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Yu Y, Lin K, Wu H, Hu M, Yang X, Wang J, Grillari J, Chen J. Targeting senescent cells in aging and COVID-19: from cellular mechanisms to therapeutic opportunities. CELL REGENERATION (LONDON, ENGLAND) 2024; 13:20. [PMID: 39358480 DOI: 10.1186/s13619-024-00201-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 09/10/2024] [Indexed: 10/04/2024]
Abstract
The COVID-19 pandemic has caused a global health crisis and significant social economic burden. While most individuals experience mild or non-specific symptoms, elderly individuals are at a higher risk of developing severe symptoms and life-threatening complications. Exploring the key factors associated with clinical severity highlights that key characteristics of aging, such as cellular senescence, immune dysregulation, metabolic alterations, and impaired regenerative potential, contribute to disruption of tissue homeostasis of the lung and worse clinical outcome. Senolytic and senomorphic drugs, which are anti-aging treatments designed to eliminate senescent cells or decrease the associated phenotypes, have shown promise in alleviating age-related dysfunctions and offer a novel approach to treating diseases that share certain aspects of underlying mechanisms with aging, including COVID-19. This review summarizes the current understanding of aging in COVID-19 progression, and highlights recent findings on anti-aging drugs that could be repurposed for COVID-19 treatment to complement existing therapies.
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Affiliation(s)
- Yuan Yu
- Center for Cell Lineage and Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kaixuan Lin
- Center for Cell Lineage and Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Haoyu Wu
- Center for Cell Lineage and Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Mingli Hu
- Center for Cell Lineage and Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Xuejie Yang
- Center for Cell Lineage and Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jie Wang
- Center for Cell Lineage and Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Johannes Grillari
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
- Institute of Molecular Biotechnology, BOKU University, Vienna, Austria
- Ludwig Boltzmann Institute for Traumatology, The Research Center in Cooperation With AUVA, 1200, Vienna, Austria
| | - Jiekai Chen
- Center for Cell Lineage and Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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2
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Shan Z, Zhao Y, Chen X, Zhan G, Huang J, Yang X, Xu C, Guo N, Xiong Z, Wu F, Liu Y, Liu H, Chen B, Chen B, Sun J, He J, Guo Y, Cao S, Wu K, Mao R, Wu G, Lin L, Zou X, Wang J, Chen J. KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids. Sci Bull (Beijing) 2024:S2095-9273(24)00638-8. [PMID: 39327125 DOI: 10.1016/j.scib.2024.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/15/2024] [Accepted: 09/02/2024] [Indexed: 09/28/2024]
Abstract
KMT2D, a H3K4me1 methyltransferase primarily regulating enhancers, is a leading cause of KABUKI syndrome. This multisystem disorder leads to craniofacial and cognitive abnormalities, possibly through neural crest and neuronal lineages. However, the impacted cell-of-origin and molecular mechanism of KMT2D during the development of KABUKI disease remains unknown. Here we have optimized a brain organoid model to investigate neural crest and neuronal differentiation. To pinpoint KMT2D's enhancer target, we developed a genome-wide cis-regulatory element explorer (GREE) based on single-cell multiomic integration. Single cell RNA-seq revealed that KMT2D-knockout (KO) and patient-derived organoids exhibited neural crest deformities and GABAergic overproduction. Mechanistically, GREE identified that KMT2D targets a roof-plate-like niche cell and activates the niche cell-specific WNT3A enhancer, providing the microenvironment for neural crest and neuronal development. Interestingly, KMT2D-mutated mice displayed decreased WNT3A expression in the diencephalon roof plate, indicating impaired niche cell function. Deleting the WNT3A enhancer in the organoids presented phenotypic similarities to KMT2D-depletion, emphasizing the WNT3A enhancer as the predominant target of KMT2D. Conversely, reactivating WNT signaling in KMT2D-KO rescued the lineage defects by restoring the microenvironment. Overall, our discovery of KMT2D's primary target provides insights for reconciling complex phenotypes of KABUKI syndrome and establishes a new paradigm for dissecting the mechanisms of genetic disorders from genotype to phenotype.
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Affiliation(s)
- Ziyun Shan
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingying Zhao
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, 999077, Hong Kong Special Administrative Region of China
| | - Xiuyu Chen
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guodong Zhan
- Child Development and Behavior Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Junju Huang
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xuejie Yang
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Chongshen Xu
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Ning Guo
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Zhi Xiong
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangzhou Laboratory, Guangzhou 510005, China
| | - Fang Wu
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujian Liu
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - He Liu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou 510005, China; The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510700, China
| | - Biyuan Chen
- Child Development and Behavior Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Bingqiu Chen
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou 510005, China; Guangzhou Laboratory, Guangzhou 510005, China
| | - Yiping Guo
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | | | - Kaixin Wu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou 510005, China
| | - Rui Mao
- Animal Research Center, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | | | - Lihui Lin
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiaobing Zou
- Child Development and Behavior Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Jie Wang
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Jiekai Chen
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, 999077, Hong Kong Special Administrative Region of China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou 510005, China.
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3
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Wang M, Zhang D, Lei T, Zhou Y, Qin H, Wu Y, Liu S, Zhang L, Jia K, Dong Y, Wang S, Li Y, Fan Y, Gui L, Dong Y, Zhang W, Li Z, Hou J. Interferon-responsive neutrophils and macrophages extricate SARS-CoV-2 Omicron critical patients from the nasty fate of sepsis. J Med Virol 2024; 96:e29889. [PMID: 39206862 DOI: 10.1002/jmv.29889] [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: 04/22/2024] [Revised: 07/24/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
The SARS-CoV-2 Omicron variant is characterized by its high transmissibility, which has caused a worldwide epidemiological event. Yet, it turns ominous once the disease progression degenerates into severe pneumonia and sepsis, presenting a horrendous lethality. To elucidate the alveolar immune or inflammatory landscapes of Omicron critical-ill patients, we performed single-cell RNA-sequencing (scRNA-seq) of bronchoalveolar lavage fluid (BALF) from the patients with critical pneumonia caused by Omicron infection, and analyzed the correlation between the clinical severity scores and different immune cell subpopulations. In the BALF of Omicron critical patients, the alveolar violent myeloid inflammatory environment was determined. ISG15+ neutrophils and CXCL10+ macrophages, both expressed the interferon-stimulated genes (ISGs), were negatively correlated with clinical pulmonary infection score, while septic CST7+ neutrophils and inflammatory VCAN+ macrophages were positively correlated with sequential organ failure assessment. The percentages of ISG15+ neutrophils were associated with more protective alveolar epithelial cells, and may reshape CD4+ T cells to the exhaustive phenotype, thus preventing immune injuries. The CXCL10+ macrophages may promote plasmablast/plasma cell survival and activation as well as the production of specific antibodies. As compared to the previous BALF scRNA-seq data from SARS-CoV-2 wild-type/Alpha critical patients, the subsets of neutrophils and macrophages with pro-inflammatory and immunoregulatory features presented obvious distinctions, suggesting an immune disparity in Omicron variants. Overall, this study provides a BALF single-cell atlas of Omicron critical patients, and suggests that alveolar interferon-responsive neutrophils and macrophages may extricate SARS-CoV-2 Omicron critical patients from the nasty fate of sepsis.
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Affiliation(s)
- Mu Wang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Dingji Zhang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Ting Lei
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Ye Zhou
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Hao Qin
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Second Military Medical University, Shanghai, China
| | - Yanfeng Wu
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Shuxun Liu
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Liyuan Zhang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Kaiwei Jia
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Yue Dong
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Suyuan Wang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Yunhui Li
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Yiwen Fan
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Liangchen Gui
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Yuchao Dong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Second Military Medical University, Shanghai, China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Second Military Medical University, Shanghai, China
| | - Zhixuan Li
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Jin Hou
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
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4
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Haoyu W, Meiqin L, Jiaoyang S, Guangliang H, Haofeng L, Pan C, Xiongzhi Q, Kaixin W, Mingli H, Xuejie Y, Lämmermann I, Grillari J, Zhengli S, Jiekai C, Guangming W. Premature aging effects on COVID-19 pathogenesis: new insights from mouse models. Sci Rep 2024; 14:19703. [PMID: 39181932 PMCID: PMC11344828 DOI: 10.1038/s41598-024-70612-2] [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: 04/24/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024] Open
Abstract
Aging is identified as a significant risk factor for severe coronavirus disease-2019 (COVID-19), often resulting in profound lung damage and mortality. Yet, the biological relationship between aging, aging-related comorbidities, and COVID-19 remains incompletely understood. This study aimed to elucidate the age-related COVID19 pathogenesis using an Hutchinson-Gilford progeria syndrome (HGPS) mouse model, a premature aging disease model, with humanized ACE2 receptors. Pathological features were compared between young, aged, and HGPS hACE2 mice following SARS-CoV-2 challenge. We demonstrated that young mice display robust interferon response and antiviral activity, whereas this response is attenuated in aged mice. Viral infection in aged mice results in severe respiratory tract hemorrhage, likely contributing a higher mortality rate. In contrast, HGPS hACE2 mice exhibit milder disease manifestations characterized by minor immune cell infiltration and dysregulation of multiple metabolic processes. Comprehensive transcriptome analysis revealed both shared and unique gene expression dynamics among different mouse groups. Collectively, our studies evaluated the impact of SARS-CoV-2 infection on progeroid syndromes using a HGPS hACE2 mouse model, which holds promise as a useful tool for investigating COVID-19 pathogenesis in individuals with premature aging.
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Affiliation(s)
- Wu Haoyu
- Center for Cell Lineage Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Liu Meiqin
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory Clinical Base, Guangzhou Medical University, Guangzhou, China
| | - Sun Jiaoyang
- Division of Basic Research, Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Hong Guangliang
- Division of Basic Research, Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Lin Haofeng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Chen Pan
- Center for Cell Lineage Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Quan Xiongzhi
- Center for Cell Lineage Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Wu Kaixin
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Hu Mingli
- Center for Cell Lineage Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yang Xuejie
- Center for Cell Lineage Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | | | - Johannes Grillari
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
- Institute of Molecular Biotechnology, BOKU University, Vienna, Austria
- Ludwig Boltzmann Institute for Traumatology, The Research Center in Cooperation with AUVA, 1200, Vienna, Austria
| | - Shi Zhengli
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Chen Jiekai
- Center for Cell Lineage Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Kowloon, 999077, Hong Kong SAR, China.
| | - Wu Guangming
- Division of Basic Research, Guangzhou National Laboratory, Guangzhou, 510005, China.
- The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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Song Y, Lu J, Qin P, Chen H, Chen L. Interferon-I modulation and natural products: Unraveling mechanisms and therapeutic potential in severe COVID-19. Cytokine Growth Factor Rev 2024:S1359-6101(24)00066-2. [PMID: 39261232 DOI: 10.1016/j.cytogfr.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 08/20/2024] [Indexed: 09/13/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to pose a significant global public health threat, particularly to older adults, pregnant women, and individuals with underlying chronic conditions. Dysregulated immune responses to SARS-CoV-2 infection are believed to contribute to the progression of COVID-19 in severe cases. Previous studies indicates that a deficiency in type I interferon (IFN-I) immunity accounts for approximately 15 %-20 % of patients with severe pneumonia caused by COVID-19, highlighting the potential therapeutic importance of modulating IFN-I signals. Natural products and their derivatives, due to their structural diversity and novel scaffolds, play a crucial role in drug discovery. Some of these natural products targeting IFN-I have demonstrated applications in infectious diseases and inflammatory conditions. However, the immunomodulatory potential of IFN-I in critical COVID-19 pneumonia and the natural compounds regulating the related signal pathway remain not fully understood. In this review, we offer a comprehensive assessment of the association between IFN-I and severe COVID-19, exploring its mechanisms and integrating information on natural compounds effective for IFN-I regulation. Focusing on the primary targets of IFN-I, we also summarize the regulatory mechanisms of natural products, their impact on IFNs, and their therapeutic roles in viral infections. Collectively, by synthesizing these findings, our goal is to provide a valuable reference for future research and to inspire innovative treatment strategies for COVID-19.
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Affiliation(s)
- Yuheng Song
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Pengcheng Qin
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; School of Pharmacy, Henan University, Kaifeng 475001, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai 200032, China
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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Dai X, Xu R, Li N. The Interplay between Airway Cilia and Coronavirus Infection, Implications for Prevention and Control of Airway Viral Infections. Cells 2024; 13:1353. [PMID: 39195243 DOI: 10.3390/cells13161353] [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: 07/23/2024] [Revised: 08/10/2024] [Accepted: 08/12/2024] [Indexed: 08/29/2024] Open
Abstract
Coronaviruses (CoVs) are a class of respiratory viruses with the potential to cause severe respiratory diseases by infecting cells of the upper respiratory tract, bronchial epithelium, and lung. The airway cilia are distributed on the surface of respiratory epithelial cells, forming the first point of contact between the host and the inhaled coronaviruses. The function of the airway cilia is to oscillate and sense, thereby defending against and removing pathogens to maintain the cleanliness and patency of the respiratory tract. Following infection of the respiratory tract, coronaviruses exploit the cilia to invade and replicate in epithelial cells while also damaging the cilia to facilitate the spread and exacerbation of respiratory diseases. It is therefore imperative to investigate the interactions between coronaviruses and respiratory cilia, as well as to elucidate the functional mechanism of respiratory cilia following coronavirus invasion, in order to develop effective strategies for the prevention and treatment of respiratory viral infections. This review commences with an overview of the fundamental characteristics of airway cilia, and then, based on the interplay between airway cilia and coronavirus infection, we propose that ciliary protection and restoration may represent potential therapeutic approaches in emerging and re-emerging coronavirus pandemics.
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Affiliation(s)
- Xuyao Dai
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ruodan Xu
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ning Li
- Department of Biomedical Engineering and Technology, Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
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7
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Sasso-Cerri E, Martinelli VD, de Oliveira SA, da Silva AAS, de Moraes JCG, Cerri PS. Submandibular Gland Pathogenesis Following SARS-CoV-2 Infection and Implications for Xerostomia. Int J Mol Sci 2024; 25:6820. [PMID: 38999930 PMCID: PMC11241347 DOI: 10.3390/ijms25136820] [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: 05/09/2024] [Revised: 06/10/2024] [Accepted: 06/15/2024] [Indexed: 07/14/2024] Open
Abstract
Although SARS-CoV-2 induces mucin hypersecretion in the respiratory tract, hyposalivation/xerostomia has been reported by COVID-19 patients. We evaluate the submandibular gland (SMGs) pathogenesis in SARS-CoV-2-infected K18-hACE2 mice, focusing on the impact of infection on the mucin production and structural integrity of acini, ductal system, myoepithelial cells (MECs) and telocytes. The spike protein, the nucleocapsid protein, hACE2, actin, EGF, TNF-α and IL-1β were detected by immunofluorescence, and the Egfr and Muc5b expression was evaluated. In the infected animals, significant acinar hypertrophy was observed in contrast to ductal atrophy. Nucleocapsid proteins and/or viral particles were detected in the SMG cells, mainly in the nuclear membrane-derived vesicles, confirming the nuclear role in the viral formation. The acinar cells showed intense TNF-α and IL-1β immunoexpression, and the EGF-EGFR signaling increased, together with Muc5b upregulation. This finding explains mucin hypersecretion and acinar hypertrophy, which compress the ducts. Dying MECs and actin reduction were also observed, indicating failure of contraction and acinar support, favoring acinar hypertrophy. Viral assembly was found in the dying telocytes, pointing to these intercommunicating cells as viral transmitters in SMGs. Therefore, EGF-EGFR-induced mucin hypersecretion was triggered by SARS-CoV-2 in acinar cells, likely mediated by cytokines. The damage to telocytes and MECs may have favored the acinar hypertrophy, leading to ductal obstruction, explaining xerostomia in COVID-19 patients. Thus, acinar cells, telocytes and MECs may be viral targets, which favor replication and cell-to-cell viral transmission in the SMG, corroborating the high viral load in saliva of infected individuals.
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Affiliation(s)
- Estela Sasso-Cerri
- Laboratory of Histology and Embryology, Department of Morphology, Genetics, Orthodontics and Pediatric Dentistry, Dental School–São Paulo State University (UNESP), Araraquara 14801-903, Brazil; (V.D.M.); (J.C.G.d.M.)
| | - Vitor Dallacqua Martinelli
- Laboratory of Histology and Embryology, Department of Morphology, Genetics, Orthodontics and Pediatric Dentistry, Dental School–São Paulo State University (UNESP), Araraquara 14801-903, Brazil; (V.D.M.); (J.C.G.d.M.)
| | - Salmo Azambuja de Oliveira
- Department of Morphology and Genetics, Federal University of São Paulo, São Paulo 04023-900, Brazil; (S.A.d.O.); (A.A.S.d.S.)
| | - André Acácio Souza da Silva
- Department of Morphology and Genetics, Federal University of São Paulo, São Paulo 04023-900, Brazil; (S.A.d.O.); (A.A.S.d.S.)
| | - Juliana Cerini Grassi de Moraes
- Laboratory of Histology and Embryology, Department of Morphology, Genetics, Orthodontics and Pediatric Dentistry, Dental School–São Paulo State University (UNESP), Araraquara 14801-903, Brazil; (V.D.M.); (J.C.G.d.M.)
| | - Paulo Sérgio Cerri
- Laboratory of Histology and Embryology, Department of Morphology, Genetics, Orthodontics and Pediatric Dentistry, Dental School–São Paulo State University (UNESP), Araraquara 14801-903, Brazil; (V.D.M.); (J.C.G.d.M.)
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8
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Tomassetti S, Ciani L, Luzzi V, Gori L, Trigiani M, Giuntoli L, Lavorini F, Poletti V, Ravaglia C, Torrego A, Maldonado F, Lentz R, Annunziato F, Maggi L, Rossolini GM, Pollini S, Para O, Ciurleo G, Casini A, Rasero L, Bartoloni A, Spinicci M, Munavvar M, Gasparini S, Comin C, Cerinic MM, Peired A, Henket M, Ernst B, Louis R, Corhay JL, Nardi C, Guiot J. Utility of bronchoalveolar lavage for COVID-19: a perspective from the Dragon consortium. Front Med (Lausanne) 2024; 11:1259570. [PMID: 38371516 PMCID: PMC10869531 DOI: 10.3389/fmed.2024.1259570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 01/09/2024] [Indexed: 02/20/2024] Open
Abstract
Diagnosing COVID-19 and treating its complications remains a challenge. This review reflects the perspective of some of the Dragon (IMI 2-call 21, #101005122) research consortium collaborators on the utility of bronchoalveolar lavage (BAL) in COVID-19. BAL has been proposed as a potentially useful diagnostic tool to increase COVID-19 diagnosis sensitivity. In both critically ill and non-critically ill COVID-19 patients, BAL has a relevant role in detecting other infections or supporting alternative diagnoses and can change management decisions in up to two-thirds of patients. BAL is used to guide steroid and immunosuppressive treatment and to narrow or discontinue antibiotic treatment, reducing the use of unnecessary broad antibiotics. Moreover, cellular analysis and novel multi-omics techniques on BAL are of critical importance for understanding the microenvironment and interaction between epithelial cells and immunity, revealing novel potential prognostic and therapeutic targets. The BAL technique has been described as safe for both patients and healthcare workers in more than a thousand procedures reported to date in the literature. Based on these preliminary studies, we recognize that BAL is a feasible procedure in COVID-19 known or suspected cases, useful to properly guide patient management, and has great potential for research.
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Affiliation(s)
- Sara Tomassetti
- Interventional Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Luca Ciani
- Interventional Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Valentina Luzzi
- Interventional Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Leonardo Gori
- Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Marco Trigiani
- Interventional Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Leonardo Giuntoli
- Interventional Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Federico Lavorini
- Pulmonology Unit, Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - Venerino Poletti
- Department of Diseases of the Thorax, GB Morgagni Hospital, Forlì, Italy
| | - Claudia Ravaglia
- Department of Diseases of the Thorax, GB Morgagni Hospital, Forlì, Italy
| | - Alfons Torrego
- Respiratory Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Fabien Maldonado
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Robert Lentz
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Simona Pollini
- Department of Experimental Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Ombretta Para
- Internal Medicine Unit 1, AOU Careggi, Florence, Italy
| | - Greta Ciurleo
- Internal Medicine Unit 2, AOU Careggi, Florence, Italy
| | | | - Laura Rasero
- Department of Health Science, Clinical Innovations and Research Unit, Careggi University Hospital, Florence, Italy
| | - Alessandro Bartoloni
- Infectious and Tropical Diseases Unit, Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Michele Spinicci
- Infectious and Tropical Diseases Unit, Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Mohammed Munavvar
- School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
- Department of Respiratory, Lancashire Teaching Hospital NHS Foundation Trust, Preston, United Kingdom
| | - Stefano Gasparini
- Interventional Pulmonology Unit, University Hospital Riuniti di Ancona, Ancona, Italy
| | - Camilla Comin
- Department of Experimental and Clinical Medicine Section of Surgery, Histopathology, and Molecular Pathology, University of Florence, Florence, Italy
| | - Marco Matucci Cerinic
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Anna Peired
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
| | - Monique Henket
- Department of Respiratory Medicine, Universitary Hospital of Liège, Liège, Belgium
| | - Benoit Ernst
- Department of Respiratory Medicine, Universitary Hospital of Liège, Liège, Belgium
| | - Renaud Louis
- Department of Respiratory Medicine, Universitary Hospital of Liège, Liège, Belgium
| | - Jean-louis Corhay
- Department of Respiratory Medicine, Universitary Hospital of Liège, Liège, Belgium
| | - Cosimo Nardi
- Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit n. 2, University of Florence, Florence, Italy
| | - Julien Guiot
- Department of Respiratory Medicine, Universitary Hospital of Liège, Liège, Belgium
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9
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Chang YY, Wei AC. Transcriptome and machine learning analysis of the impact of COVID-19 on mitochondria and multiorgan damage. PLoS One 2024; 19:e0297664. [PMID: 38295140 PMCID: PMC10830027 DOI: 10.1371/journal.pone.0297664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
The effects of coronavirus disease 2019 (COVID-19) primarily concern the respiratory tract and lungs; however, studies have shown that all organs are susceptible to infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 may involve multiorgan damage from direct viral invasion through angiotensin-converting enzyme 2 (ACE2), through inflammatory cytokine storms, or through other secondary pathways. This study involved the analysis of publicly accessible transcriptome data from the Gene Expression Omnibus (GEO) database for identifying significant differentially expressed genes related to COVID-19 and an investigation relating to the pathways associated with mitochondrial, cardiac, hepatic, and renal toxicity in COVID-19. Significant differentially expressed genes were identified and ranked by statistical approaches, and the genes derived by biological meaning were ranked by feature importance; both were utilized as machine learning features for verification. Sample set selection for machine learning was based on the performance, sample size, imbalanced data state, and overfitting assessment. Machine learning served as a verification tool by facilitating the testing of biological hypotheses by incorporating gene list adjustment. A subsequent in-depth study for gene and pathway network analysis was conducted to explore whether COVID-19 is associated with cardiac, hepatic, and renal impairments via mitochondrial infection. The analysis showed that potential cardiac, hepatic, and renal impairments in COVID-19 are associated with ACE2, inflammatory cytokine storms, and mitochondrial pathways, suggesting potential medical interventions for COVID-19-induced multiorgan damage.
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Affiliation(s)
- Yu-Yu Chang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - An-Chi Wei
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
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10
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Bankoti K, Wang W, Amonkar GM, Xiong L, Shui JE, Zhao C, Van E, Mwase C, Park JA, Mou H, Fang Y, Que J, Bai Y, Lerou PH, Ai X. Airway Basal Stem Cells in COVID-19 Exhibit a Proinflammatory Signature and Impaired Mucocililary Differentiation. Am J Respir Cell Mol Biol 2024; 70:26-38. [PMID: 37699145 PMCID: PMC10768838 DOI: 10.1165/rcmb.2023-0104oc] [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: 03/20/2023] [Accepted: 09/12/2023] [Indexed: 09/14/2023] Open
Abstract
Airway basal stem cells (BSCs) play a critical role in epithelial regeneration. Whether coronavirus disease (COVID-19) affects BSC function is unknown. Here, we derived BSC lines from patients with COVID-19 using tracheal aspirates (TAs) to circumvent the biosafety concerns of live-cell derivation. We show that BSCs derived from the TAs of control patients are bona fide bronchial BSCs. TA BSCs from patients with COVID-19 tested negative for severe acute respiratory syndrome coronavirus 2 RNA; however, these so-termed COVID-19-exposed BSCs in vitro resemble a predominant BSC subpopulation uniquely present in patients with COVID-19, manifested by a proinflammatory gene signature and STAT3 hyperactivation. Furthermore, the sustained STAT3 hyperactivation drives goblet cell differentiation of COVID-19-exposed BSCs in an air-liquid interface. Last, these phenotypes of COVID-19-exposed BSCs can be induced in control BSCs by cytokine cocktail pretreatment. Taken together, acute inflammation in COVID-19 exerts a long-term impact on mucociliary differentiation of BSCs.
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Affiliation(s)
- Kamakshi Bankoti
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Wei Wang
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gaurang M. Amonkar
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Linjie Xiong
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jessica E. Shui
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Caiqi Zhao
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric Van
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Chimwemwe Mwase
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Jin-Ah Park
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Hongmei Mou
- The Mucosal Immunology and Biology Research Center, Massachusetts General Hospital for Children, Boston, Massachusetts; and
| | - Yinshan Fang
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, New York
| | - Jianwen Que
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, New York
| | - Yan Bai
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Paul H. Lerou
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xingbin Ai
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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11
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Xiao SQ, Wen TZ, Chen XY, Chen HY, Li Z, He ZC, Luo T, Tang R, Fu WJ, Cao MF, Chen L, Niu Q, Wang S, Lan Y, Ge J, Li QR, Guo HT, Wang YX, Ping YF, Shen H, Wang Y, Ding YQ, Bian XW, Yao XH. Autopsy analysis reveals increased macrophage infiltration and cell apoptosis in COVID-19 patients with severe pulmonary fibrosis. Pathol Res Pract 2023; 252:154920. [PMID: 37948998 DOI: 10.1016/j.prp.2023.154920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Clinical data indicates that SARS-CoV-2 infection-induced respiratory failure is a fatal condition for severe COVID-19 patients. However, the pathological alterations of different types of respiratory failure remained unknown for severe COVID-19 patients. This study aims to evaluate whether there are differences in the performance of various types of respiratory failure in severe COVID-19 patients and investigate the pathological basis for these differences. The lung tissue sections of severe COVID-19 patients were assessed for the degree of injury and immune responses. Transcriptome data were used to analyze the molecular basis in severe COVID-19 patients. Severe COVID-19 patients with combined oxygenation and ventilatory failure presented more severe pulmonary fibrosis, airway obstruction, and prolonged disease course. The number of M2 macrophages increased with the degree of fibrosis in patients, suggesting that it may be closely related to the development of pulmonary fibrosis. The co-existence of pro-inflammatory and anti-inflammatory cytokines in the pulmonary environment could also participate in the progression of pulmonary fibrosis. Furthermore, the increased apoptosis in the lungs of COVID-19 patients with severe pulmonary fibrosis may represent a critical factor linking sustained inflammatory responses to fibrosis. Our findings indicate that during the extended phase of COVID-19, antifibrotic and antiapoptotic treatments should be considered in conjunction with the progression of the disease.
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Affiliation(s)
- Shi-Qi Xiao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Tian-Zi Wen
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Xin-Yu Chen
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - He-Yuan Chen
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Zhuang Li
- Department of Neurology, Armed Corps Police Hospital of Chongqing, Chongqing, China
| | - Zhi-Cheng He
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Tao Luo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Rui Tang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Wen-Juan Fu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Mian-Fu Cao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Lu Chen
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Qin Niu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Shuai Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Yang Lan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Jia Ge
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Qing-Rui Li
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Hai-Tao Guo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Yan-Xia Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Yi-Fang Ping
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Hong Shen
- Department of Pathology, Southern Medical University, Guangzhou, China
| | - Yan Wang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Yan-Qing Ding
- Department of Pathology, Southern Medical University, Guangzhou, China
| | - Xiu-Wu Bian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Xiao-Hong Yao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China.
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12
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Karmaus PWF, Tata A, Meacham JM, Day F, Thrower D, Tata PR, Fessler MB. Meta-Analysis of COVID-19 BAL Single-Cell RNA Sequencing Reveals Alveolar Epithelial Transitions and Unique Alveolar Epithelial Cell Fates. Am J Respir Cell Mol Biol 2023; 69:623-637. [PMID: 37523502 DOI: 10.1165/rcmb.2023-0077oc] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/31/2023] [Indexed: 08/02/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) of BAL cells has provided insights into coronavirus disease (COVID-19). However, reports have been limited by small patient cohorts. We performed a meta-analysis of BAL scRNA-seq data from healthy control subjects (n = 13) and patients with COVID-19 (n = 20), sourced from six independent studies (167,280 high-quality cells in total). Consistent with the source reports, increases in infiltrating leukocyte subtypes were noted, several with type I IFN signatures and unique gene expression signatures associated with transcellular chemokine signaling. Noting dramatic reductions of inferred NKX2-1 and NR4A1 activity in alveolar epithelial type II (AT-II) cells, we modeled pseudotemporal AT-II-to-AT-I progression. This revealed changes in inferred AT-II cell metabolic activity, increased transitional cells, and a previously undescribed AT-I state. This cell state was conspicuously marked by the induction of genes of the epidermal differentiation complex, including the cornified envelope protein SPRR3 (small proline-rich protein 3), upregulation of multiple KRT (keratin) genes, inferred mitochondrial dysfunction, and cell death signatures including apoptosis and ferroptosis. Immunohistochemistry of lungs from patients with COVID-19 confirmed upregulation and colocalization of KRT13 and SPRR3 in the distal airspaces. Forced overexpression of SPRR3 in human alveolar epithelial cells ex vivo did not activate caspase-3 or upregulate KRT13, suggesting that SPRR3 marks an AT-I cornification program in COVID-19 but is not sufficient for phenotypic changes.
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Affiliation(s)
| | - Aleksandra Tata
- Department of Cell Biology, School of Medicine, Duke University, Durham, North Carolina
| | | | - Frank Day
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; and
| | - David Thrower
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; and
| | - Purushothama Rao Tata
- Department of Cell Biology, School of Medicine, Duke University, Durham, North Carolina
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13
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Pi P, Zeng Z, Zeng L, Han B, Bai X, Xu S. Molecular mechanisms of COVID-19-induced pulmonary fibrosis and epithelial-mesenchymal transition. Front Pharmacol 2023; 14:1218059. [PMID: 37601070 PMCID: PMC10436482 DOI: 10.3389/fphar.2023.1218059] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/25/2023] [Indexed: 08/22/2023] Open
Abstract
As the outbreak of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first broke out in Hubei Province, China, at the end of 2019. It has brought great challenges and harms to global public health. SARS-CoV-2 mainly affects the lungs and is mainly manifested as pulmonary disease. However, one of the biggest crises arises from the emergence of COVID-19-induced fibrosis. At present, there are still many questions about how COVID-19 induced pulmonary fibrosis (PF) occurs and how to treat and regulate its long-term effects. In addition, as an important process of fibrosis, the effect of COVID-19 on epithelial-mesenchymal transition (EMT) may be an important factor driving PF. This review summarizes the main pathogenesis and treatment mechanisms of COVID-19 related to PF. Starting with the basic mechanisms of PF, such as EMT, transforming growth factor-β (TGF-β), fibroblasts and myofibroblasts, inflammation, macrophages, innate lymphoid cells, matrix metalloproteinases and tissue inhibitors of metalloproteinases, hedgehog pathway as well as Notch signaling. Further, we highlight the importance of COVID-19-induced EMT in the process of PF and provide an overview of the related molecular mechanisms, which will facilitate future research to propose new clinical therapeutic solutions for the treatment of COVID-19-induced PF.
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Affiliation(s)
- Peng Pi
- School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, China
| | - Zhipeng Zeng
- School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, China
| | - Liqing Zeng
- School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, China
| | - Bing Han
- School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, China
| | - Xizhe Bai
- College of Physical Education and Health, East China Normal University, Shanghai, China
| | - Shousheng Xu
- School of Sports Engineering, Beijing Sport University, Beijing, China
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14
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Chatterjee M, Huang LZX, Mykytyn AZ, Wang C, Lamers MM, Westendorp B, Wubbolts RW, van Putten JPM, Bosch BJ, Haagmans BL, Strijbis K. Glycosylated extracellular mucin domains protect against SARS-CoV-2 infection at the respiratory surface. PLoS Pathog 2023; 19:e1011571. [PMID: 37561789 PMCID: PMC10464970 DOI: 10.1371/journal.ppat.1011571] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/29/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Mucins play an essential role in protecting the respiratory tract against microbial infections while also acting as binding sites for bacterial and viral adhesins. The heavily O-glycosylated gel-forming mucins MUC5AC and MUC5B eliminate pathogens by mucociliary clearance. Transmembrane mucins MUC1, MUC4, and MUC16 can restrict microbial invasion at the apical surface of the epithelium. In this study, we determined the impact of host mucins and mucin glycans on epithelial entry of SARS-CoV-2. Human lung epithelial Calu-3 cells express the SARS-CoV-2 entry receptor ACE2 and high levels of glycosylated MUC1, but not MUC4 and MUC16, on their cell surface. The O-glycan-specific mucinase StcE specifically removed the glycosylated part of the MUC1 extracellular domain while leaving the underlying SEA domain and cytoplasmic tail intact. StcE treatment of Calu-3 cells significantly enhanced infection with SARS-CoV-2 pseudovirus and authentic virus, while removal of terminal mucin glycans sialic acid and fucose from the epithelial surface did not impact viral entry. In Calu-3 cells, the transmembrane mucin MUC1 and ACE2 are located to the apical surface in close proximity and StcE treatment results in enhanced binding of purified spike protein. Both MUC1 and MUC16 are expressed on the surface of human organoid-derived air-liquid interface (ALI) differentiated airway cultures and StcE treatment led to mucin removal and increased levels of SARS-CoV-2 replication. In these cultures, MUC1 was highly expressed in non-ciliated cells while MUC16 was enriched in goblet cells. In conclusion, the glycosylated extracellular domains of different transmembrane mucins might have similar protective functions in different respiratory cell types by restricting SARS-CoV-2 binding and entry.
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Affiliation(s)
- Maitrayee Chatterjee
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Liane Z. X. Huang
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Anna Z. Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Chunyan Wang
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Mart M. Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart Westendorp
- Department of Biomolecular Health Sciences, Division Cell Biology, Metabolism and Cancer, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Jos P. M. van Putten
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Berend-Jan Bosch
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Bart L. Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Karin Strijbis
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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15
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Parimon T, Espindola M, Marchevsky A, Rampolla R, Chen P, Hogaboam CM. Potential mechanisms for lung fibrosis associated with COVID-19 infection. QJM 2023; 116:487-492. [PMID: 36018274 PMCID: PMC10382189 DOI: 10.1093/qjmed/hcac206] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Indexed: 11/13/2022] Open
Abstract
Pulmonary fibrosis is a sequelae of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection that currently lacks effective preventative or therapeutic measures. Post-viral lung fibrosis due to SARS-CoV-2 has been shown to be progressive on selected patients using imaging studies. Persistent infiltration of macrophages and monocytes, a main feature of SARS-CoV-2 pulmonary fibrosis, and long-lived circulating inflammatory monocytes might be driving factors promoting the profibrotic milieu in the lung. The upstream signal(s) that regulates the presence of these immune cells (despite complete viral clearance) remains to be explored. Current data indicate that much of the stimulating signals are localized in the lungs. However, an ongoing low-grade systemic inflammation in long Coronavirus Disease 2019 (COVID-19) symptoms suggests that certain non-pulmonary regulators such as epigenetic changes in hematopoietic stem cells might be critical to the chronic inflammatory response. Since nearly one-third of the world population have been infected, a timely understanding of the underlying pathogenesis leading to tissue remodeling is required. Herein, we review the potential pathogenic mechanisms driving lung fibrosis following SARS-CoV-2 infection based upon available studies and our preliminary findings (Graphical abstract).
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Affiliation(s)
- T Parimon
- From the Cedars-Sinai Medical Center, Women’s Guild Lung Institute, 127 San Vicente Blvd, Los Angeles, CA 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical, Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - M Espindola
- From the Cedars-Sinai Medical Center, Women’s Guild Lung Institute, 127 San Vicente Blvd, Los Angeles, CA 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical, Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - A Marchevsky
- Pathology Department, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - R Rampolla
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical, Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - P Chen
- From the Cedars-Sinai Medical Center, Women’s Guild Lung Institute, 127 San Vicente Blvd, Los Angeles, CA 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical, Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - C M Hogaboam
- From the Cedars-Sinai Medical Center, Women’s Guild Lung Institute, 127 San Vicente Blvd, Los Angeles, CA 90048, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical, Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
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16
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Udomsinprasert W, Nontawong N, Saengsiwaritt W, Panthan B, Jiaranai P, Thongchompoo N, Santon S, Runcharoen C, Sensorn I, Jittikoon J, Chaikledkaew U, Chantratita W. Host genetic polymorphisms involved in long-term symptoms of COVID-19. Emerg Microbes Infect 2023:2239952. [PMID: 37497655 PMCID: PMC10392286 DOI: 10.1080/22221751.2023.2239952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Host genetic polymorphisms are recognized as a critical determinant of diversity in clinical symptoms of Coronavirus disease 2019 (COVID-19). Accordingly, this study aimed to determine possible associations between single nucleotide polymorphisms (SNPs) in 37 candidate genes and clinical consequences of COVID-19 - especially long-term symptoms, Long COVID. A total of 260 COVID-19 patients, divided into mild (n=239) and severe (n=21) and further categorized based on the presence of Long COVID (no, n=211; yes, n=49), were recruited. Genotyping of selected polymorphisms in 37 genes responsible for viral entry, immune response, and inflammation was performed using MassARRAY system. Out of 37 SNPs, 9 including leucine zipper transcription factor like-1 (LZTFL1) rs10490770 C allele, LZTFL1 rs11385942 dupA allele, nicotinamide adenine dinucleotide synthetase-1 (NADSYN1) rs12785878 TT genotype, plexin A-4 (PLXNA4) rs1424597 AA genotype, LZTFL1 rs17713054 A allele, interleukin-10 (IL10) rs1800896 TC genotype and C allele, angiotensin converting enzyme-2 (ACE2) rs2285666 T allele, and plasmanylethanolamine desaturase-1 (PEDS1) rs6020298 GG genotype and G allele were significantly associated with an increased risk of developing Long COVID, whereas interleukin-10 receptor subunit beta (IL10RB) rs8178562 GG genotype was significantly associated with a reduced risk of Long COVID. Kaplan-Meier curve displayed that polymorphisms in the above genes were significantly associated with cumulative rate of Long COVID occurrence. Polymorphisms in LZTFL1 rs10490770, LZTFL1 rs11385942, LZTFL1 rs17713054, NADSYN1 rs12785878, PLXNA4 rs1424597, IL10 rs1800896, ACE2 rs2285666, PEDS1 rs6020298, and IL10RB rs8178562 appear to be genetic factors involved in development of Long COVID.
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Affiliation(s)
- Wanvisa Udomsinprasert
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | | | | | - Bhakbhoom Panthan
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Poramate Jiaranai
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Nartthawee Thongchompoo
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Siwalee Santon
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Chakkaphan Runcharoen
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Insee Sensorn
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Jiraphun Jittikoon
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Usa Chaikledkaew
- Social and Administrative Pharmacy Division, Department of Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Mahidol University Health Technology Assessment (MUHTA) Graduate Program, Mahidol University, Bangkok 10400, Thailand
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
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17
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Sahin ME, Gökçek A, Satar S, Ergün P. Relation of impulse oscillometry and spirometry with quantitative thorax computed tomography after COVID-19 pneumonia. REVISTA DA ASSOCIACAO MEDICA BRASILEIRA (1992) 2023; 69:e20221427. [PMID: 37222321 DOI: 10.1590/1806-9282.20221427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/23/2023] [Indexed: 05/25/2023]
Abstract
OBJECTIVE This study aimed to investigate if there is any correlation between the quantitative computed tomography and the impulse oscillometry or spirometry results of post-COVID-19 patients. METHODS The study comprised 47 post-COVID-19 patients who had spirometry, impulse oscillometry, and high-resolution computed tomography examinations at the same time. The study group consisted of 33 patients with quantitative computed tomography involvement, while the control group included 14 patients who did not have CT findings. The quantitative computed tomography technology was used to calculate percentages of density range volumes. The relationship between percentages of density range volumes for different quantitative computed tomography density ranges and impulse oscillometry-spirometry findings was statistically analyzed. RESULTS In quantitative computed tomography, the percentage of relatively high-density lung parenchyma, including fibrotic areas, was 1.76±0.43 and 5.65±3.73 in the control and study groups, respectively. The percentages of primarily ground-glass parenchyma areas were found to be 7.60±2.86 and 29.25±16.50 in the control and study groups, respectively. In the correlation analysis, the forced vital capacity% predicted in the study group was correlated with DRV%[(-750)-(-500)] (volume of the lung parenchyma that has density between (-750)-(-500) Hounsfield units), but no correlation with DRV%[(-500)-0] was detected. Also, reactance area and resonant frequency were correlated with DRV%[(-750)-(-500)], while X5 was correlated with both DRV%[(-500)-0] and DRV%[(-750)-(-500)] density. Modified Medical Research Council score was correlated with predicted percentages of forced vital capacity and X5. CONCLUSION After COVID-19, forced vital capacity, reactance area, resonant frequency, and X5 correlated with the percentages of density range volumes of ground-glass opacity areas in the quantitative computed tomography. X5 was the only parameter correlated with density ranges consistent with both ground-glass opacity and fibrosis. Furthermore, the percentages of forced vital capacity and X5 were shown to be associated with the perception of dyspnea.
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Affiliation(s)
- Mustafa Engin Sahin
- University of Health Sciences, Ankara Atatürk Sanatoryum Training and Research Hospital - Ankara, Turkey
| | - Atila Gökçek
- University of Health Sciences, Ankara Atatürk Sanatoryum Training and Research Hospital - Ankara, Turkey
| | - Seher Satar
- University of Health Sciences, Ankara Atatürk Sanatoryum Training and Research Hospital - Ankara, Turkey
| | - Pınar Ergün
- University of Health Sciences, Ankara Atatürk Sanatoryum Training and Research Hospital - Ankara, Turkey
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18
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Qin S, Yao X, Li W, Wang C, Xu W, Gan Z, Yang Y, Zhong A, Wang B, He Z, Wu J, Wu Q, Jiang W, Han Y, Wang F, Wang Z, Ke Y, Zhao J, Gao J, Qu L, Jin P, Guan M, Xia X, Bian X. Novel insight into the underlying dysregulation mechanisms of immune cell-to-cell communication by analyzing multitissue single-cell atlas of two COVID-19 patients. Cell Death Dis 2023; 14:286. [PMID: 37087411 PMCID: PMC10122452 DOI: 10.1038/s41419-023-05814-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/28/2023] [Accepted: 04/14/2023] [Indexed: 04/24/2023]
Abstract
How does SARS-CoV-2 cause lung microenvironment disturbance and inflammatory storm is still obscure. We here performed the single-cell transcriptome sequencing from lung, blood, and bone marrow of two dead COVID-19 patients and detected the cellular communication among them. Our results demonstrated that SARS-CoV-2 infection increase the frequency of cellular communication between alveolar type I cells (AT1) or alveolar type II cells (AT2) and myeloid cells triggering immune activation and inflammation microenvironment and then induce the disorder of fibroblasts, club, and ciliated cells, which may cause increased pulmonary fibrosis and mucus accumulation. Further study showed that the increase of T cells in the lungs may be mainly recruited by myeloid cells through ligands/receptors (e.g., ANXA1/FPR1, C5AR1/RPS19, and CCL5/CCR1). Interestingly, we also found that certain ligands/receptors (e.g., ANXA1/FPR1, CD74/COPA, CXCLs/CXCRs, ALOX5/ALOX5AP, CCL5/CCR1) are significantly activated and shared among lungs, blood and bone marrow of COVID-19 patients, implying that the dysregulation of ligands/receptors may lead to immune cell's activation, migration, and the inflammatory storm in different tissues of COVID-19 patients. Collectively, our study revealed a possible mechanism by which the disorder of cell communication caused by SARS-CoV-2 infection results in the lung inflammatory microenvironment and systemic immune responses across tissues in COVID-19 patients.
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Affiliation(s)
- Shijie Qin
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
- Laboratory for Comparative Genomics and Bioinformatics, College of Life Science, Nanjing Normal University, 210046, Nanjing, Jiangsu, China
| | - Xiaohong Yao
- Institute of Pathology, Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
| | - Weiwei Li
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Canbiao Wang
- Laboratory for Comparative Genomics and Bioinformatics, College of Life Science, Nanjing Normal University, 210046, Nanjing, Jiangsu, China
| | - Weijun Xu
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
- Department of Gastroenterology, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Zhenhua Gan
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
| | - Yang Yang
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Aifang Zhong
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
- Medical Technical Support Division, the 904th Hospital, 213003, Changzhou, Jiangsu, China
| | - Bin Wang
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
- Department of Gastroenterology, Daping Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Zhicheng He
- Institute of Pathology, Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
| | - Jian Wu
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Qiuyue Wu
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Weijun Jiang
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Ying Han
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Fan Wang
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Zhihua Wang
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
- Department of Laboratory Medicine and Blood Transfusion, the 907th Hospital, 350702, Nanping, Fujian, China
| | - Yuehua Ke
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
- Chinese PLA Center for Disease Control and Prevention, 100070, Beijing, China
| | - Jun Zhao
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Junyin Gao
- Pulmonary and Critical Care Medicine, Yancheng No.1 People's Hospital, 224000, Yancheng, Jiangsu, China
| | - Liang Qu
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
- Department of Laboratory Medicine, 920 Hospital of the Joint Service Support Force of the Chinese People's Liberation Army, 650032, Kunming, Yunnan, China
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics, College of Life Science, Nanjing Normal University, 210046, Nanjing, Jiangsu, China
| | - Miao Guan
- Laboratory for Comparative Genomics and Bioinformatics, College of Life Science, Nanjing Normal University, 210046, Nanjing, Jiangsu, China.
| | - Xinyi Xia
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China.
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China.
| | - Xiuwu Bian
- Institute of Pathology, Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China.
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China.
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19
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Buckley PR, Lee CH, Antanaviciute A, Simmons A, Koohy H. A systems approach evaluating the impact of SARS-CoV-2 variant of concern mutations on CD8+ T cell responses. IMMUNOTHERAPY ADVANCES 2023; 3:ltad005. [PMID: 37082106 PMCID: PMC10112682 DOI: 10.1093/immadv/ltad005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/02/2023] [Indexed: 03/17/2023] Open
Abstract
T cell recognition of SARS-CoV-2 antigens after vaccination and/or natural infection has played a central role in resolving SARS-CoV-2 infections and generating adaptive immune memory. However, the clinical impact of SARS-CoV-2-specific T cell responses is variable and the mechanisms underlying T cell interaction with target antigens are not fully understood. This is especially true given the virus' rapid evolution, which leads to new variants with immune escape capacity. In this study, we used the Omicron variant as a model organism and took a systems approach to evaluate the impact of mutations on CD8+ T cell immunogenicity. We computed an immunogenicity potential score for each SARS-CoV-2 peptide antigen from the ancestral strain and Omicron, capturing both antigen presentation and T cell recognition probabilities. By comparing ancestral vs. Omicron immunogenicity scores, we reveal a divergent and heterogeneous landscape of impact for CD8+ T cell recognition of mutated targets in Omicron variants. While T cell recognition of Omicron peptides is broadly preserved, we observed mutated peptides with deteriorated immunogenicity that may assist breakthrough infection in some individuals. We then combined our scoring scheme with an in silico mutagenesis, to characterise the position- and residue-specific theoretical mutational impact on immunogenicity. While we predict many escape trajectories from the theoretical landscape of substitutions, our study suggests that Omicron mutations in T cell epitopes did not develop under cell-mediated pressure. Our study provides a generalisable platform for fostering a deeper understanding of existing and novel variant impact on antigen-specific vaccine- and/or infection-induced T cell immunity.
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Affiliation(s)
- Paul R Buckley
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Chloe H Lee
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Agne Antanaviciute
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Alison Simmons
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Hashem Koohy
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Alan Turing Fellow in Health and Medicine
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20
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Barnett KC, Xie Y, Asakura T, Song D, Liang K, Taft-Benz SA, Guo H, Yang S, Okuda K, Gilmore RC, Loome JF, Oguin Iii TH, Sempowski GD, Randell SH, Heise MT, Lei YL, Boucher RC, Ting JPY. An epithelial-immune circuit amplifies inflammasome and IL-6 responses to SARS-CoV-2. Cell Host Microbe 2023; 31:243-259.e6. [PMID: 36563691 PMCID: PMC9731922 DOI: 10.1016/j.chom.2022.12.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/12/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
Elevated levels of cytokines IL-1β and IL-6 are associated with severe COVID-19. Investigating the underlying mechanisms, we find that while primary human airway epithelia (HAE) have functional inflammasomes and support SARS-CoV-2 replication, they are not the source of IL-1β released upon infection. In leukocytes, the SARS-CoV-2 E protein upregulates inflammasome gene transcription via TLR2 to prime, but not activate, inflammasomes. SARS-CoV-2-infected HAE supply a second signal, which includes genomic and mitochondrial DNA, to stimulate leukocyte IL-1β release. Nuclease treatment, STING, and caspase-1 inhibition but not NLRP3 inhibition blocked leukocyte IL-1β release. After release, IL-1β stimulates IL-6 secretion from HAE. Therefore, infection alone does not increase IL-1β secretion by either cell type. Rather, bi-directional interactions between the SARS-CoV-2-infected epithelium and immune bystanders stimulates both IL-1β and IL-6, creating a pro-inflammatory cytokine circuit. Consistent with these observations, patient autopsy lungs show elevated myeloid inflammasome gene signatures in severe COVID-19.
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Affiliation(s)
- Katherine C Barnett
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yuying Xie
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA; Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
| | - Takanori Asakura
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dingka Song
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kaixin Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Oral and Craniofacial Biomedicine Program, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sharon A Taft-Benz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Haitao Guo
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shuangshuang Yang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenichi Okuda
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rodney C Gilmore
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jennifer F Loome
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Scott H Randell
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
| | - Mark T Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yu Leo Lei
- Department of Periodontics and Oral Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48104, USA; Department of Otolaryngology-Head and Neck Surgery, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jenny P-Y Ting
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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21
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Li Q, Vijaykumar K, Phillips SE, Hussain SS, Huynh NV, Fernandez-Petty CM, Lever JEP, Foote JB, Ren J, Campos-Gómez J, Daya FA, Hubbs NW, Kim H, Onuoha E, Boitet ER, Fu L, Leung HM, Yu L, Detchemendy TW, Schaefers LT, Tipper JL, Edwards LJ, Leal SM, Harrod KS, Tearney GJ, Rowe SM. Mucociliary transport deficiency and disease progression in Syrian hamsters with SARS-CoV-2 infection. JCI Insight 2023; 8:e163962. [PMID: 36625345 PMCID: PMC9870055 DOI: 10.1172/jci.insight.163962] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/16/2022] [Indexed: 01/10/2023] Open
Abstract
Substantial clinical evidence supports the notion that ciliary function in the airways is important in COVID-19 pathogenesis. Although ciliary damage has been observed in both in vitro and in vivo models, the extent or nature of impairment of mucociliary transport (MCT) in in vivo models remains unknown. We hypothesize that SARS-CoV-2 infection results in MCT deficiency in the airways of golden Syrian hamsters that precedes pathological injury in lung parenchyma. Micro-optical coherence tomography was used to quantitate functional changes in the MCT apparatus. Both genomic and subgenomic viral RNA pathological and physiological changes were monitored in parallel. We show that SARS-CoV-2 infection caused a 67% decrease in MCT rate as early as 2 days postinfection (dpi) in hamsters, principally due to 79% diminished airway coverage of motile cilia. Correlating quantitation of physiological, virological, and pathological changes reveals steadily descending infection from the upper airways to lower airways to lung parenchyma within 7 dpi. Our results indicate that functional deficits of the MCT apparatus are a key aspect of COVID-19 pathogenesis, may extend viral retention, and could pose a risk factor for secondary infection. Clinically, monitoring abnormal ciliated cell function may indicate disease progression. Therapies directed toward the MCT apparatus deserve further investigation.
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Affiliation(s)
- Qian Li
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | | | - Scott E. Phillips
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | - Shah S. Hussain
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | | | | | | | | | | | | | - Farah Abou Daya
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | - Nathaniel W. Hubbs
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | - Harrison Kim
- Gregory Fleming James Cystic Fibrosis Research Center
- Department of Radiology, and
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ezinwanne Onuoha
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Evan R. Boitet
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | - Lianwu Fu
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
| | - Hui Min Leung
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Linhui Yu
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Levi T. Schaefers
- Department of Microbiology
- Department of Anesthesiology and Perioperative Medicine
| | | | | | - Sixto M. Leal
- Department of Microbiology
- Department of Anesthesiology and Perioperative Medicine
| | | | - Guillermo J. Tearney
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven M. Rowe
- Department of Medicine
- Gregory Fleming James Cystic Fibrosis Research Center
- Department of Pediatrics
- Department of Cell Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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22
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Yang Q, Tang J, Cao J, Liu F, Fu M, Xue B, Zhou A, Chen S, Liu J, Zhou Y, Shi Y, Peng W, Chen X. SARS-CoV-2 infection activates CREB/CBP in cellular cyclic AMP-dependent pathways. J Med Virol 2023; 95:e28383. [PMID: 36477795 PMCID: PMC9877775 DOI: 10.1002/jmv.28383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/15/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global coronavirus disease 2019 (COVID-19) pandemic that has affected the lives of billions of individuals. However, the host-virus interactions still need further investigation to reveal the underling mechanism of SARS-CoV-2 pathogenesis. Here, transcriptomics analysis of SARS-CoV-2 infection highlighted possible correlation between host-associated signaling pathway and virus. In detail, cAMP-protein kinase (PKA) pathway has an essential role in SARS-CoV-2 infection, followed by the interaction between cyclic AMP response element binding protein (CREB) and CREB-binding protein (CBP) could be induced and leading to the enhancement of CREB/CBP transcriptional activity. The replication of Delta and Omicron BA.5 were inhibited by about 49.4% and 44.7% after knockdown of CREB and CBP with small interfering RNAs, respectively. Furthermore, a small organic molecule naphthol AS-E (nAS-E), which targets on the interaction between CREB and CBP, potently inhibited SARS-CoV-2 wild-type (WT) infection with comparable the half-maximal effective concentration (EC50 ) 1.04 μM to Remdesivir 0.57 μM. Compared with WT virus, EC50 in Calu-3 cells against Delta, Omicron BA.2, and Omicron BA.5 were, on average, 1.5-fold, 1.1-fold, and 1.5-fold higher, respectively, nAS-E had a satisfied antiviral effect against Omicron variants. Taken together, our study demonstrated the importance of CREB/CBP induced by cAMP-PKA pathway during SARS-CoV-2 infection, and further provided a novel CREB/CBP interaction therapeutic drug targets for COVID-19.
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Affiliation(s)
- Qi Yang
- Chen Xinwen Lab in Department of Basic ResearchGuangzhou LaboratoryGuangzhouChina,Hepatitis Virus and Gene Therapy Lab, State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Jielin Tang
- Chen Xinwen Lab in Department of Basic ResearchGuangzhou LaboratoryGuangzhouChina,Hepatitis Virus and Gene Therapy Lab, State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina,Center for Infection & Immunity, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Juan Cao
- Hepatitis Virus and Gene Therapy Lab, State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Fengjiang Liu
- Chen Xinwen Lab in Department of Basic ResearchGuangzhou LaboratoryGuangzhouChina
| | - Muqing Fu
- Center for Infection & Immunity, Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina
| | - Bao Xue
- Chen Xinwen Lab in Department of Basic ResearchGuangzhou LaboratoryGuangzhouChina,Hepatitis Virus and Gene Therapy Lab, State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Anqi Zhou
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouChina
| | - Sijie Chen
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouChina
| | - Junjun Liu
- Chen Xinwen Lab in Department of Basic ResearchGuangzhou LaboratoryGuangzhouChina
| | - Yuan Zhou
- Chen Xinwen Lab in Department of Basic ResearchGuangzhou LaboratoryGuangzhouChina,Hepatitis Virus and Gene Therapy Lab, State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Yongxia Shi
- Guangzhou Customs District Technology CenterGuangzhouChina
| | - Wei Peng
- Chen Xinwen Lab in Department of Basic ResearchGuangzhou LaboratoryGuangzhouChina,Guangzhou Medical UniversityGuangzhouChina
| | - Xinwen Chen
- Chen Xinwen Lab in Department of Basic ResearchGuangzhou LaboratoryGuangzhouChina,Hepatitis Virus and Gene Therapy Lab, State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina,Guangzhou Medical UniversityGuangzhouChina
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23
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Kato T, Asakura T, Edwards CE, Dang H, Mikami Y, Okuda K, Chen G, Sun L, Gilmore RC, Hawkins P, De la Cruz G, Cooley MR, Bailey AB, Hewitt SM, Chertow DS, Borczuk AC, Salvatore S, Martinez FJ, Thorne LB, Askin FB, Ehre C, Randell SH, O’Neal WK, Baric RS, Boucher RC. Prevalence and Mechanisms of Mucus Accumulation in COVID-19 Lung Disease. Am J Respir Crit Care Med 2022; 206:1336-1352. [PMID: 35816430 PMCID: PMC9746856 DOI: 10.1164/rccm.202111-2606oc] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 07/06/2022] [Indexed: 01/27/2023] Open
Abstract
Rationale: The incidence and sites of mucus accumulation and molecular regulation of mucin gene expression in coronavirus (COVID-19) lung disease have not been reported. Objectives: To characterize the incidence of mucus accumulation and the mechanisms mediating mucin hypersecretion in COVID-19 lung disease. Methods: Airway mucus and mucins were evaluated in COVID-19 autopsy lungs by Alcian blue and periodic acid-Schiff staining, immunohistochemical staining, RNA in situ hybridization, and spatial transcriptional profiling. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected human bronchial epithelial (HBE) cultures were used to investigate mechanisms of SARS-CoV-2-induced mucin expression and synthesis and test candidate countermeasures. Measurements and Main Results: MUC5B and variably MUC5AC RNA concentrations were increased throughout all airway regions of COVID-19 autopsy lungs, notably in the subacute/chronic disease phase after SARS-CoV-2 clearance. In the distal lung, MUC5B-dominated mucus plugging was observed in 90% of subjects with COVID-19 in both morphologically identified bronchioles and microcysts, and MUC5B accumulated in damaged alveolar spaces. SARS-CoV-2-infected HBE cultures exhibited peak titers 3 days after inoculation, whereas induction of MUC5B/MUC5AC peaked 7-14 days after inoculation. SARS-CoV-2 infection of HBE cultures induced expression of epidermal growth factor receptor (EGFR) ligands and inflammatory cytokines (e.g., IL-1α/β) associated with mucin gene regulation. Inhibiting EGFR/IL-1R pathways or administration of dexamethasone reduced SARS-CoV-2-induced mucin expression. Conclusions: SARS-CoV-2 infection is associated with a high prevalence of distal airspace mucus accumulation and increased MUC5B expression in COVID-19 autopsy lungs. HBE culture studies identified roles for EGFR and IL-1R signaling in mucin gene regulation after SARS-CoV-2 infection. These data suggest that time-sensitive mucolytic agents, specific pathway inhibitors, or corticosteroid administration may be therapeutic for COVID-19 lung disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Daniel S. Chertow
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland; and
| | | | | | | | - Leigh B. Thorne
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Frederic B. Askin
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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24
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Ma Q, Ma W, Song TZ, Wu Z, Liu Z, Hu Z, Han JB, Xu L, Zeng B, Wang B, Sun Y, Yu DD, Wu Q, Yao YG, Zheng YT, Wang X. Single-nucleus transcriptomic profiling of multiple organs in a rhesus macaque model of SARS-CoV-2 infection. Zool Res 2022; 43:1041-1062. [PMID: 36349357 PMCID: PMC9700497 DOI: 10.24272/j.issn.2095-8137.2022.443] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/09/2022] Open
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes diverse clinical manifestations and tissue injuries in multiple organs. However, cellular and molecular understanding of SARS-CoV-2 infection-associated pathology and immune defense features in different organs remains incomplete. Here, we profiled approximately 77 000 single-nucleus transcriptomes of the lung, liver, kidney, and cerebral cortex in rhesus macaques ( Macaca mulatta) infected with SARS-CoV-2 and healthy controls. Integrated analysis of the multi-organ dataset suggested that the liver harbored the strongest global transcriptional alterations. We observed prominent impairment in lung epithelial cells, especially in AT2 and ciliated cells, and evident signs of fibrosis in fibroblasts. These lung injury characteristics are similar to those reported in patients with coronavirus disease 2019 (COVID-19). Furthermore, we found suppressed MHC class I/II molecular activity in the lung, inflammatory response in the liver, and activation of the kynurenine pathway, which induced the development of an immunosuppressive microenvironment. Analysis of the kidney dataset highlighted tropism of tubule cells to SARS-CoV-2, and we found membranous nephropathy (an autoimmune disease) caused by podocyte dysregulation. In addition, we identified the pathological states of astrocytes and oligodendrocytes in the cerebral cortex, providing molecular insights into COVID-19-related neurological implications. Overall, our multi-organ single-nucleus transcriptomic survey of SARS-CoV-2-infected rhesus macaques broadens our understanding of disease features and antiviral immune defects caused by SARS-CoV-2 infection, which may facilitate the development of therapeutic interventions for COVID-19.
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Affiliation(s)
- Qiang Ma
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenji Ma
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tian-Zhang Song
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Zhaobo Wu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zeyuan Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenxiang Hu
- LivzonBio, Inc., Zhuhai, Guangdong 519045, China
| | - Jian-Bao Han
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Ling Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Bo Zeng
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bosong Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
| | - Yinuo Sun
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dan-Dan Yu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China. E-mail:
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China. E-mail:
| | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
- Advanced Innovation Center for Human Brain Protection, Beijing Institute for Brain Disorders, Capital Medical University, Beijing 100069, China. E-mail:
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25
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Sage SE, Nicholson P, Peters LM, Leeb T, Jagannathan V, Gerber V. Single-cell gene expression analysis of cryopreserved equine bronchoalveolar cells. Front Immunol 2022; 13:929922. [PMID: 36105804 PMCID: PMC9467276 DOI: 10.3389/fimmu.2022.929922] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/08/2022] [Indexed: 12/21/2022] Open
Abstract
The transcriptomic profile of a cell population can now be studied at the cellular level using single-cell mRNA sequencing (scRNA-seq). This novel technique provides the unprecedented opportunity to explore the cellular composition of the bronchoalveolar lavage fluid (BALF) of the horse, a species for which cell type markers are poorly described. Here, scRNA-seq technology was applied to cryopreserved equine BALF cells. Analysis of 4,631 cells isolated from three asthmatic horses in remission identified 16 cell clusters belonging to six major cell types: monocytes/macrophages, T cells, B/plasma cells, dendritic cells, neutrophils and mast cells. Higher resolution analysis of the constituents of the major immune cell populations allowed deep annotation of monocytes/macrophages, T cells and B/plasma cells. A significantly higher lymphocyte/macrophage ratio was detected with scRNA-seq compared to conventional cytological differential cell count. For the first time in horses, we detected a transcriptomic signature consistent with monocyte-lymphocyte complexes. Our findings indicate that scRNA-seq technology is applicable to cryopreserved equine BALF cells, allowing the identification of its major (cytologically differentiated) populations as well as previously unexplored T cell and macrophage subpopulations. Single-cell gene expression analysis has the potential to facilitate understanding of the immunological mechanisms at play in respiratory disorders of the horse, such as equine asthma.
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Affiliation(s)
- Sophie E. Sage
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- *Correspondence: Sophie E. Sage,
| | - Pamela Nicholson
- Next Generation Sequencing Platform, University of Bern, Bern, Switzerland
| | - Laureen M. Peters
- Clinical Diagnostic Laboratory, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Next Generation Sequencing Platform, University of Bern, Bern, Switzerland
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vinzenz Gerber
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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26
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Vijaykumar K, Leung HM, Barrios A, Fernandez-Petty CM, Solomon GM, Hathorne HY, Wade JD, Monroe K, Slaten KB, Li Q, Leal SM, Moates DB, Pierce HM, Olson KR, Currier P, Foster S, Marsden D, Tearney GJ, Rowe SM. COVID-19 Causes Ciliary Dysfunction as Demonstrated by Human Intranasal Micro-Optical Coherence Tomography Imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.07.08.499336. [PMID: 35860227 PMCID: PMC9298131 DOI: 10.1101/2022.07.08.499336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-2), causative agent of coronavirus disease 2019 (COVID-19), binds via ACE2 receptors, highly expressed in ciliated cells of the nasal epithelium. Micro-optical coherence tomography (μOCT) is a minimally invasive intranasal imaging technique that can determine cellular and functional dynamics of respiratory epithelia at 1-μm resolution, enabling real time visualization and quantification of epithelial anatomy, ciliary motion, and mucus transport. We hypothesized that respiratory epithelial cell dysfunction in COVID-19 will manifest as reduced ciliated cell function and mucociliary abnormalities, features readily visualized by μOCT. Symptomatic outpatients with SARS-CoV-2 aged ≥ 18 years were recruited within 14 days of symptom onset. Data was interpreted for subjects with COVID-19 (n=13) in comparison to healthy controls (n=8). Significant reduction in functional cilia, diminished ciliary beat frequency, and abnormal ciliary activity were evident. Other abnormalities included denuded epithelium, presence of mucus rafts, and increased inflammatory cells. Our results indicate that subjects with mild but symptomatic COVID-19 exhibit functional abnormalities of the respiratory mucosa underscoring the importance of mucociliary health in viral illness and disease transmission. Ciliary imaging enables investigation of early pathogenic mechanisms of COVID-19 and may be useful for evaluating disease progression and therapeutic response. Graphical abstract
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27
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Zhao P, Zou J, Zhou F, Zhu Y, Song Q, Yu D, Li X. Immune features of COVID-19 convalescent individuals revealed by a single-cell RNA sequencing. Int Immunopharmacol 2022; 108:767. [PMID: 35453072 PMCID: PMC9013654 DOI: 10.1016/j.intimp.2022.108767] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/22/2022] [Accepted: 04/05/2022] [Indexed: 02/05/2023]
Abstract
It remains unclear whether immune responses following natural infection can be sustained or potentially prove critical for long-term immune protection against SARS-CoV-2 reinfection. Here, we systematically mapped the phenotypic landscape of SARS-CoV-2-specific immune responses in peripheral blood samples of convalescent patients with COVID-19 by single-cell RNA sequencing. The relative percentage of the CD8 + effector memory subset was increased in both convalescent moderate and severe cases, but NKT-CD160 and marginal zone B clusters were decreased. Innate immune responses were attenuated reflected by decreased expression of genes involved in interferon-gamma, leukocyte migration and neutrophil mediated immune response in convalescent COVID-19 patients. Functions of T cell were strengthened in convalescent COVID-19 patients by clear endorsement of increased expression of genes involved in biological processes of regulation of T cell activation, differentiation and cell-cell adhesion. In addition, T cell mediated immune responses were enhanced with remarkable clonal expansions of TCR and increased transition of CD4 + effector memory and CD8 + effector-GNLY in severe subjects. B cell immune responses displayed complicated and dualfunctions during convalescence of COVID-19, providing a novel mechanism that B cell activation was observed especially in moderate while humoral immune response was weakened. Interestingly, HLA class I genes displayed downregulation while HLA class II genes upregulation in both T and B cell subsets in convalescent individuals. Our results showed that innate immunity was declined but SARS-CoV-2-specific T cell responses were retained even strengthened whereas complicated and dualfunctions of B cells, including declined humoral immunity were presented at several months following infections.
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Affiliation(s)
- Pingsen Zhao
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
- Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025 China
| | - Jiahua Zou
- Cancer Center, Huanggang Hospital of Traditional Chinese Medicine, Huanggang 438000, China
| | - Fan Zhou
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025 China
| | - Yanyan Zhu
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan 512025 China
| | - Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Dongdong Yu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Xiangpan Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China
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28
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Ciurkiewicz M, Armando F, Schreiner T, de Buhr N, Pilchová V, Krupp-Buzimikic V, Gabriel G, von Köckritz-Blickwede M, Baumgärtner W, Schulz C, Gerhauser I. Ferrets are valuable models for SARS-CoV-2 research. Vet Pathol 2022; 59:661-672. [PMID: 35001763 PMCID: PMC9207987 DOI: 10.1177/03009858211071012] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulted in an ongoing pandemic with millions of deaths worldwide. Infection of humans can be asymptomatic or result in fever, fatigue, dry cough, dyspnea, and acute respiratory distress syndrome with multiorgan failure in severe cases. The pathogenesis of COVID-19 is not fully understood, and various models employing different species are currently applied. Ferrets can be infected with SARS-CoV-2 and efficiently transmit the virus to contact animals. In contrast to hamsters, ferrets usually show mild disease and viral replication restricted to the upper airways. Most reports have used the intranasal inoculation route, while the intratracheal infection model is not well characterized. Herein, we present clinical, virological, and pathological data from young ferrets intratracheally inoculated with SARS-CoV-2. Infected animals showed no significant clinical signs, and had transient infection with peak viral RNA loads at 4 days postinfection, mild to moderate rhinitis, and pulmonary endothelialitis/vasculitis. Viral antigen was exclusively found in the respiratory epithelium of the nasal cavity, indicating a particular tropism for cells in this location. Viral antigen was associated with epithelial damage and influx of inflammatory cells, including activated neutrophils releasing neutrophil extracellular traps. Scanning electron microscopy of the nasal respiratory mucosa revealed loss of cilia, shedding, and rupture of epithelial cells. The currently established ferret SARS-CoV-2 infection models are comparatively discussed with SARS-CoV-2 pathogenesis in mink, and the advantages and disadvantages of both species as research models for zoonotic betacoronaviruses are highlighted.
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Affiliation(s)
| | - Federico Armando
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Tom Schreiner
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Nicole de Buhr
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Veronika Pilchová
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Vanessa Krupp-Buzimikic
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Gülşah Gabriel
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | | | - Claudia Schulz
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Ingo Gerhauser
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
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Abstract
Coronavirus disease 2019 (COVID-19) is a worldwide pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has affected millions of lives. Individuals who survive severe COVID-19 can experience sustained respiratory symptoms that persist for months after initial infection. In other airway diseases, abnormal airway mucus contributes to sustained airway symptoms. However, the impact of SARS-CoV-2 on airway mucus has received limited attention. In the current review, we assess literature describing the impact of SARS-CoV-2 on airway pathophysiology with specific emphasis on mucus production. Accumulating evidence suggests that the 2 major secreted airway mucin glycoproteins, MUC5AC and MUC5B, are abnormal in some patients with COVID-19. Aberrations in MUC5AC or MUC5B in response to SARS-CoV-2 infection are likely due to inflammation, though the responsible mechanisms have yet to be determined. Thus, we also provide a proposed model highlighting mechanisms that can contribute to acute and sustained mucus abnormalities in SARS-CoV-2, with an emphasis on inflammatory cells and mediators, including mast cells and histamine. Last, we bring to light the challenges of studying abnormal mucus production in SARS-CoV-2 infections and discuss the strengths and limitations of model systems commonly used to study COVID-19. The evidence to date suggests that ferrets, nonhuman primates, and cats may have advantages over other models to investigate mucus in COVID-19.
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30
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He J, Lin L, Chen J. Practical bioinformatics pipelines for single-cell RNA-seq data analysis. BIOPHYSICS REPORTS 2022; 8:158-169. [PMID: 37288243 PMCID: PMC10189648 DOI: 10.52601/bpr.2022.210041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/01/2022] [Indexed: 11/05/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool to explore cells. With an increasing number of scRNA-seq data analysis tools that have been developed, it is challenging for users to choose and compare their performance. Here, we present an overview of the workflow for computational analysis of scRNA-seq data. We detail the steps of a typical scRNA-seq analysis, including experimental design, pre-processing and quality control, feature selection, dimensionality reduction, cell clustering and annotation, and downstream analysis including batch correction, trajectory inference and cell-cell communication. We provide guidelines according to our best practice. This review will be helpful for the experimentalists interested in analyzing their data, and will aid the users seeking to update their analysis pipelines.
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Affiliation(s)
- Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Lihui Lin
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiekai Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
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31
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Reay WR, Geaghan MP, Cairns MJ. The genetic architecture of pneumonia susceptibility implicates mucin biology and a relationship with psychiatric illness. Nat Commun 2022; 13:3756. [PMID: 35768473 PMCID: PMC9243103 DOI: 10.1038/s41467-022-31473-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/17/2022] [Indexed: 01/25/2023] Open
Abstract
Pneumonia remains one of the leading causes of death worldwide. In this study, we use genome-wide meta-analysis of lifetime pneumonia diagnosis (N = 391,044) to identify four association signals outside of the previously implicated major histocompatibility complex region. Integrative analyses and finemapping of these signals support clinically tractable targets, including the mucin MUC5AC and tumour necrosis factor receptor superfamily member TNFRSF1A. Moreover, we demonstrate widespread evidence of genetic overlap with pneumonia susceptibility across the human phenome, including particularly significant correlations with psychiatric phenotypes that remain significant after testing differing phenotype definitions for pneumonia or genetically conditioning on smoking behaviour. Finally, we show how polygenic risk could be utilised for precision treatment formulation or drug repurposing through pneumonia risk scores constructed using variants mapped to pathways with known drug targets. In summary, we provide insights into the genetic architecture of pneumonia susceptibility and genetics informed targets for drug development or repositioning.
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Affiliation(s)
- William R Reay
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Program, Hunter Medical Research Institute, Newcastle, NSW, 2305, Australia
| | - Michael P Geaghan
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Program, Hunter Medical Research Institute, Newcastle, NSW, 2305, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, 2308, Australia.
- Precision Medicine Program, Hunter Medical Research Institute, Newcastle, NSW, 2305, Australia.
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32
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Wang L, Liu C, Yang B, Zhang H, Jiao J, Zhang R, Liu S, Xiao S, Chen Y, Liu B, Ma Y, Duan X, Guo Y, Guo M, Wu B, Wang X, Huang X, Yang H, Gui Y, Fang M, Zhang L, Duo S, Guo X, Li W. SARS-CoV-2 ORF10 impairs cilia by enhancing CUL2ZYG11B activity. J Biophys Biochem Cytol 2022; 221:213272. [PMID: 35674692 PMCID: PMC9184850 DOI: 10.1083/jcb.202108015] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 03/02/2022] [Accepted: 04/27/2022] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causal pathogen of the ongoing global pandemic of coronavirus disease 2019 (COVID-19). Loss of smell and taste are symptoms of COVID-19, and may be related to cilia dysfunction. Here, we found that the SARS-CoV-2 ORF10 increases the overall E3 ligase activity of the CUL2ZYG11B complex by interacting with ZYG11B. Enhanced CUL2ZYG11B activity by ORF10 causes increased ubiquitination and subsequent proteasome-mediated degradation of an intraflagellar transport (IFT) complex B protein, IFT46, thereby impairing both cilia biogenesis and maintenance. Further, we show that exposure of the respiratory tract of hACE2 mice to SARS-CoV-2 or SARS-CoV-2 ORF10 alone results in cilia-dysfunction-related phenotypes, and the ORF10 expression in primary human nasal epithelial cells (HNECs) also caused a rapid loss of the ciliary layer. Our study demonstrates how SARS-CoV-2 ORF10 hijacks CUL2ZYG11B to eliminate IFT46 and leads to cilia dysfunction, thereby offering a powerful etiopathological explanation for how SARS-CoV-2 causes multiple cilia-dysfunction-related symptoms specific to COVID-19.
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Affiliation(s)
- Liying Wang
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China 1
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China 4
| | - Chao Liu
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China 1
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China 4
| | - Bo Yang
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China 5
| | - Haotian Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China 2
| | - Jian Jiao
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China 9
- Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China 10
| | - Ruidan Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China 4
| | - Shujun Liu
- Laboratory Animal Center, Institute of Zoology, Chinese Academy of Sciences, Beijing, China 3
| | - Sai Xiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China 4
| | - Yinghong Chen
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China 1
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China 4
| | - Bo Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China 4
| | - Yanjie Ma
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China 1
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China 4
| | - Xuefeng Duan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China 6
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China 2
| | - Mengmeng Guo
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China 1
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China 4
| | - Bingbing Wu
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China 1
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China 4
| | - Xiangdong Wang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China 9
- Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China 10
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China 8
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China 7
| | - Yaoting Gui
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China 5
| | - Min Fang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China 6
| | - Luo Zhang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China 9
- Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China 10
| | - Shuguang Duo
- Laboratory Animal Center, Institute of Zoology, Chinese Academy of Sciences, Beijing, China 3
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China 2
| | - Wei Li
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China 1
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Sciences, Beijing, China 4
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33
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Prasher P, Sharma M. Targeting mucin hypersecretion in COVID-19 therapy. Future Med Chem 2022; 14:681-684. [PMID: 35315705 PMCID: PMC8939459 DOI: 10.4155/fmc-2021-0111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 03/11/2022] [Indexed: 01/11/2023] Open
Affiliation(s)
- Parteek Prasher
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar, 143005, India
- Department of Chemistry, University of Petroleum & Energy Studies, Energy Acres, Dehradun, 248007, India
| | - Mousmee Sharma
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar, 143005, India
- Department of Chemistry, Uttaranchal University, Arcadia Grant, Dehradun, 248007, India
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34
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Buckley PR, Lee CH, Pereira Pinho M, Ottakandathil Babu R, Woo J, Antanaviciute A, Simmons A, Ogg G, Koohy H. HLA-dependent variation in SARS-CoV-2 CD8 + T cell cross-reactivity with human coronaviruses. Immunology 2022; 166:78-103. [PMID: 35143694 PMCID: PMC9111820 DOI: 10.1111/imm.13451] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/26/2021] [Accepted: 01/17/2022] [Indexed: 11/29/2022] Open
Abstract
The conditions and extent of cross-protective immunity between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and common-cold human coronaviruses (HCoVs) remain open despite several reports of pre-existing T cell immunity to SARS-CoV-2 in individuals without prior exposure. Using a pool of functionally evaluated SARS-CoV-2 peptides, we report a map of 126 immunogenic peptides with high similarity to 285 MHC-presented peptides from at least one HCoV. Employing this map of SARS-CoV-2-non-homologous and homologous immunogenic peptides, we observe several immunogenic peptides with high similarity to human proteins, some of which have been reported to have elevated expression in severe COVID-19 patients. After combining our map with SARS-CoV-2-specific TCR repertoire data from COVID-19 patients and healthy controls, we show that public repertoires for the majority of convalescent patients are dominated by TCRs cognate to non-homologous SARS-CoV-2 peptides. We find that for a subset of patients, >50% of their public SARS-CoV-2-specific repertoires consist of TCRs cognate to homologous SARS-CoV-2-HCoV peptides. Further analysis suggests that this skewed distribution of TCRs cognate to homologous or non-homologous peptides in COVID-19 patients is likely to be HLA-dependent. Finally, we provide 10 SARS-CoV-2 peptides with known cognate TCRs that are conserved across multiple coronaviruses and are predicted to be recognized by a high proportion of the global population. These findings may have important implications for COVID-19 heterogeneity, vaccine-induced immune responses, and robustness of immunity to SARS-CoV-2 and its variants.
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Affiliation(s)
- Paul R. Buckley
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Chloe H. Lee
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Mariana Pereira Pinho
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Rosana Ottakandathil Babu
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Jeongmin Woo
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Agne Antanaviciute
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Alison Simmons
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Graham Ogg
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Hashem Koohy
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
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35
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Multi-omics evaluation of SARS-CoV-2 infected mouse lungs reveals dynamics of host responses. iScience 2022; 25:103967. [PMID: 35224468 PMCID: PMC8863311 DOI: 10.1016/j.isci.2022.103967] [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: 10/09/2021] [Revised: 01/04/2022] [Accepted: 02/17/2022] [Indexed: 12/27/2022] Open
Abstract
The outbreak of Coronavirus disease 2019 (COVID-19) throughout the world has caused millions of death, while the dynamics of host responses and the underlying regulation mechanisms during SARS-CoV-2 infection are not well depicted. Lung tissues from a mouse model sensitized to SARS-CoV-2 infection were serially collected at different time points for evaluation of transcriptome, proteome, and phosphoproteome. We showed the ebb and flow of several host responses in the lung across the viral infection. The signaling pathways and kinases regulating networks were alternated at different phases of infection. This multiplex evaluation also revealed that many kinases of the CDK and MAPK family were interactive and served as functional hubs in mediating the signal transduction during SARS-CoV-2 infection. Our study not only revealed the dynamics of lung pathophysiology and their underlying molecular mechanisms during SARS-CoV-2 infection, but also highlighted some molecules and signaling pathways that might guide future investigations on COVID-19 therapies. Multi-omics analysis profiles temporal host responses in SARS-CoV-2 infected lungs Signaling pathways and kinase regulating networks are dynamically altered The CDK and MAPK family are interactive and involved in regulating host responses
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36
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Tiezzi M, Morra S, Seminerio J, Van Muylem A, Godefroid A, Law-Weng-Sam N, Van Praet A, Corbière V, Orte Cano C, Karimi S, Del Marmol V, Bondue B, Benjelloun M, Lavis P, Mascart F, van de Borne P, Cardozo AK. SP-D and CC-16 Pneumoproteins' Kinetics and Their Predictive Role During SARS-CoV-2 Infection. Front Med (Lausanne) 2022; 8:761299. [PMID: 35211479 PMCID: PMC8863171 DOI: 10.3389/fmed.2021.761299] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022] Open
Abstract
Background Surfactant protein D (SP-D) and pulmonary club cell protein 16 (CC-16) are called “pneumoproteins” and are involved in host defense against oxidative stress, inflammation, and viral outbreak. This study aimed to determine the predictive value of these pneumoproteins on the incidence of acute respiratory distress syndrome (ARDS) or death in patients with coronavirus disease-2019 (COVID-19). Methods This retrospective study included 87 patients admitted to an emergency department. Blood samples were collected on three time points (days 1, 5, and 14 from hospital admission). SP-D and CC-16 serum levels were determined, and univariate and multivariate analyses considering confounding variables (age, body mass index, tobacco use, dyspnea, hypertension, diabetes mellitus, neutrophil-to-lymphocyte ratio) were performed. Results Based on the multivariate analysis, SP-D level on D1 was positively and slightly correlated with subsequent development of ARDS, independent of body mass index, dyspnea, and diabetes mellitus. CC-16 level on D1 was modestly and positively correlated with fatal outcome. A rise in SP-D between D1 and D5 and D1 and D14 had a strong negative association with incidence of ARDS. These associations were independent of tobacco use and neutrophil-to-lymphocyte ratio. Conclusions Overall, our data reveal that increase in SP-D levels is a good prognostic factor for patients with COVID-19, and that initial CC-16 levels correlated with slightly higher risk of death. SP-D and CC-16 may prove useful to predict outcomes in patients with COVID-19.
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Affiliation(s)
- Margherita Tiezzi
- Department of Cardiology, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium.,Inflammation and Cell Death Signalling Group, Experimental Gastroenterology Laboratory and Endotools-Medical Faculty, ULB, Brussels, Belgium
| | - Sofia Morra
- Department of Cardiology, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium.,Institute for Translational Research in Cardiovascular and Respiratory Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Jimmy Seminerio
- Department of Cardiology, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Alain Van Muylem
- Department of Respiratory Medicine, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Audrey Godefroid
- Laboratory of Vaccinology and Mucosal Immunity, Université Libre de Bruxelles, Brussels, Belgium
| | - Noémie Law-Weng-Sam
- Laboratory of Vaccinology and Mucosal Immunity, Université Libre de Bruxelles, Brussels, Belgium
| | - Anne Van Praet
- Laboratory of Vaccinology and Mucosal Immunity, Université Libre de Bruxelles, Brussels, Belgium
| | - Véronique Corbière
- Laboratory of Vaccinology and Mucosal Immunity, Université Libre de Bruxelles, Brussels, Belgium
| | - Carmen Orte Cano
- Department of Dermatology, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Sina Karimi
- Department of Internal Medicine, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Véronique Del Marmol
- Department of Dermatology, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Benjamin Bondue
- Department of Respiratory Medicine, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Mariam Benjelloun
- Department of Cardiology, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium.,Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Philomène Lavis
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Françoise Mascart
- Laboratory of Vaccinology and Mucosal Immunity, Université Libre de Bruxelles, Brussels, Belgium.,Immunobiology Clinic, Erasme University Hospital, Université libre de Bruxelles, Brussels, Belgium
| | - Philippe van de Borne
- Department of Cardiology, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium.,Institute for Translational Research in Cardiovascular and Respiratory Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Alessandra K Cardozo
- Inflammation and Cell Death Signalling Group, Experimental Gastroenterology Laboratory and Endotools-Medical Faculty, ULB, Brussels, Belgium
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37
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Li Q, Vijaykumar K, Philips SE, Hussain SS, Huynh VN, Fernandez-Petty CM, Lever JEP, Foote JB, Ren J, Campos-Gómez J, Daya FA, Hubbs NW, Kim H, Onuoha E, Boitet ER, Fu L, Leung HM, Yu L, Detchemendy TW, Schaefers LT, Tipper JL, Edwards LJ, Leal SM, Harrod KS, Tearney GJ, Rowe SM. Mucociliary Transport Deficiency and Disease Progression in Syrian Hamsters with SARS-CoV-2 Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.16.476016. [PMID: 35075457 PMCID: PMC8786228 DOI: 10.1101/2022.01.16.476016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Substantial clinical evidence supports the notion that ciliary function in the airways plays an important role in COVID-19 pathogenesis. Although ciliary damage has been observed in both in vitro and in vivo models, consequent impaired mucociliary transport (MCT) remains unknown for the intact MCT apparatus from an in vivo model of disease. Using golden Syrian hamsters, a common animal model that recapitulates human COVID-19, we quantitatively followed the time course of physiological, virological, and pathological changes upon SARS-CoV-2 infection, as well as the deficiency of the MCT apparatus using micro-optical coherence tomography, a novel method to visualize and simultaneously quantitate multiple aspects of the functional microanatomy of intact airways. Corresponding to progressive weight loss up to 7 days post-infection (dpi), viral detection and histopathological analysis in both the trachea and lung revealed steadily descending infection from the upper airways, as the main target of viral invasion, to lower airways and parenchymal lung, which are likely injured through indirect mechanisms. SARS-CoV-2 infection caused a 67% decrease in MCT rate as early as 2 dpi, largely due to diminished motile ciliation coverage, but not airway surface liquid depth, periciliary liquid depth, or cilia beat frequency of residual motile cilia. Further analysis indicated that the fewer motile cilia combined with abnormal ciliary motion of residual cilia contributed to the delayed MCT. The time course of physiological, virological, and pathological progression suggest that functional deficits of the MCT apparatus predispose to COVID-19 pathogenesis by extending viral retention and may be a risk factor for secondary infection. As a consequence, therapies directed towards the MCT apparatus deserve further investigation as a treatment modality.
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Affiliation(s)
- Qian Li
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kadambari Vijaykumar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Scott E Philips
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Shah S Hussain
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Van N Huynh
- Department of Graduate Biomedical Sciences Program, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Courtney M Fernandez-Petty
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jacelyn E Peabody Lever
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jeremy B Foote
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Janna Ren
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Javier Campos-Gómez
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Farah Abou Daya
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Nathaniel W Hubbs
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Harrison Kim
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ezinwanne Onuoha
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Evan R Boitet
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Lianwu Fu
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Hui Min Leung
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Linhui Yu
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Thomas W Detchemendy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
- Departments of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Levi T Schaefers
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
- Departments of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jennifer L Tipper
- Departments of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Lloyd J Edwards
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Sixto M Leal
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
- Departments of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kevin S Harrod
- Departments of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Guillermo J Tearney
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Steven M Rowe
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, United States
- Departments of Cell Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
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38
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Walentek P. Signaling Control of Mucociliary Epithelia: Stem Cells, Cell Fates, and the Plasticity of Cell Identity in Development and Disease. Cells Tissues Organs 2022; 211:736-753. [PMID: 33902038 PMCID: PMC8546001 DOI: 10.1159/000514579] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/19/2021] [Indexed: 01/25/2023] Open
Abstract
Mucociliary epithelia are composed of multiciliated, secretory, and stem cells and line various organs in vertebrates such as the respiratory tract. By means of mucociliary clearance, those epithelia provide a first line of defense against inhaled particles and pathogens. Mucociliary clearance relies on the correct composition of cell types, that is, the proper balance of ciliated and secretory cells. A failure to generate and to maintain correct cell type composition and function results in impaired clearance and high risk to infections, such as in congenital diseases (e.g., ciliopathies) as well as in acquired diseases, including asthma, chronic obstructive pulmonary disease (COPD), and idiopathic pulmonary fibrosis (IPF). While it remains incompletely resolved how precisely cell types are specified and maintained in development and disease, many studies have revealed important mechanisms regarding the signaling control in mucociliary cell types in various species. Those studies not only provided insights into the signaling contribution to organ development and regeneration but also highlighted the remarkable plasticity of cell identity encountered in mucociliary maintenance, including frequent trans-differentiation events during homeostasis and specifically in disease. This review will summarize major findings and provide perspectives regarding the future of mucociliary research and the treatment of chronic airway diseases associated with tissue remodeling.
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Affiliation(s)
- Peter Walentek
- Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Freiburg, Germany.,CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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39
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Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection. Nat Genet 2022; 54:1078-1089. [PMID: 35879412 PMCID: PMC9355872 DOI: 10.1038/s41588-022-01131-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/10/2022] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a range of symptoms in infected individuals, from mild respiratory illness to acute respiratory distress syndrome. A systematic understanding of host factors influencing viral infection is critical to elucidate SARS-CoV-2-host interactions and the progression of Coronavirus disease 2019 (COVID-19). Here, we conducted genome-wide CRISPR knockout and activation screens in human lung epithelial cells with endogenous expression of the SARS-CoV-2 entry factors ACE2 and TMPRSS2. We uncovered proviral and antiviral factors across highly interconnected host pathways, including clathrin transport, inflammatory signaling, cell-cycle regulation, and transcriptional and epigenetic regulation. We further identified mucins, a family of high molecular weight glycoproteins, as a prominent viral restriction network that inhibits SARS-CoV-2 infection in vitro and in murine models. These mucins also inhibit infection of diverse respiratory viruses. This functional landscape of SARS-CoV-2 host factors provides a physiologically relevant starting point for new host-directed therapeutics and highlights airway mucins as a host defense mechanism.
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40
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Single-Cell Genomics: Enabling the Functional Elucidation of Infectious Diseases in Multi-Cell Genomes. Pathogens 2021; 10:pathogens10111467. [PMID: 34832622 PMCID: PMC8624509 DOI: 10.3390/pathogens10111467] [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: 06/14/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022] Open
Abstract
Since the time when detection of gene expression in single cells by microarrays to the Next Generation Sequencing (NGS) enabled Single Cell Genomics (SCG), it has played a pivotal role to understand and elucidate the functional role of cellular heterogeneity. Along this journey to becoming a key player in the capture of the individuality of cells, SCG overcame many milestones, including scale, speed, sensitivity and sample costs (4S). There have been many important experimental and computational innovations in the efficient analysis and interpretation of SCG data. The increasing role of AI in SCG data analysis has further enhanced its applicability in building models for clinical intervention. Furthermore, SCG has been instrumental in the delineation of the role of cellular heterogeneity in specific diseases, including cancer and infectious diseases. The understanding of the role of differential immune responses in driving coronavirus disease-2019 (COVID-19) disease severity and clinical outcomes has been greatly aided by SCG. With many variants of concern (VOC) in sight, it would be of great importance to further understand the immune response specificity vis-a-vis the immune cell repertoire, the identification of novel cell types, and antibody response. Given the potential of SCG to play an integral part in the multi-omics approach to the study of the host-pathogen interaction and its outcomes, our review attempts to highlight its strengths, its implications for infectious disease biology, and its current limitations. We conclude that the application of SCG would be a critical step towards future pandemic preparedness.
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41
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Downes DJ, Cross AR, Hua P, Roberts N, Schwessinger R, Cutler AJ, Munis AM, Brown J, Mielczarek O, de Andrea CE, Melero I, Gill DR, Hyde SC, Knight JC, Todd JA, Sansom SN, Issa F, Davies JOJ, Hughes JR. Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus. Nat Genet 2021; 53:1606-1615. [PMID: 34737427 PMCID: PMC7611960 DOI: 10.1038/s41588-021-00955-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 09/22/2021] [Indexed: 12/21/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) disease (COVID-19) pandemic has caused millions of deaths worldwide. Genome-wide association studies identified the 3p21.31 region as conferring a twofold increased risk of respiratory failure. Here, using a combined multiomics and machine learning approach, we identify the gain-of-function risk A allele of an SNP, rs17713054G>A, as a probable causative variant. We show with chromosome conformation capture and gene-expression analysis that the rs17713054-affected enhancer upregulates the interacting gene, leucine zipper transcription factor like 1 (LZTFL1). Selective spatial transcriptomic analysis of lung biopsies from patients with COVID-19 shows the presence of signals associated with epithelial-mesenchymal transition (EMT), a viral response pathway that is regulated by LZTFL1. We conclude that pulmonary epithelial cells undergoing EMT, rather than immune cells, are likely responsible for the 3p21.31-associated risk. Since the 3p21.31 effect is conferred by a gain-of-function, LZTFL1 may represent a therapeutic target.
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Affiliation(s)
- Damien J Downes
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Amy R Cross
- Nuffield Department of Surgical Sciences, Transplantation Research and Immunology Group,University of Oxford, Oxford, UK
| | - Peng Hua
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nigel Roberts
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine Centre for Computational Biology, University of Oxford, Oxford, UK
| | - Antony J Cutler
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Immunology Research Unit, GlaxoSmithKline, Stevenage, UK
| | - Altar M Munis
- Department of Medicine, Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe University of Oxford, Oxford, UK
| | - Jill Brown
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Olga Mielczarek
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Carlos E de Andrea
- Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ignacio Melero
- Division of Immunology and Immunotherapy, Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Deborah R Gill
- Department of Medicine, Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe University of Oxford, Oxford, UK
| | - Stephen C Hyde
- Department of Medicine, Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe University of Oxford, Oxford, UK
| | - Julian C Knight
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - John A Todd
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen N Sansom
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Fadi Issa
- Nuffield Department of Surgical Sciences, Transplantation Research and Immunology Group,University of Oxford, Oxford, UK
- Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - James O J Davies
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK.
| | - Jim R Hughes
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine Centre for Computational Biology, University of Oxford, Oxford, UK.
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42
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Kumar SS, Binu A, Devan AR, Nath LR. Mucus targeting as a plausible approach to improve lung function in COVID-19 patients. Med Hypotheses 2021; 156:110680. [PMID: 34592563 PMCID: PMC8440041 DOI: 10.1016/j.mehy.2021.110680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 06/27/2021] [Accepted: 09/12/2021] [Indexed: 02/06/2023]
Abstract
COVID-19 (SARS-CoV-2) has emerged as one of the worst pandemics that have tormented the globe due to its highly contagious nature. Even if the disease manifests fever-like symptoms mostly, the disease may progress to the pulmonary-hyper inflammatory phase, with severe pneumonia, hypoxia and subsequent multiple organ infection. This subsequently creates a huge burden to the health care systems across the globe for an immediate arrangement of ventilator facilities, oxygen supply and advanced health care. We evaluated the pathological similarity of COVID-19 with other airway obstructive disorders such as COPD and asthma and found typical mucus hypersecretion and mucus plugging in COVID-19 subjects. From several bronchoscopy and clinical autopsy carried out in COVID-19 patients, the overexpression of mucin gene was evident which play a significant role in mucus hypersecretion and accumulation, leading to airway obstruction and further to respiratory distress. In the present work, we highlight the need for intense research inputs to elucidate the exact role the mucus plays in worsening COVID-19 symptoms. This will further help to find a proper approach to quantify the airway mucus plugging in each patient and to develop an appropriate therapy either to inhibit mucus secretion or to improve mucus clearance through well-designed clinical trials.
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Affiliation(s)
- Sarath S Kumar
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
| | - Aiswarya Binu
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
| | - Aswathy R Devan
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
| | - Lekshmi R Nath
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India.
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43
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Silveira CP, Schneid ADC, Ribeiro IRS, Galdino FE, Cardoso MB. A nano perspective behind the COVID-19 pandemic. NANOSCALE HORIZONS 2021; 6:842-855. [PMID: 34382995 DOI: 10.1039/d1nh00135c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The global pandemic scenario has definitely pushed the scientific community to develop COVID-19 vaccines at unprecedented speed. Nevertheless, a worldwide vaccination campaign is still far from being achieved, making the usual precautionary measures as necessary as at the beginning of the outbreak. Many aspects of the SARS-CoV-2 infectious potential and disease severity do not solely rely on interactions at the molecular level but also on physical-chemical parameters that often involve nanoscale effects. Here the SARS-CoV-2 journey to infect a susceptible host is reviewed, focusing on the nanoscale aspects that play a role in the viral infectivity and disease progression. These nanoscale-driven interactions are essential to establish mitigation-related strategies.
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Affiliation(s)
- Camila Pedroso Silveira
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Postal Code 13083-970, Campinas, Brazil.
| | - Andressa da Cruz Schneid
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Postal Code 13083-970, Campinas, Brazil.
| | - Iris Renata Sousa Ribeiro
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Postal Code 13083-970, Campinas, Brazil.
- Institute of Chemistry (IQ), University of Campinas (UNICAMP), Post Office Box 6154, Postal Code 13083-970, Campinas, SP, Brazil
| | - Flávia Elisa Galdino
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Postal Code 13083-970, Campinas, Brazil.
- Institute of Chemistry (IQ), University of Campinas (UNICAMP), Post Office Box 6154, Postal Code 13083-970, Campinas, SP, Brazil
| | - Mateus Borba Cardoso
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Postal Code 13083-970, Campinas, Brazil.
- Institute of Chemistry (IQ), University of Campinas (UNICAMP), Post Office Box 6154, Postal Code 13083-970, Campinas, SP, Brazil
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44
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Garg M, Li X, Moreno P, Papatheodorou I, Shu Y, Brazma A, Miao Z. Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses. Sci Rep 2021; 11:20833. [PMID: 34675242 PMCID: PMC8531356 DOI: 10.1038/s41598-021-00121-z] [Citation(s) in RCA: 9] [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: 05/01/2021] [Accepted: 09/28/2021] [Indexed: 01/07/2023] Open
Abstract
Several single-cell RNA sequencing (scRNA-seq) studies analyzing immune response to COVID-19 infection have been recently published. Most of these studies have small sample sizes, which limits the conclusions that can be made with high confidence. By re-analyzing these data in a standardized manner, we validated 8 of the 20 published results across multiple datasets. In particular, we found a consistent decrease in T-cells with increasing COVID-19 infection severity, upregulation of type I Interferon signal pathways, presence of expanded B-cell clones in COVID-19 patients but no consistent trend in T-cell clonal expansion. Overall, our results show that the conclusions drawn from scRNA-seq data analysis of small cohorts of COVID-19 patients need to be treated with some caution.
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Affiliation(s)
- Manik Garg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Xu Li
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, China
| | - Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, China.
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Zhichao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, 200081, China.
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45
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Li Y, Tang XX. Abnormal Airway Mucus Secretion Induced by Virus Infection. Front Immunol 2021; 12:701443. [PMID: 34650550 PMCID: PMC8505958 DOI: 10.3389/fimmu.2021.701443] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/06/2021] [Indexed: 12/23/2022] Open
Abstract
The airway mucus barrier is a primary defensive layer at the airway surface. Mucins are the major structural components of airway mucus that protect the respiratory tract. Respiratory viruses invade human airways and often induce abnormal mucin overproduction and airway mucus secretion, leading to airway obstruction and disease. The mechanism underlying the virus-induced abnormal airway mucus secretion has not been fully studied so far. Understanding the mechanisms by which viruses induce airway mucus hypersecretion may open new avenues to treatment. In this article, we elaborate the clinical and experimental evidence that respiratory viruses cause abnormal airway mucus secretion, review the underlying mechanisms, and also discuss the current research advance as well as potential strategies to treat the abnormal airway mucus secretion caused by SARS-CoV-2.
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Affiliation(s)
- Yao Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiao Xiao Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Laboratory, Bio-island, Guangzhou, China
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46
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Smet A, Breugelmans T, Michiels J, Lamote K, Arras W, De Man JG, Heyndrickx L, Hauner A, Huizing M, Malhotra-Kumar S, Lammens M, Hotterbeekx A, Kumar-Singh S, Verstraeten A, Loeys B, Verhoeven V, Jacobs R, Dams K, Coenen S, Ariën KK, Jorens PG, De Winter BY. A dynamic mucin mRNA signature associates with COVID-19 disease presentation and severity. JCI Insight 2021; 6:e151777. [PMID: 34448730 PMCID: PMC8525642 DOI: 10.1172/jci.insight.151777] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/25/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND SARS-CoV-2 infection induces mucin overexpression, further promoting disease. Given that mucins are critical components of innate immunity, unraveling their expression profiles that dictate the course of disease could greatly enhance our understanding and management of COVID-19. METHODS Using validated RT-PCR assays, we assessed mucin mRNA expression in the blood of patients with symptomatic COVID-19 compared with symptomatic patients without COVID-19 and healthy controls and correlated the data with clinical outcome parameters. Additionally, we analyzed mucin expression in mucus and lung tissue from patients with COVID-19 and investigated the effect of drugs for COVID-19 treatment on SARS-CoV-2–induced mucin expression in pulmonary epithelial cells. RESULTS We identified a dynamic blood mucin mRNA signature that clearly distinguished patients with symptomatic COVID-19 from patients without COVID-19 based on expression of MUC1, MUC2, MUC4, MUC6, MUC13, MUC16, and MUC20 (AUCROC of 91.8%; sensitivity and specificity of 90.6% and 93.3%, respectively) and that discriminated between mild and critical COVID-19 based on the expression of MUC16, MUC20, and MUC21 (AUCROC of 89.1%; sensitivity and specificity of 90.0% and 85.7%, respectively). Differences in the transcriptional landscape of mucins in critical cases compared with mild cases identified associations with COVID-19 symptoms, respiratory support, organ failure, secondary infections, and mortality. Furthermore, we identified different mucins in the mucus and lung tissue of critically ill COVID-19 patients and showed the ability of baricitinib, tocilizumab, favipiravir, and remdesivir to suppress expression of SARS-CoV-2–induced mucins. CONCLUSION This multifaceted blood mucin mRNA signature showed the potential role of mucin profiling in diagnosing, estimating severity, and guiding treatment options in patients with COVID-19. FUNDING The Antwerp University Research and the Research Foundation Flanders COVID-19 funds.
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Affiliation(s)
- Annemieke Smet
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Tom Breugelmans
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Johan Michiels
- Virology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Kevin Lamote
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium.,Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Wout Arras
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Joris G De Man
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Leo Heyndrickx
- Virology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Anne Hauner
- Virology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Manon Huizing
- Biobank Antwerpen, Antwerp University Hospital, Edegem, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Martin Lammens
- Department of Histopathology, Antwerp University Hospital, Edegem, Belgium
| | - An Hotterbeekx
- Laboratory of Cell Biology and Histology, Molecular Pathology Group, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Samir Kumar-Singh
- Laboratory of Cell Biology and Histology, Molecular Pathology Group, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Aline Verstraeten
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Bart Loeys
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Veronique Verhoeven
- Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Rita Jacobs
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium.,Critical Care Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Karolien Dams
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium.,Critical Care Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Samuel Coenen
- Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Kevin K Ariën
- Virology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Philippe G Jorens
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium.,Critical Care Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Benedicte Y De Winter
- Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, and.,Infla-med, Centre of Excellence, University of Antwerp, Antwerp, Belgium.,Division of Gastroenterology and Hepatology, Antwerp University Hospital, Edegem, Belgium
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47
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Wang X, Xu G, Liu X, Liu Y, Zhang S, Zhang Z. Multiomics: unraveling the panoramic landscapes of SARS-CoV-2 infection. Cell Mol Immunol 2021; 18:2313-2324. [PMID: 34471261 PMCID: PMC8408367 DOI: 10.1038/s41423-021-00754-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
In response to emerging infectious diseases, such as the recent pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is critical to quickly identify and understand responsible pathogens, risk factors, host immune responses, and pathogenic mechanisms at both the molecular and cellular levels. The recent development of multiomic technologies, including genomics, proteomics, metabolomics, and single-cell transcriptomics, has enabled a fast and panoramic grasp of the pathogen and the disease. Here, we systematically reviewed the major advances in the virology, immunology, and pathogenic mechanisms of SARS-CoV-2 infection that have been achieved via multiomic technologies. Based on well-established cohorts, omics-based methods can greatly enhance the mechanistic understanding of diseases, contributing to the development of new diagnostics, drugs, and vaccines for emerging infectious diseases, such as COVID-19.
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Affiliation(s)
- Xin Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Gang Xu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Xiaoju Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yang Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
- Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen, Guangdong Province, China.
- Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen, Guangdong Province, China.
- Shenzhen Bay Laboratory, Shenzhen, Guangdong Province, China.
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48
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Cinnamon and its possible impact on COVID-19: The viewpoint of traditional and conventional medicine. Biomed Pharmacother 2021; 143:112221. [PMID: 34563952 PMCID: PMC8452493 DOI: 10.1016/j.biopha.2021.112221] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/18/2022] Open
Abstract
The COVID-19 global epidemic caused by coronavirus has affected the health and other aspects of life for more than one year. Despite the current pharmacotherapies, there is still no specific treatment, and studies are in progress to find a proper therapy with high efficacy and low side effects. In this way, Traditional Persian Medicine (TPM), due to its holistic view, can provide recommendations for the prevention and treatment of new diseases such as COVID-19. The muco-obstruction of the airway, which occurs in SARS-CoV-2, has similar features in TPM textbooks that can lead us to new treatment approaches. Based on TPM and pharmacological studies, Cinnamomum verum (Darchini)'s potential effective functions can contribute to SARS-CoV-2 infection treatment and has been known to be effective in corona disease in Public beliefs. From the viewpoint of TPM theories, Cinnamon can be effective in SARS-CoV-2 improvement and treatment through its anti-obstructive, diuretic, tonic and antidote effects. In addition, there is pharmacological evidence on anti-viral, anti-inflammatory, antioxidant, organ-o-protective and anti-depression effects of Cinnamon that are in line with the therapeutic functions mentioned in TPM.Overall, Cinnamon and its ingredients can be recommended for SARS-CoV2 management due to multi-targeting therapies. This review provides basic information for future studies on this drug's effectiveness in preventing and treating COVID-19 and similar diseases.
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Robinot R, Hubert M, de Melo GD, Lazarini F, Bruel T, Smith N, Levallois S, Larrous F, Fernandes J, Gellenoncourt S, Rigaud S, Gorgette O, Thouvenot C, Trébeau C, Mallet A, Duménil G, Gobaa S, Etournay R, Lledo PM, Lecuit M, Bourhy H, Duffy D, Michel V, Schwartz O, Chakrabarti LA. SARS-CoV-2 infection induces the dedifferentiation of multiciliated cells and impairs mucociliary clearance. Nat Commun 2021; 12:4354. [PMID: 34272374 PMCID: PMC8285531 DOI: 10.1038/s41467-021-24521-x] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/21/2021] [Indexed: 01/08/2023] Open
Abstract
Understanding how SARS-CoV-2 spreads within the respiratory tract is important to define the parameters controlling the severity of COVID-19. Here we examine the functional and structural consequences of SARS-CoV-2 infection in a reconstructed human bronchial epithelium model. SARS-CoV-2 replication causes a transient decrease in epithelial barrier function and disruption of tight junctions, though viral particle crossing remains limited. Rather, SARS-CoV-2 replication leads to a rapid loss of the ciliary layer, characterized at the ultrastructural level by axoneme loss and misorientation of remaining basal bodies. Downregulation of the master regulator of ciliogenesis Foxj1 occurs prior to extensive cilia loss, implicating this transcription factor in the dedifferentiation of ciliated cells. Motile cilia function is compromised by SARS-CoV-2 infection, as measured in a mucociliary clearance assay. Epithelial defense mechanisms, including basal cell mobilization and interferon-lambda induction, ramp up only after the initiation of cilia damage. Analysis of SARS-CoV-2 infection in Syrian hamsters further demonstrates the loss of motile cilia in vivo. This study identifies cilia damage as a pathogenic mechanism that could facilitate SARS-CoV-2 spread to the deeper lung parenchyma.
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Grants
- Institut Pasteur
- This work was supported by : Institut Pasteur TASK FORCE SARS COV2 (TROPICORO and COROCHIP projects), DIM ELICIT Region Ile-de-France, and Agence Nationale de Recherche sur le SIDA et les Maladies Infectieuses Emergentes (ANRS; project 19052) (L.A.C.); the Vaccine Research Institute (ANR-10-LABX-77), ANRS, Labex IBEID (ANR-10-LABX-62-IBEID), the French National Research Agency (ANR; projects “TIMTAMDEN” ANR-14-CE14-0029, “CHIKV-Viro-Immuno” ANR-14-CE14-0015-01), the Gilead HIV cure program, ANR/Fondation pour la Recherche Médicale (FRM) Flash Covid PROTEO-SARS-CoV-2 and IDISCOVR (O.S.); Institut Pasteur TASK FORCE SARS COV2 and ANR Flash Covid CoVarImm (D.D.); Institut Pasteur TASK FORCE SARS COV2 (Neuro-Covid project) (H.B.). The Lledo lab is supported by the life insurance company "AG2R-La-Mondiale". The UtechS Photonic BioImaging (Imagopole) and the UtechS Ultrastructural BioImaging (UBI) are supported by the ANR (France BioImaging; ANR-10–INSB–04; Investments for the Future). R.R. is the recipient of a Sidaction fellowship, N.S. of a Pasteur-Roux-Cantarini fellowship, and St.G. of a MESR/Ecole Doctorale B3MI, Université de Paris fellowship. S.L. is supported by FRM (fellowship ECO201906009119) and by “Ecole Doctorale FIRE – Programme Bettencourt”.
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Affiliation(s)
- Rémy Robinot
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569 CNRS, Paris, France
| | - Mathieu Hubert
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569 CNRS, Paris, France
| | | | - Françoise Lazarini
- Perception and Memory Unit, Institut Pasteur, Paris, France
- UMR 3571 CNRS, Paris, France
| | - Timothée Bruel
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569 CNRS, Paris, France
| | - Nikaïa Smith
- Translational Immunology Lab, Department of Immunology, Institut Pasteur, Paris, France
| | - Sylvain Levallois
- Biology of Infection Unit, Institut Pasteur, Paris, France
- INSERM U1117, Paris, France
| | - Florence Larrous
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Paris, France
| | - Julien Fernandes
- UtechS Photonics BioImaging, C2RT, Institut Pasteur, Paris, France
| | - Stacy Gellenoncourt
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569 CNRS, Paris, France
| | | | - Olivier Gorgette
- UtechS Ultrastructural BioImaging UBI, C2RT, Institut Pasteur, Paris, France
| | - Catherine Thouvenot
- UtechS Ultrastructural BioImaging UBI, C2RT, Institut Pasteur, Paris, France
| | - Céline Trébeau
- Institut de l'Audition, Institut Pasteur, INSERM, Paris, France
| | - Adeline Mallet
- UtechS Ultrastructural BioImaging UBI, C2RT, Institut Pasteur, Paris, France
| | - Guillaume Duménil
- UtechS Ultrastructural BioImaging UBI, C2RT, Institut Pasteur, Paris, France
| | - Samy Gobaa
- Biomaterials and Microfluidics Core Facility, Institut Pasteur, Paris, France
| | | | - Pierre-Marie Lledo
- Perception and Memory Unit, Institut Pasteur, Paris, France
- UMR 3571 CNRS, Paris, France
| | - Marc Lecuit
- Biology of Infection Unit, Institut Pasteur, Paris, France
- INSERM U1117, Paris, France
- Université de Paris, Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, Paris, France
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Paris, France
| | - Darragh Duffy
- Translational Immunology Lab, Department of Immunology, Institut Pasteur, Paris, France
| | - Vincent Michel
- Institut de l'Audition, Institut Pasteur, INSERM, Paris, France.
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.
- UMR 3569 CNRS, Paris, France.
- Vaccine Research Institute, Créteil, France.
| | - Lisa A Chakrabarti
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.
- UMR 3569 CNRS, Paris, France.
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Discovery of potential imaging and therapeutic targets for severe inflammation in COVID-19 patients. Sci Rep 2021; 11:14151. [PMID: 34239034 PMCID: PMC8266867 DOI: 10.1038/s41598-021-93743-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 06/30/2021] [Indexed: 12/15/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19) has been spreading worldwide with rapidly increased number of deaths. Hyperinflammation mediated by dysregulated monocyte/macrophage function is considered to be the key factor that triggers severe illness in COVID-19. However, no specific targeting molecule has been identified for detecting or treating hyperinflammation related to dysregulated macrophages in severe COVID-19. In this study, previously published single-cell RNA-sequencing data of bronchoalveolar lavage fluid cells from thirteen COVID-19 patients were analyzed with publicly available databases for surface and imageable targets. Immune cell composition according to the severity was estimated with the clustering of gene expression data. Expression levels of imaging target molecules for inflammation were evaluated in macrophage clusters from single-cell RNA-sequencing data. In addition, candidate targetable molecules enriched in severe COVID-19 associated with hyperinflammation were filtered. We found that expression of SLC2A3, which can be imaged by [18F]fluorodeoxyglucose, was higher in macrophages from severe COVID-19 patients. Furthermore, by integrating the surface target and drug-target binding databases with RNA-sequencing data of severe COVID-19, we identified candidate surface and druggable targets including CCR1 and FPR1 for drug delivery as well as molecular imaging. Our results provide a resource in the development of specific imaging and therapy for COVID-19-related hyperinflammation.
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