in the TBK1 gene have been associated with severe COVID-19, and the variant in the TNFRSF13B gene has been associated with common variable immunodeficiency (CVID). We suggest that the identified variants, the autoinflammatory disorder and its treatment, or a combination of these factors probably predisposed to lethal COVID-19 in the present case.
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Affiliation(s)
- Axel Schmidt
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Alexej Knaus
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Hemmen Sabir
- Neonatology and Pediatric Intensive Care, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Frauke Hamsen
- Department of Pediatric Hematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Carlo Maj
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Julia Fazaal
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Sugirthan Sivalingam
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, Bonn, Germany
| | - Oleksandr Savchenko
- Department of Diagnostic and Interventional Radiology, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Aakash Mantri
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Dirk Holzinger
- Department of Pediatric Hematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Ulrich Neudorf
- Department of Pediatric Hematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Andreas Müller
- Neonatology and Pediatric Intensive Care, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Peter M Krawitz
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.
| | - Soyhan Bagci
- Neonatology and Pediatric Intensive Care, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
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46
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Zhuang X, Tsukuda S, Wrensch F, Wing PA, Schilling M, Harris JM, Borrmann H, Morgan SB, Cane JL, Mailly L, Thakur N, Conceicao C, Sanghani H, Heydmann L, Bach C, Ashton A, Walsh S, Tan TK, Schimanski L, Huang KYA, Schuster C, Watashi K, Hinks TS, Jagannath A, Vausdevan SR, Bailey D, Baumert TF, McKeating JA. The circadian clock component BMAL1 regulates SARS-CoV-2 entry and replication in lung epithelial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.20.436163. [PMID: 33758862 PMCID: PMC7987021 DOI: 10.1101/2021.03.20.436163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2 coronavirus, is a global health issue with unprecedented challenges for public health. SARS-CoV-2 primarily infects cells of the respiratory tract, via Spike glycoprotein binding angiotensin-converting enzyme (ACE2). Circadian rhythms coordinate an organism’s response to its environment and can regulate host susceptibility to virus infection. We demonstrate a circadian regulation of ACE2 in lung epithelial cells and show that silencing BMAL1 or treatment with a synthetic REV-ERB agonist SR9009 reduces ACE2 expression and inhibits SARS-CoV-2 entry. Treating infected cells with SR9009 limits viral replication and secretion of infectious particles, showing that post-entry steps in the viral life cycle are influenced by the circadian system. Transcriptome analysis revealed that Bmal1 silencing induced a wide spectrum of interferon stimulated genes in Calu-3 lung epithelial cells, providing a mechanism for the circadian pathway to dampen SARS-CoV-2 infection. Our study suggests new approaches to understand and improve therapeutic targeting of SARS-CoV-2.
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