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Zhu J, Xing F, Li Y, Wu C, Li S, Wang Q, Huang J, Zhang Y, Zheng X, Liu Z, Rao J, Hong R, Tian S, Xiong S, Tan L, Chen X, Li Y, He W, Hong X, Xia J, Zhou Q, Zhang Z. Exploring the causes of variability in quality of oropharyngeal swab sampling for SARS-CoV-2 nucleic acid testing and proposed improvement measures: a multicenter, double-blind study. Microbiol Spectr 2024:e0156724. [PMID: 39382280 DOI: 10.1128/spectrum.01567-24] [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: 06/26/2024] [Accepted: 09/09/2024] [Indexed: 10/10/2024] Open
Abstract
Although coronavirus disease 2019 (COVID-19) has not been considered a public health emergency of international concern since last year, intermittent regional impacts still persist, and accurate testing remains crucial. Ribonuclease P protein subunit P30 (RPP30) RNA, known for its broad and stable expression in tissue cells, was used to evaluate samples from 10 hospitals with over 3,000 negative nucleic acid tests. The results revealed that the overall pass rate for the collected samples was consistently low and exhibited significant heterogeneity. After reassessing the evaluative effectiveness of RPP30 RNA Ct values from the samples of 132 positive individuals under quarantine observation, it was used to identify factors affecting sampling quality. These factors included different stages ranging from sample collection to PCR processing, various characteristics of both samplers and individuals being sampled, as well as sampling season and location. The results indicated that post-sampling handling had minimal impact, winter and fever clinic samples showed higher quality, whereas children's samples had lower quality. The key finding was that the characteristics of samplers were closely related to sampling quality, emphasizing the role of subjectivity. Quality control warnings led to substantial improvements, confirming this finding. Consequently, although there are various factors during the testing process, the most critical aspect is to improve, supervise, and maintain standardized practices among sampling staff.IMPORTANCEThis study further confirmed the reliability of internal references (IRs) in assessing sample quality, and utilized a large sample IR data to comprehensively and multidimensionally identify significant interference factors in nucleic acid test results. By further reminding and intervening in the subjective practices of specimen collectors, good results could be achieved.
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Affiliation(s)
- Jie Zhu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Yunzhu Li
- Department of Infectious Diseases, The Third Affiliated Hospital of Anhui Medical University, The First People's Hospital of Hefei, Hefei, China
| | - Chunchen Wu
- Department of Laboratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shasha Li
- Division of Liver Disease, The Second People's Hospital of Fuyang City, Fuyang, China
| | - Qin Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jinyue Huang
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Yafei Zhang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaowei Zheng
- Department of Infectious Diseases, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Zhenjun Liu
- Department of Infectious Diseases, Anqing Municipal Hospital, Anqing, China
| | - Jianguo Rao
- Department of Infectious Diseases, The Lu'an Affiliated Hospital of Anhui Medical University, Lu'an People's Hospital, Lu'an, China
| | - Rui Hong
- Department of Infectious Diseases, Tongling Municipal Hospital, Tongling, China
| | - Shuilin Tian
- Division of Liver Disease, Traditional Chinese Hospital of LuAn, Anhui University of Traditional Chinese Medicine, Lu'an, China
| | - Shuangyun Xiong
- Department of Infectious Diseases, Funan County People's Hospital, Fuyang, China
| | - Lin Tan
- Division of Liver Disease, The Second People's Hospital of Fuyang City, Fuyang, China
| | - Xinlei Chen
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yanwu Li
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wei He
- Division of Liver Disease, Traditional Chinese Hospital of LuAn, Anhui University of Traditional Chinese Medicine, Lu'an, China
| | - Xiaodan Hong
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jianbo Xia
- Department of Laboratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiang Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhenhua Zhang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
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Liu Z, Petinrin OO, Chen N, Toseef M, Liu F, Zhu Z, Qi F, Wong KC. Identification and evaluation of candidate COVID-19 critical genes and medicinal drugs related to plasma cells. BMC Infect Dis 2024; 24:1099. [PMID: 39363208 PMCID: PMC11451256 DOI: 10.1186/s12879-024-10000-3] [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: 12/25/2023] [Accepted: 09/25/2024] [Indexed: 10/05/2024] Open
Abstract
The ongoing COVID-19 pandemic, caused by the SARS-CoV-2 virus, represents one of the most significant global health crises in recent history. Despite extensive research into the immune mechanisms and therapeutic options for COVID-19, there remains a paucity of studies focusing on plasma cells. In this study, we utilized the DESeq2 package to identify differentially expressed genes (DEGs) between COVID-19 patients and controls using datasets GSE157103 and GSE152641. We employed the xCell algorithm to perform immune infiltration analyses, revealing notably elevated levels of plasma cells in COVID-19 patients compared to healthy individuals. Subsequently, we applied the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm to identify COVID-19 related plasma cell module genes. Further, positive cluster biomarker genes for plasma cells were extracted from single-cell RNA sequencing data (GSE171524), leading to the identification of 122 shared genes implicated in critical biological processes such as cell cycle regulation and viral infection pathways. We constructed a robust protein-protein interaction (PPI) network comprising 89 genes using Cytoscape, and identified 20 hub genes through cytoHubba. These genes were validated in external datasets (GSE152418 and GSE179627). Additionally, we identified three potential small molecules (GSK-1070916, BRD-K89997465, and idarubicin) that target key hub genes in the network, suggesting a novel therapeutic approach. These compounds were characterized by their ability to down-regulate AURKB, KIF11, and TOP2A effectively, as evidenced by their low free binding energies determined through computational analyses using cMAP and AutoDock. This study marks the first comprehensive exploration of plasma cells' role in COVID-19, offering new insights and potential therapeutic targets. It underscores the importance of a systematic approach to understanding and treating COVID-19, expanding the current body of knowledge and providing a foundation for future research.
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Affiliation(s)
- Zhe Liu
- Institute for Hepatology, The Second Affiliated Hospital, School of Medicine, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, China
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | | | - Nanjun Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Muhammad Toseef
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Fang Liu
- Rocgene (Beijing) Technology Co., Ltd, Beijing, Beijing, 102200, China
| | - Zhongxu Zhu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China.
| | - Furong Qi
- Institute for Hepatology, The Second Affiliated Hospital, School of Medicine, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, China.
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China.
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China.
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Sun Y, Wang H, Wang H, Cai J, Yuan G, Zhang H, Zhao J, Xue Q, Jiang X, Ying H, Zhang Y, Yang Y, Jin J, Zhang W, Lu J, Ai J, Wang S. Aging brought additional immune response alterations after breakthrough infections with the Omicron BA.5/BF.7 variants: Protein immune mechanism. Int J Biol Macromol 2024:136183. [PMID: 39357723 DOI: 10.1016/j.ijbiomac.2024.136183] [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] [Revised: 09/20/2024] [Accepted: 09/29/2024] [Indexed: 10/04/2024]
Abstract
The global spread of the Omicron variant strain BA.5/BF.7 has led to an increase in breakthrough infections. The elderly population shows different immune responses after infection due to the aging of the immune system, which has not been fully studied. The aim of this study was to investigate the effect of aging on immune response after breakthrough infection of Omicron BA.5/BF.7 variant, especially the changes of protein immune mechanism. The study analyzed the concentration of antibodies in serum and their ability to neutralize the mutant strain by comparing the immune response of the elderly population and the young population after infection. Proteomics techniques were used to assess differences in the expression of key proteins in immune cells of different age groups. The study found that older subjects produced lower levels of antibodies after infection than younger subjects and showed a significantly reduced ability to neutralize against BA.5/BF.7. In addition, proteomic analysis showed that the expression of proteins related to inflammation and apoptosis significantly increased in the immune cells of the elderly, while the proteins related to antiviral response and cell repair significantly decreased. These findings provide new ideas for immune intervention strategies in the elderly population, and emphasize the targeted research of anti-virus vaccines.
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Affiliation(s)
- Yuhan Sun
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Hongyu Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Hua Wang
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 200336, China
| | - Jianpeng Cai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Guanmin Yuan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Haocheng Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China; Shanghai Sci-Tech InnoCenter for Infection and Immunity, Shanghai 20052, China
| | - Jingjing Zhao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Quanlin Xue
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Xiaochun Jiang
- Community Health Service Center of Xianghuaqiao Street, Qingpu District, Shanghai, China
| | - Huang Ying
- Community Health Service Center of Baihe Street, Qingpu District, Shanghai, China
| | - Yeting Zhang
- Community Health Service Center of Chonggu Town, Qingpu District, Shanghai, China
| | - Yongfeng Yang
- Community Health Service Center of Huaxin Town, Qingpu District, Shanghai, China
| | - Jialin Jin
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China; Shanghai Sci-Tech InnoCenter for Infection and Immunity, Shanghai 20052, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China; Shanghai Sci-Tech InnoCenter for Infection and Immunity, Shanghai 20052, China; Institute of Infection and Health, Fudan University, Shanghai 200040, China
| | - Jiahuan Lu
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 200336, China.
| | - Jingwen Ai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China; Shanghai Sci-Tech InnoCenter for Infection and Immunity, Shanghai 20052, China.
| | - Sen Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China; Shanghai Sci-Tech InnoCenter for Infection and Immunity, Shanghai 20052, China.
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Lim FY, Lea HG, Dostie A, Kim SY, van Neel T, Hassan G, Takezawa MG, Starita LM, Adams K, Boeckh M, Schiffer JT, Hyrien O, Waghmare A, Berthier E, Theberge AB. homeRNA self-blood collection enables high-frequency temporal profiling of presymptomatic host immune kinetics to respiratory viral infection: a prospective cohort study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.12.23296835. [PMID: 37873251 PMCID: PMC10593056 DOI: 10.1101/2023.10.12.23296835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background Early host immunity to acute respiratory infections (ARIs) is heterogenous, dynamic, and critical to an individual's infection outcome. Due to limitations in sampling frequency/timepoints, kinetics of early immune dynamics in natural human infections remain poorly understood. In this nationwide prospective cohort study, we leveraged a Tasso-SST based self-blood collection and stabilization tool (homeRNA) to profile detailed kinetics of the presymptomatic to convalescence host immunity to contemporaneous respiratory pathogens. Methods We enrolled non-symptomatic adults with recent exposure to ARIs who subsequently tested negative (exposed-uninfected) or positive for respiratory pathogens. Participants self-collected blood and nasal swabs daily for seven consecutive days followed by weekly blood collection for up to seven additional weeks. Symptom burden was assessed during each collection. Nasal swabs were tested for SARS-CoV-2 and common respiratory pathogens. 92 longitudinal blood samples spanning the presymptomatic to convalescence phase of eight SARS-CoV-2-infected participants and 40 interval-matched samples from four exposed-uninfected participants were subjected to high-frequency longitudinal profiling of 785 immune genes. Generalized additive mixed models (GAMM) were used to identify temporally dynamic genes from the longitudinal samples and linear mixed models (LMM) were used to identify baseline differences between exposed-infected (n = 8), exposed-uninfected (n = 4), and uninfected (n = 13) participant groups. Findings Between June 2021 - April 2022, 68 participants across 26 U.S. states completed the study and self-collected a total of 691 and 466 longitudinal blood and nasal swab samples along with 688 symptom surveys. SARS-CoV-2 was detected in 17 out of 22 individuals with study-confirmed respiratory infection, of which five were still presymptomatic or pre-shedding, enabling us to profile detailed expression kinetics of the earliest blood transcriptional response to contemporaneous variants of concern. 51% of the genes assessed were found to be temporally dynamic during COVID-19 infection. During the pre-shedding phase, a robust but transient response consisting of genes involved in cell migration, stress response, and T cell activation were observed. This is followed by a rapid induction of many interferon-stimulated genes (ISGs), concurrent to onset of viral shedding and increase in nasal viral load and symptom burden. Finally, elevated baseline expression of antimicrobial peptides were observed in exposed-uninfected individuals. Interpretation We demonstrated that unsupervised self-collection and stabilization of capillary blood can be applied to natural infection studies to characterize detailed early host immune kinetics at a temporal resolution comparable to that of human challenge studies. The remote (decentralized) study framework enables conduct of large-scale population-wide longitudinal mechanistic studies. Funding This study was funded by R35GM128648 to ABT for in-lab developments of homeRNA and data analysis, a Packard Fellowship for Science and Engineering from the David and Lucile Packard Foundation to ABT, and R01AI153087 to AW.
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Affiliation(s)
- Fang Yun Lim
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, U.S.A
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
| | - Hannah G. Lea
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
- Department of Therapeutic Radiology, Yale University School of Medicine; New Haven, CT, U.S.A
| | - Ashley Dostie
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
| | - Soo-Young Kim
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, U.S.A
| | - Tammi van Neel
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
| | - Grant Hassan
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
| | - Meg G. Takezawa
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
| | - Lea M. Starita
- Brotman Baty Institute, University of Washington; Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington, U.S.A
| | - Karen Adams
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
- Institute of Translational Health Sciences, School of Medicine, University of Washington, Seattle, WA, U.S.A
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, U.S.A
- Department of Medicine, University of Washington; Seattle, Washington, U.S.A
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, U.S.A
- Department of Medicine, University of Washington; Seattle, Washington, U.S.A
| | - Ollivier Hyrien
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, U.S.A
| | - Alpana Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, U.S.A
- Department of Pediatrics, University of Washington; Seattle, Washington, U.S.A
- Seattle Children’s Research Institute; Seattle, Washington, U.S.A
| | - Erwin Berthier
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
| | - Ashleigh B. Theberge
- Department of Chemistry, University of Washington; Seattle, WA, U.S.A
- Department of Urology, University of Washington; Seattle, Washington, U.S.A
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Mińko A, Turoń-Skrzypińska A, Rył A, Mańkowska K, Cymbaluk-Płoska A, Rotter I. The Importance of the Concentration of Selected Cytokines (IL-6, IL-10, IL-12, IL-15, TNF-α) and Inflammatory Markers (CRP, NLR, PLR, LMR, SII) in Predicting the Course of Rehabilitation for Patients after COVID-19 Infection. Biomedicines 2024; 12:2055. [PMID: 39335569 PMCID: PMC11429050 DOI: 10.3390/biomedicines12092055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 08/31/2024] [Accepted: 09/08/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND/OBJECTIVES In the course of COVID-19, there may be an excessive immune response of the body with the release of large amounts of pro-inflammatory cytokines, causing a "cytokine storm", also known as cytokine release syndrome (CRS). The COVID-19 pandemic has shown how important an integrated approach to health care is, with physiotherapy being one of its fundamental aspects. The aim of this study was to analyze the potential relationship between the level of selected cytokines (IL-6, IL-10, IL-12, IL-15, TNF-α) and inflammatory markers (CRP, NLR, PLR, LMR, SII) and the duration of rehabilitation in patients after COVID-19. METHODS The examined patients participated in a comprehensive rehabilitation program, which included breathing exercises, aerobic training, and strength and endurance training. Peripheral venous blood samples were also collected from each patient. RESULTS Factors such as gender, smoking status, IL-10, and the presence of pneumonia during infection were significantly associated with the length of rehabilitation after COVID-19. CONCLUSIONS The course of rehabilitation after COVID-19 may depend on many factors, including smoking, the presence of pneumonia due to infection, and some parameters of inflammation.
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Affiliation(s)
- Alicja Mińko
- Department of Medical Rehabilitation and Clinical Physiotherapy, Pomeranian Medical University, 71-210 Szczecin, Poland; (A.T.-S.); (A.R.); (I.R.)
| | - Agnieszka Turoń-Skrzypińska
- Department of Medical Rehabilitation and Clinical Physiotherapy, Pomeranian Medical University, 71-210 Szczecin, Poland; (A.T.-S.); (A.R.); (I.R.)
| | - Aleksandra Rył
- Department of Medical Rehabilitation and Clinical Physiotherapy, Pomeranian Medical University, 71-210 Szczecin, Poland; (A.T.-S.); (A.R.); (I.R.)
| | - Katarzyna Mańkowska
- Department of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Aneta Cymbaluk-Płoska
- Department of Reconstructive Surgery and Gynecological Oncology, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Iwona Rotter
- Department of Medical Rehabilitation and Clinical Physiotherapy, Pomeranian Medical University, 71-210 Szczecin, Poland; (A.T.-S.); (A.R.); (I.R.)
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Hsieh LL, Looney M, Figueroa A, Massaccesi G, Stavrakis G, Anaya EU, D'Alessio FR, Ordonez AA, Pekosz AS, DeFilippis VR, Karakousis PC, Karaba AH, Cox AL. Bystander monocytic cells drive infection-independent NLRP3 inflammasome response to SARS-CoV-2. mBio 2024:e0081024. [PMID: 39240187 DOI: 10.1128/mbio.00810-24] [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: 03/25/2024] [Accepted: 06/26/2024] [Indexed: 09/07/2024] Open
Abstract
The pathogenesis of COVID-19 is associated with a hyperinflammatory immune response. Monocytes and macrophages play a central role in this hyperinflammatory response to SARS-CoV-2. NLRP3 inflammasome activation has been observed in monocytes of patients with COVID-19, but the mechanism and consequences of inflammasome activation require further investigation. In this study, we inoculated a macrophage-like THP-1 cell line, primary differentiated human nasal epithelial cell (hNEC) cultures, and primary monocytes with SARS-CoV-2. We found that the activation of the NLRP3 inflammasome in macrophages does not rely on viral replication, receptor-mediated entry, or actin-dependent entry. SARS-CoV-2 productively infected hNEC cultures without triggering the production of inflammasome cytokines IL-18 and IL-1β. Importantly, these cytokines did not inhibit viral replication in hNEC cultures. SARS-CoV-2 inoculation of primary monocytes led to inflammasome activation and induced a macrophage phenotype in these cells. Monocytic cells from bronchoalveolar lavage (BAL) fluid, but not from peripheral blood, of patients with COVID-19, showed evidence of inflammasome activation, expressed the proinflammatory marker CD11b, and displayed oxidative burst. These findings highlight the central role of activated macrophages, as a result of direct viral sensing, in COVID-19 and support the inhibition of IL-1β and IL-18 as potential therapeutic strategies to reduce immunopathology without increasing viral replication. IMPORTANCE Inflammasome activation is associated with severe COVID-19. The impact of inflammasome activation on viral replication and mechanistic details of this activation are not clarified. This study advances our understanding of the role of inflammasome activation in macrophages by identifying TLR2, NLRP3, ASC, and caspase-1 as dependent factors in this activation. Further, it highlights that SARS-CoV-2 inflammasome activation is not a feature of nasal epithelial cells but rather activation of bystander macrophages in the airway. Finally, we demonstrate that two pro inflammatory cytokines produced by inflammasome activation, IL-18 and IL-1β, do not restrict viral replication and are potential targets to ameliorate pathological inflammation in severe COVID-19.
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Affiliation(s)
- Leon L Hsieh
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Monika Looney
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alexis Figueroa
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Guido Massaccesi
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Georgia Stavrakis
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Eduardo U Anaya
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Franco R D'Alessio
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alvaro A Ordonez
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew S Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Victor R DeFilippis
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Petros C Karakousis
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew H Karaba
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrea L Cox
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
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7
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Lee HJ, Kim MJ, Kim JS, Lee YC, Jeong JS. Prior respiratory syncytial viral infection contributes to severe COVID-19 illness: A nationwide cohort study. Allergy 2024; 79:2534-2537. [PMID: 38577792 DOI: 10.1111/all.16118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/08/2024] [Accepted: 03/24/2024] [Indexed: 04/06/2024]
Affiliation(s)
- Hwan Jin Lee
- Department of Internal Medicine, Research Center for Pulmonary Disorders, Jeonbuk National University Hospital, Jeonju, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea
| | - Min Ji Kim
- Department of Medical Informatics, Jeonbuk National University Medical School, Jeonju, Republic of Korea
| | - Jong Seung Kim
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea
- Department of Medical Informatics, Jeonbuk National University Medical School, Jeonju, Republic of Korea
- Department of Otorhinolaryngology-Head and Neck Surgery, Jeonbuk National University Hospital, Jeonju, Republic of Korea
- Respiratory Drug Development Research Institute, Jeonbuk National University Medical School, Jeonju, Republic of Korea
| | - Yong Chul Lee
- Department of Internal Medicine, Research Center for Pulmonary Disorders, Jeonbuk National University Hospital, Jeonju, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea
- Respiratory Drug Development Research Institute, Jeonbuk National University Medical School, Jeonju, Republic of Korea
| | - Jae Seok Jeong
- Department of Internal Medicine, Research Center for Pulmonary Disorders, Jeonbuk National University Hospital, Jeonju, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea
- Respiratory Drug Development Research Institute, Jeonbuk National University Medical School, Jeonju, Republic of Korea
- Laboratory of Respiratory Immunology and Infectious Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea
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Bost P, Drayman N. Dissecting viral infections, one cell at a time, by single-cell technologies. Microbes Infect 2024; 26:105268. [PMID: 38008398 PMCID: PMC11161131 DOI: 10.1016/j.micinf.2023.105268] [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: 05/31/2023] [Revised: 10/22/2023] [Accepted: 11/21/2023] [Indexed: 11/28/2023]
Abstract
The meteoric rise of single-cell genomic technologies, especially of single-cell RNA-sequencing (scRNA-seq), has revolutionized several fields of cellular biology, especially immunology, oncology, neuroscience and developmental biology. While the field of virology has been relatively slow to adopt these technological advances, many works have shed new light on the fascinating interactions of viruses with their hosts using single cell technologies. One clear example is the multitude of studies dissecting viral infections by single-cell sequencing technologies during the recent COVID-19 pandemic. In this review we will detail the advantages of studying viral infections at a single-cell level, how scRNA-seq technologies can be used to achieve this goal and the associated technical limitations, challenges and solutions. We will highlight recent biological discoveries and breakthroughs in virology enabled by single-cell analyses and will end by discussing possible future directions of the field. Given the rate of publications in this exciting new frontier of virology, we have likely missed some important works and we apologize in advance to the researchers whose work we have failed to cite.
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Affiliation(s)
- Pierre Bost
- University of Zurich, Department of Quantitative Biomedicine, Zurich, 8057, Switzerland; ETH Zurich, Institute for Molecular Health Sciences, Zurich, 8093 Switzerland.
| | - Nir Drayman
- The Department of Molecular Biology and Biochemistry, The Center for Virus Research and The Center for Complex Biological Systems, The University of California, Irvine, CA, 92697, USA
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9
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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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10
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Thiede JM, Dick JK, Jarjour NN, Krishna VD, Qian L, Sangala J, Benzow K, Karanjeet K, Chin S, Rainwater O, Cheeran MCJ, Hogquist KA, Jameson SC, Hart GT, Bold TD, Koob MD. Human ACE2 Gene Replacement Mice Support SARS-CoV-2 Viral Replication and Nonlethal Disease Progression. Immunohorizons 2024; 8:712-720. [PMID: 39287601 PMCID: PMC11447706 DOI: 10.4049/immunohorizons.2400030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 08/06/2024] [Indexed: 09/19/2024] Open
Abstract
Many mouse models of SARS-CoV-2 infection involve expression of the human ACE2 protein, the entry receptor for SARS-CoV-2 Spike protein, in mouse tissues. However, most of these models suffer from nonphysiological regulation of ACE2 expression, which can lead to atypically severe infections and aberrant sites of viral replication. In this report, we developed and characterized an ACE2 gene replacement (ACE2-GR) mouse strain in which the mouse Ace2 genomic locus was replaced by the entire human ACE2 gene locus, and we investigated the ability of these animals to respond to SARS-CoV-2 infection. We show that ACE2-GR mice support SARS-CoV-2 viral replication, but, in stark contrast to the widely used K18-hACE2 transgenic model, this infection leads to a mild disease with no detectable involvement of the CNS. Thus, ACE2-GR mice provide a novel, to our knowledge, model to explore immune responses and long-term consequences of SARS-CoV-2 infection.
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Affiliation(s)
- Joshua M. Thiede
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
| | - Jenna K. Dick
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
| | - Nicholas N. Jarjour
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Venkatramana D. Krishna
- Department of Veterinary Population Medicine, University of Minnesota College of Veterinary Medicine, St. Paul, MN
| | - Lily Qian
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Jules Sangala
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
| | - Kellie Benzow
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Kul Karanjeet
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Shine Chin
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Orion Rainwater
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Maxim C.-J. Cheeran
- Department of Veterinary Population Medicine, University of Minnesota College of Veterinary Medicine, St. Paul, MN
| | - Kristin A. Hogquist
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Stephen C. Jameson
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Geoffrey T. Hart
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
| | - Tyler D. Bold
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
| | - Michael D. Koob
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
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11
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Zong YH, Cao JF, Zhao Y, Gao M, Chen WL, Wu M, Xu X, Xu ZY, Zhang XQ, Tang JZ, Liu Y, Hu XS, Wang SQ, Zhang X. Mechanism of Lian Hua Qing Wen capsules regulates the inflammatory response caused by M 1 macrophage based on cellular experiments and computer simulations. Acta Trop 2024; 257:107320. [PMID: 39002739 DOI: 10.1016/j.actatropica.2024.107320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 07/01/2024] [Accepted: 07/04/2024] [Indexed: 07/15/2024]
Abstract
PURPOSE The polarization of macrophages with the resulting inflammatory response play a crucial part in tissue and organ damage due to inflammatory. Study has proved Lian Hua Qing Wen capsules (LHQW) can reduce activation of inflammatory response and damage of tissue derived from the inflammatory reactions. However, the mechanism of LHQW regulates the macrophage-induced inflammatory response is unclear. Therefore, we investigated the mechanism of LHQW regulated the inflammatory response of M1 macrophages by cellular experiments and computer simulations. METHODS This study has analysed the targets and mechanisms of macrophage regulating inflammatory response at gene and protein levels through bioinformatics. The monomeric components of LHQW were analyzed by High Performance Liquid Chromatography (HPLC). We established the in vitro cell model by M1 macrophages (Induction of THP-1 cells into M1 macrophages). RT-qPCR and immunofluorescence were used to detect changes in gene and protein levels of key targets after LHQW treatment. Computer simulations were utilized to verify the binding stability of monomeric components and protein targets. RESULTS Macrophages had 140,690 gene targets, inflammatory response had 12,192 gene targets, intersection gene targets were 11,772. Key monomeric components (including: Pinocembrin, Fargesone-A, Nodakenin and Bowdichione) of LHQW were screened by HPLC. The results of cellular experiments indicated that LHQW could significantly reduce the mRNA expression of CCR5, CSF2, IFNG and TNF, thereby alleviating the inflammatory response caused by M1 macrophage. The computer simulations further validated the binding stability and conformation of key monomeric components and key protein targets, and IFNG/Nodakenin was able to form the most stable binding conformation for its action. CONCLUSION In this study, the mechanism of LHQW inhibits the polarization of macrophages and the resulting inflammatory response was investigated by computer simulations and cellular experiments. We found that LHQW may not only reduce cell damage and death by acting on TNF and CCR5, but also inhibit the immune recognition process and inflammatory response by regulating CSF2 and IFNG to prevent polarization of macrophages. Therefore, these results suggested that LHQW may act through multiple targets to inhibit the polarization of macrophages and the resulting inflammatory response.
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Affiliation(s)
| | - Jun-Feng Cao
- College of Medicine, Southwest Jiaotong University, Chengdu, PR China
| | | | - Miao Gao
- Chengdu Medical College, Chengdu, PR China
| | | | - Mei Wu
- Chengdu Medical College, Chengdu, PR China
| | - Xiang Xu
- Chengdu Medical College, Chengdu, PR China
| | | | | | | | - Yulin Liu
- Chengdu Medical College, Chengdu, PR China
| | | | | | - Xiao Zhang
- Chengdu Medical College, Chengdu, PR China.
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12
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Friedrich VD, Pennitz P, Wyler E, Adler JM, Postmus D, Müller K, Teixeira Alves LG, Prigann J, Pott F, Vladimirova D, Hoefler T, Goekeri C, Landthaler M, Goffinet C, Saliba AE, Scholz M, Witzenrath M, Trimpert J, Kirsten H, Nouailles G. Neural network-assisted humanisation of COVID-19 hamster transcriptomic data reveals matching severity states in human disease. EBioMedicine 2024:105312. [PMID: 39317638 DOI: 10.1016/j.ebiom.2024.105312] [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: 04/05/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 09/26/2024] Open
Abstract
BACKGROUND Translating findings from animal models to human disease is essential for dissecting disease mechanisms, developing and testing precise therapeutic strategies. The coronavirus disease 2019 (COVID-19) pandemic has highlighted this need, particularly for models showing disease severity-dependent immune responses. METHODS Single-cell transcriptomics (scRNAseq) is well poised to reveal similarities and differences between species at the molecular and cellular level with unprecedented resolution. However, computational methods enabling detailed matching are still scarce. Here, we provide a structured scRNAseq-based approach that we applied to scRNAseq from blood leukocytes originating from humans and hamsters affected with moderate or severe COVID-19. FINDINGS Integration of data from patients with COVID-19 with two hamster models that develop moderate (Syrian hamster, Mesocricetus auratus) or severe (Roborovski hamster, Phodopus roborovskii) disease revealed that most cellular states are shared across species. A neural network-based analysis using variational autoencoders quantified the overall transcriptomic similarity across species and severity levels, showing highest similarity between neutrophils of Roborovski hamsters and patients with severe COVID-19, while Syrian hamsters better matched patients with moderate disease, particularly in classical monocytes. We further used transcriptome-wide differential expression analysis to identify which disease stages and cell types display strongest transcriptional changes. INTERPRETATION Consistently, hamsters' response to COVID-19 was most similar to humans in monocytes and neutrophils. Disease-linked pathways found in all species specifically related to interferon response or inhibition of viral replication. Analysis of candidate genes and signatures supported the results. Our structured neural network-supported workflow could be applied to other diseases, allowing better identification of suitable animal models with similar pathomechanisms across species. FUNDING This work was supported by German Federal Ministry of Education and Research, (BMBF) grant IDs: 01ZX1304B, 01ZX1604B, 01ZX1906A, 01ZX1906B, 01KI2124, 01IS18026B and German Research Foundation (DFG) grant IDs: 14933180, 431232613.
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Affiliation(s)
- Vincent D Friedrich
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany; Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Leipzig, Germany
| | - Peter Pennitz
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany
| | - Emanuel Wyler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Julia M Adler
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
| | - Dylan Postmus
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Liverpool School of Tropical Medicine, Department of Tropical Disease Biology, Liverpool, United Kingdom
| | - Kristina Müller
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany
| | - Luiz Gustavo Teixeira Alves
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Julia Prigann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Gladstone Institutes, San Francisco, USA
| | - Fabian Pott
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Thomas Hoefler
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
| | - Cengiz Goekeri
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany; Cyprus International University, Faculty of Medicine, Nicosia, Cyprus
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany; Humboldt-Universität zu Berlin, Institut fuer Biologie, Berlin, Germany
| | - Christine Goffinet
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Liverpool School of Tropical Medicine, Department of Tropical Disease Biology, Liverpool, United Kingdom
| | - Antoine-Emmanuel Saliba
- Faculty of Medicine, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Markus Scholz
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany; University of Leipzig, Faculty of Mathematics and Computer Science, Leipzig, Germany
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany; German Center for Lung Research (DZL), Berlin, Germany
| | - Jakob Trimpert
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
| | - Holger Kirsten
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany.
| | - Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany.
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13
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Zhao M, Li J, Liu X, Ma K, Tang J, Guo F. A gene regulatory network-aware graph learning method for cell identity annotation in single-cell RNA-seq data. Genome Res 2024; 34:1036-1051. [PMID: 39134412 PMCID: PMC11368180 DOI: 10.1101/gr.278439.123] [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: 08/28/2023] [Accepted: 07/23/2024] [Indexed: 08/22/2024]
Abstract
Cell identity annotation for single-cell transcriptome data is a crucial process for constructing cell atlases, unraveling pathogenesis, and inspiring therapeutic approaches. Currently, the efficacy of existing methodologies is contingent upon specific data sets. Nevertheless, such data are often sourced from various batches, sequencing technologies, tissues, and even species. Notably, the gene regulatory relationship remains unaffected by the aforementioned factors, highlighting the extensive gene interactions within organisms. Therefore, we propose scHGR, an automated annotation tool designed to leverage gene regulatory relationships in constructing gene-mediated cell communication graphs for single-cell transcriptome data. This strategy helps reduce noise from diverse data sources while establishing distant cellular connections, yielding valuable biological insights. Experiments involving 22 scenarios demonstrate that scHGR precisely and consistently annotates cell identities, benchmarked against state-of-the-art methods. Crucially, scHGR uncovers novel subtypes within peripheral blood mononuclear cells, specifically from CD4+ T cells and cytotoxic T cells. Furthermore, by characterizing a cell atlas comprising 56 cell types for COVID-19 patients, scHGR identifies vital factors like IL1 and calcium ions, offering insights for targeted therapeutic interventions.
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Affiliation(s)
- Mengyuan Zhao
- College of Computer Science and Control Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Jiawei Li
- College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
| | - Xiaoyi Liu
- Computer Science and Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Ke Ma
- College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jijun Tang
- College of Computer Science and Control Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
| | - Fei Guo
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
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14
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Thompson MD, Reiner-Link D, Berghella A, Rana BK, Rovati GE, Capra V, Gorvin CM, Hauser AS. G protein-coupled receptor (GPCR) pharmacogenomics. Crit Rev Clin Lab Sci 2024:1-44. [PMID: 39119983 DOI: 10.1080/10408363.2024.2358304] [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: 06/15/2023] [Revised: 09/03/2023] [Accepted: 05/18/2024] [Indexed: 08/10/2024]
Abstract
The field of pharmacogenetics, the investigation of the influence of one or more sequence variants on drug response phenotypes, is a special case of pharmacogenomics, a discipline that takes a genome-wide approach. Massively parallel, next generation sequencing (NGS), has allowed pharmacogenetics to be subsumed by pharmacogenomics with respect to the identification of variants associated with responders and non-responders, optimal drug response, and adverse drug reactions. A plethora of rare and common naturally-occurring GPCR variants must be considered in the context of signals from across the genome. Many fundamentals of pharmacogenetics were established for G protein-coupled receptor (GPCR) genes because they are primary targets for a large number of therapeutic drugs. Functional studies, demonstrating likely-pathogenic and pathogenic GPCR variants, have been integral to establishing models used for in silico analysis. Variants in GPCR genes include both coding and non-coding single nucleotide variants and insertion or deletions (indels) that affect cell surface expression (trafficking, dimerization, and desensitization/downregulation), ligand binding and G protein coupling, and variants that result in alternate splicing encoding isoforms/variable expression. As the breadth of data on the GPCR genome increases, we may expect an increase in the use of drug labels that note variants that significantly impact the clinical use of GPCR-targeting agents. We discuss the implications of GPCR pharmacogenomic data derived from the genomes available from individuals who have been well-phenotyped for receptor structure and function and receptor-ligand interactions, and the potential benefits to patients of optimized drug selection. Examples discussed include the renin-angiotensin system in SARS-CoV-2 (COVID-19) infection, the probable role of chemokine receptors in the cytokine storm, and potential protease activating receptor (PAR) interventions. Resources dedicated to GPCRs, including publicly available computational tools, are also discussed.
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Affiliation(s)
- Miles D Thompson
- Krembil Brain Institute, Toronto Western Hospital, Toronto, Ontario, Canada
| | - David Reiner-Link
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alessandro Berghella
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Brinda K Rana
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - G Enrico Rovati
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Valerie Capra
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Caroline M Gorvin
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom
| | - Alexander S Hauser
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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15
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Malireddi RKS, Kanneganti TD. Chromatin Regulator SMARCA4 Is Essential for MHV-Induced Inflammatory Cell Death, PANoptosis. Viruses 2024; 16:1261. [PMID: 39205235 PMCID: PMC11359047 DOI: 10.3390/v16081261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 08/04/2024] [Indexed: 09/04/2024] Open
Abstract
The innate immune system serves as the first line of defense against β-coronaviruses (β-CoVs), a family of viruses that includes SARS-CoV-2. Viral sensing via pattern recognition receptors triggers inflammation and cell death, which are essential components of the innate immune response that facilitate viral clearance. However, excessive activation of the innate immune system and inflammatory cell death can result in uncontrolled release of proinflammatory cytokines, resulting in cytokine storm and pathology. PANoptosis, innate immune, inflammatory cell death initiated by innate immune sensors and driven by caspases and RIPKs through PANoptosome complexes, has been implicated in the pathology of viral infections. Therefore, understanding the molecular mechanisms regulating PANoptosis in response to β-CoV infection is critical for identifying new therapeutic targets that can mitigate disease severity. In the current study, we analyzed findings from a cell death-based CRISPR screen with archetypal β-CoV mouse hepatitis virus (MHV) as the trigger to characterize host molecules required for inflammatory cell death. As a result, we identified SMARCA4, a chromatin regulator, as a putative host factor required for PANoptosis in response to MHV. Furthermore, we observed that gRNA-mediated deletion of Smarca4 inhibited MHV-induced PANoptotic cell death in macrophages. These findings have potential translational and clinical implications for the advancement of treatment strategies for β-CoVs and other infections.
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16
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Suzuki H, Tanaka T, Li G, Ouchida T, Kaneko MK, Kato Y. Development of a Sensitive Anti-Mouse CCR5 Monoclonal Antibody for Flow Cytometry. Monoclon Antib Immunodiagn Immunother 2024; 43:96-100. [PMID: 38836505 DOI: 10.1089/mab.2024.0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024] Open
Abstract
C-C chemokine receptor 5 (CCR5), a member of the G protein-coupled receptor family, is the most common coreceptor for the human immunodeficiency virus type 1. CCR5 is also involved in the pathogenesis of tumors and inflammatory diseases. The CCR5 antagonists including monoclonal antibodies (mAbs) have been developed and evaluated in clinical trials. In this study, we developed novel mAbs for mouse CCR5 (mCCR5) using the Cell-Based Immunization and Screening (CBIS) method. One of the established anti-mCCR5 mAbs, C5Mab-2 (rat IgG2b, kappa), reacted with mCCR5-overexpressed Chinese hamster ovary-K1 (CHO/mCCR5) and an endogenously mCCR5-expressing cell line (L1210) by flow cytometry. Using flow cytometry, the dissociation constant (KD) of C5Mab-2 for CHO/mCCR5 was determined as 4.3 × 10-8 M. These results indicated that C5Mab-2 is useful for the detection of mCCR5 in flow cytometry and may be applicable to obtain the proof of concept in preclinical studies.
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Affiliation(s)
- Hiroyuki Suzuki
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomohiro Tanaka
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Guanjie Li
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tsunenori Ouchida
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mika K Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
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17
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Ubukata R, Suzuki H, Tanaka T, Li G, Kaneko MK, Kato Y. Development of Sensitive Anti-Mouse CCR5 Monoclonal Antibodies Using the N-Terminal Peptide Immunization. Monoclon Antib Immunodiagn Immunother 2024; 43:112-118. [PMID: 38868984 DOI: 10.1089/mab.2024.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
One of the G protein-coupled receptors, C-C chemokine receptor 5 (CCR5), is an important regulator for the activation of T and B lymphocytes, dendritic cells, natural killer cells, and macrophages. Upon binding to its ligands, CCR5 activates downstream signaling, which is an important regulator in the innate and adaptive immune response through the promotion of lymphocyte migration and the secretion of proinflammatory cytokines. Anti-CCR5 monoclonal antibodies (mAbs) have been developed and evaluated in clinical trials for tumors and inflammatory diseases. In this study, we developed novel mAbs for mouse CCR5 (mCCR5) using the N-terminal peptide immunization. Among the established anti-mCCR5 mAbs, C5Mab-4 (rat IgG2a, kappa) and C5Mab-8 (rat IgG1, kappa), recognized mCCR5-overexpressing Chinese hamster ovary-K1 (CHO/mCCR5) and an endogenously mCCR5-expressing cell line (L1210) by flow cytometry. The dissociation constant (KD) values of C5Mab-4 and C5Mab-8 for CHO/mCCR5 were determined as 3.5 × 10-8 M and 7.3 × 10-9 M, respectively. Furthermore, both C5Mab-4 and C5Mab-8 could detect mCCR5 by western blotting. These results indicated that C5Mab-4 and C5Mab-8 are useful for detecting mCCR5 by flow cytometry and western blotting and provide a possibility to obtain the proof of concept in preclinical studies.
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Affiliation(s)
| | | | - Tomohiro Tanaka
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Guanjie Li
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mika K Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
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18
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Antos D, Parks OB, Duray AM, Abraham N, Michel JJ, Kupul S, Westcott R, Alcorn JF. Cell-intrinsic regulation of phagocyte function by interferon lambda during pulmonary viral, bacterial super-infection. PLoS Pathog 2024; 20:e1012498. [PMID: 39178311 PMCID: PMC11376568 DOI: 10.1371/journal.ppat.1012498] [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: 01/25/2024] [Revised: 09/05/2024] [Accepted: 08/12/2024] [Indexed: 08/25/2024] Open
Abstract
Influenza infections result in a significant number of severe illnesses annually, many of which are complicated by secondary bacterial super-infection. Primary influenza infection has been shown to increase susceptibility to secondary methicillin-resistant Staphylococcus aureus (MRSA) infection by altering the host immune response, leading to significant immunopathology. Type III interferons (IFNs), or IFNλs, have gained traction as potential antiviral therapeutics due to their restriction of viral replication without damaging inflammation. The role of IFNλ in regulating epithelial biology in super-infection has recently been established; however, the impact of IFNλ on immune cells is less defined. In this study, we infected wild-type and IFNLR1-/- mice with influenza A/PR/8/34 followed by S. aureus USA300. We demonstrated that global IFNLR1-/- mice have enhanced bacterial clearance through increased uptake by phagocytes, which was shown to be cell-intrinsic specifically in myeloid cells in mixed bone marrow chimeras. We also showed that depletion of IFNLR1 on CX3CR1 expressing myeloid immune cells, but not neutrophils, was sufficient to significantly reduce bacterial burden compared to mice with intact IFNLR1. These findings provide insight into how IFNλ in an influenza-infected lung impedes bacterial clearance during super-infection and show a direct cell intrinsic role for IFNλ signaling on myeloid cells.
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Affiliation(s)
- Danielle Antos
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Olivia B Parks
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexis M Duray
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nevil Abraham
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joshua J Michel
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Saran Kupul
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Rosemary Westcott
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - John F Alcorn
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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19
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Dubovik T, Lukačišin M, Starosvetsky E, LeRoy B, Normand R, Admon Y, Alpert A, Ofran Y, G'Sell M, Shen-Orr SS. Interactions between immune cell types facilitate the evolution of immune traits. Nature 2024; 632:350-356. [PMID: 38866051 PMCID: PMC11306095 DOI: 10.1038/s41586-024-07661-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 06/04/2024] [Indexed: 06/14/2024]
Abstract
An essential prerequisite for evolution by natural selection is variation among individuals in traits that affect fitness1. The ability of a system to produce selectable variation, known as evolvability2, thus markedly affects the rate of evolution. Although the immune system is among the fastest-evolving components in mammals3, the sources of variation in immune traits remain largely unknown4,5. Here we show that an important determinant of the immune system's evolvability is its organization into interacting modules represented by different immune cell types. By profiling immune cell variation in bone marrow of 54 genetically diverse mouse strains from the Collaborative Cross6, we found that variation in immune cell frequencies is polygenic and that many associated genes are involved in homeostatic balance through cell-intrinsic functions of proliferation, migration and cell death. However, we also found genes associated with the frequency of a particular cell type that are expressed in a different cell type, exerting their effect in what we term cyto-trans. The vertebrate evolutionary record shows that genes associated in cyto-trans have faced weaker negative selection, thus increasing the robustness and hence evolvability2,7,8 of the immune system. This phenomenon is similarly observable in human blood. Our findings suggest that interactions between different components of the immune system provide a phenotypic space in which mutations can produce variation with little detriment, underscoring the role of modularity in the evolution of complex systems9.
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Affiliation(s)
- Tania Dubovik
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Martin Lukačišin
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Elina Starosvetsky
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Benjamin LeRoy
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
- Nike, Beaverton, OR, USA
| | - Rachelly Normand
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Massachusetts General Hospital, Boston, MA, USA
| | - Yasmin Admon
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Ayelet Alpert
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Oncology, Rambam Health Care Campus, Haifa, Israel
| | - Yishai Ofran
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Haematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa, Israel
- Haematology and Bone Marrow Transplantation Department and the Eisenberg R&D Authority, Shaare Zedek Medical Centre, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Max G'Sell
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Shai S Shen-Orr
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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20
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Yang X, Mann KK, Wu H, Ding J. scCross: a deep generative model for unifying single-cell multi-omics with seamless integration, cross-modal generation, and in silico exploration. Genome Biol 2024; 25:198. [PMID: 39075536 PMCID: PMC11285326 DOI: 10.1186/s13059-024-03338-z] [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: 12/15/2023] [Accepted: 07/16/2024] [Indexed: 07/31/2024] Open
Abstract
Single-cell multi-omics data reveal complex cellular states, providing significant insights into cellular dynamics and disease. Yet, integration of multi-omics data presents challenges. Some modalities have not reached the robustness or clarity of established transcriptomics. Coupled with data scarcity for less established modalities and integration intricacies, these challenges limit our ability to maximize single-cell omics benefits. We introduce scCross, a tool leveraging variational autoencoders, generative adversarial networks, and the mutual nearest neighbors (MNN) technique for modality alignment. By enabling single-cell cross-modal data generation, multi-omics data simulation, and in silico cellular perturbations, scCross enhances the utility of single-cell multi-omics studies.
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Affiliation(s)
- Xiuhui Yang
- School of Software, Shandong University, 1500 Shunhua, Jinan, 250101, Shandong, China
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, H4A 3J1, QC, Canada
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Koren K Mann
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Hao Wu
- School of Software, Shandong University, 1500 Shunhua, Jinan, 250101, Shandong, China.
| | - Jun Ding
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, H4A 3J1, QC, Canada.
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, QC, H3G 1Y6, Canada.
- Mila-Quebec AI Institute, Montreal, QC, H2S 3H1, Canada.
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21
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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22
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Leibel SL, McVicar RN, Murad R, Kwong EM, Clark AE, Alvarado A, Grimmig BA, Nuryyev R, Young RE, Lee JC, Peng W, Zhu YP, Griffis E, Nowell CJ, James B, Alarcon S, Malhotra A, Gearing LJ, Hertzog PJ, Galapate CM, Galenkamp KMO, Commisso C, Smith DM, Sun X, Carlin AF, Sidman RL, Croker BA, Snyder EY. A therapy for suppressing canonical and noncanonical SARS-CoV-2 viral entry and an intrinsic intrapulmonary inflammatory response. Proc Natl Acad Sci U S A 2024; 121:e2408109121. [PMID: 39028694 PMCID: PMC11287264 DOI: 10.1073/pnas.2408109121] [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: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 07/21/2024] Open
Abstract
The prevalence of "long COVID" is just one of the conundrums highlighting how little we know about the lung's response to viral infection, particularly to syndromecoronavirus-2 (SARS-CoV-2), for which the lung is the point of entry. We used an in vitro human lung system to enable a prospective, unbiased, sequential single-cell level analysis of pulmonary cell responses to infection by multiple SARS-CoV-2 strains. Starting with human induced pluripotent stem cells and emulating lung organogenesis, we generated and infected three-dimensional, multi-cell-type-containing lung organoids (LOs) and gained several unexpected insights. First, SARS-CoV-2 tropism is much broader than previously believed: Many lung cell types are infectable, if not through a canonical receptor-mediated route (e.g., via Angiotensin-converting encyme 2(ACE2)) then via a noncanonical "backdoor" route (via macropinocytosis, a form of endocytosis). Food and Drug Administration (FDA)-approved endocytosis blockers can abrogate such entry, suggesting adjunctive therapies. Regardless of the route of entry, the virus triggers a lung-autonomous, pulmonary epithelial cell-intrinsic, innate immune response involving interferons and cytokine/chemokine production in the absence of hematopoietic derivatives. The virus can spread rapidly throughout human LOs resulting in mitochondrial apoptosis mediated by the prosurvival protein Bcl-xL. This host cytopathic response to the virus may help explain persistent inflammatory signatures in a dysfunctional pulmonary environment of long COVID. The host response to the virus is, in significant part, dependent on pulmonary Surfactant Protein-B, which plays an unanticipated role in signal transduction, viral resistance, dampening of systemic inflammatory cytokine production, and minimizing apoptosis. Exogenous surfactant, in fact, can be broadly therapeutic.
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Affiliation(s)
- Sandra L. Leibel
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
| | - Rachael N. McVicar
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Rabi Murad
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Elizabeth M. Kwong
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Alex E. Clark
- Department of Medicine, University of California San Diego, La Jolla, CA92093
| | - Asuka Alvarado
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Bethany A. Grimmig
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Ruslan Nuryyev
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Randee E. Young
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Jamie C. Lee
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Weiqi Peng
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Yanfang P. Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Eric Griffis
- Nikon Imaging Center, University of California San Diego, La Jolla, CA92093
| | - Cameron J. Nowell
- Monash Institute of Pharmaceutical Sciences, Parkville, VIC3052, Australia
| | - Brian James
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Suzie Alarcon
- La Jolla Institute for Immunology, La Jolla, CA92037
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California San Diego, La Jolla, CA92093
| | - Linden J. Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC3168, Australia
- Department of Molecular and Translational Sciences, Monash University Clayton, Clayton, VIC3168, Australia
| | - Paul J. Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC3168, Australia
- Department of Molecular and Translational Sciences, Monash University Clayton, Clayton, VIC3168, Australia
| | - Cheska M. Galapate
- Sanford Burnham Prebys Medical Discovery Institute Cell & Molecular Biology of Cancer, La Jolla, CA92037
| | - Koen M. O. Galenkamp
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
| | - Cosimo Commisso
- Sanford Burnham Prebys Medical Discovery Institute Cell & Molecular Biology of Cancer, La Jolla, CA92037
| | - Davey M. Smith
- Department of Medicine, University of California San Diego, La Jolla, CA92093
| | - Xin Sun
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Aaron F. Carlin
- Department of Medicine, University of California San Diego, La Jolla, CA92093
| | - Richard L. Sidman
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02115
| | - Ben A. Croker
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Evan Y. Snyder
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92037
- Sanford Burnham Prebys Medical Discovery Institute, Center for Stem Cells & Regenerative Medicine, La Jolla, CA92037
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23
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Caohuy H, Eidelman O, Chen T, Mungunsukh O, Yang Q, Walton NI, Pollard BS, Khanal S, Hentschel S, Florez C, Herbert AS, Pollard HB. Inflammation in the COVID-19 airway is due to inhibition of CFTR signaling by the SARS-CoV-2 spike protein. Sci Rep 2024; 14:16895. [PMID: 39043712 PMCID: PMC11266487 DOI: 10.1038/s41598-024-66473-4] [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: 12/15/2023] [Accepted: 07/01/2024] [Indexed: 07/25/2024] Open
Abstract
SARS-CoV-2-contributes to sickness and death in COVID-19 patients partly by inducing a hyper-proinflammatory immune response in the host airway. This hyper-proinflammatory state involves activation of signaling by NFκB, and unexpectedly, ENaC, the epithelial sodium channel. Post-infection inflammation may also contribute to "Long COVID"/PASC. Enhanced signaling by NFκB and ENaC also marks the airway of patients suffering from cystic fibrosis, a life-limiting proinflammatory genetic disease due to inactivating mutations in the CFTR gene. We therefore hypothesized that inflammation in the COVID-19 airway might similarly be due to inhibition of CFTR signaling by SARS-CoV-2 spike protein, and therefore activation of both NFκB and ENaC signaling. We used western blot and electrophysiological techniques, and an organoid model of normal airway epithelia, differentiated on an air-liquid-interface (ALI). We found that CFTR protein expression and CFTR cAMP-activated chloride channel activity were lost when the model epithelium was exposed to SARS-CoV-2 spike proteins. As hypothesized, the absence of CFTR led to activation of both TNFα/NFκB signaling and α and γ ENaC. We had previously shown that the cardiac glycoside drugs digoxin, digitoxin and ouabain blocked interaction of spike protein and ACE2. Consistently, addition of 30 nM concentrations of the cardiac glycoside drugs, prevented loss of both CFTR protein and CFTR channel activity. ACE2 and CFTR were found to co-immunoprecipitate in both basal cells and differentiated epithelia. Thus spike-dependent CFTR loss might involve ACE2 as a bridge between Spike and CFTR. In addition, spike exposure to the epithelia resulted in failure of endosomal recycling to return CFTR to the plasma membrane. Thus, failure of CFTR recovery from endosomal recycling might be a mechanism for spike-dependent loss of CFTR. Finally, we found that authentic SARS-CoV-2 virus infection induced loss of CFTR protein, which was rescued by the cardiac glycoside drugs digitoxin and ouabain. Based on experiments with this organoid model of small airway epithelia, and comparisons with 16HBE14o- and other cell types expressing normal CFTR, we predict that inflammation in the COVID-19 airway may be mediated by inhibition of CFTR signaling by the SARS-CoV-2 spike protein, thus inducing a cystic fibrosis-like clinical phenotype. To our knowledge this is the first time COVID-19 airway inflammation has been experimentally traced in normal subjects to a contribution from SARS-CoV-2 spike-dependent inhibition of CFTR signaling.
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Affiliation(s)
- Hung Caohuy
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Ofer Eidelman
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Tinghua Chen
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Ognoon Mungunsukh
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Center for Military Precision Health, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Qingfeng Yang
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Center for the Study of Traumatic Stress (CSTS), and Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Nathan I Walton
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | | | - Sara Khanal
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, 21702, USA
- The Geneva Foundation, Tacoma, WA, 98402, USA
| | - Shannon Hentschel
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, 21702, USA
- Cherokee Nation Assurance, Catoosa, OK, 74015, USA
| | - Catalina Florez
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, 21702, USA
- The Geneva Foundation, Tacoma, WA, 98402, USA
| | - Andrew S Herbert
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, 21702, USA
| | - Harvey B Pollard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
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24
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Wu Y, Wang Y, Wang X, Li M, Yan H, Shi H, Shi D, Chen J, Guo L, Feng L. Elevation of IL-8 secretion induced by PEDV infection via NF-κB signaling pathway. Front Cell Infect Microbiol 2024; 14:1422560. [PMID: 39104852 PMCID: PMC11298435 DOI: 10.3389/fcimb.2024.1422560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/05/2024] [Indexed: 08/07/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is associated with severe enteritis, which contributes to high mortality in piglets. The aim of this study was to describe molecular mechanisms associated with proinflammatory cytokine(s) production during PEDV infection. We showed that infection of porcine intestine epithelial cell clone J2 (IPEC-J2) with PEDV induces a gradual increase in interleukin 8 (IL-8) production at different time points, as well as infection of Vero E6 with PEDV. The secretion of IL-8 in these two cell lines infected with PEDV is related to the activation of NF-κB. Furthermore, the cells expressing PEDV M or E protein can induce the upregulation of IL-8. These findings suggest that the IL-8 production can be the initiator of inflammatory response by the host cells upon PEDV infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Longjun Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Li Feng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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25
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Toy L, Huber ME, Lee M, Bartolomé AA, Ortiz Zacarías NV, Nasser S, Scholl S, Zlotos DP, Mandour YM, Heitman LH, Szpakowska M, Chevigné A, Schiedel M. Fluorophore-Labeled Pyrrolones Targeting the Intracellular Allosteric Binding Site of the Chemokine Receptor CCR1. ACS Pharmacol Transl Sci 2024; 7:2080-2092. [PMID: 39022357 PMCID: PMC11249626 DOI: 10.1021/acsptsci.4c00182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/18/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024]
Abstract
In this study, we describe the structure-based development of the first fluorescent ligands targeting the intracellular allosteric binding site (IABS) of the CC chemokine receptor type 1 (CCR1), a G protein-coupled receptor (GPCR) that has been pursued as a drug target in inflammation and immune diseases. Starting from previously reported intracellular allosteric modulators of CCR1, tetramethylrhodamine (TAMRA)-labeled ligands were designed, synthesized, and tested for their suitability as fluorescent tracers to probe binding to the IABS of CCR1. In the course of these studies, we developed LT166 (12) as a highly versatile fluorescent CCR1 ligand, enabling cell-free as well as cellular NanoBRET-based binding studies in a nonradioactive and high-throughput manner. Besides the detection of intracellular allosteric ligands by direct competition with 12, we were also able to monitor the binding of extracellular antagonists due to their positive cooperative binding with 12. Thereby, we provide a straightforward and nonradioactive method to easily distinguish between ligands binding to the IABS of CCR1 and extracellular negative modulators. Further, we applied 12 for the identification of novel chemotypes for intracellular CCR1 inhibition that feature high binding selectivity for CCR1 over CCR2. For one of the newly identified intracellular CCR1 ligands (i.e., 23), we were able to show CCR1 over CCR2 selectivity also on a functional level and demonstrated that this compound inhibits basal β-arrestin recruitment to CCR1, thereby acting as an inverse agonist. Thus, our fluorescent CCR1 ligand 12 represents a highly promising tool for future studies of CCR1-targeted pharmacology and drug discovery.
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Affiliation(s)
- Lara Toy
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen 91058, Germany
| | - Max E. Huber
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen 91058, Germany
| | - Minhee Lee
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, Braunschweig 38106, Germany
| | - Ana Alonso Bartolomé
- Immuno-Pharmacology
and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Rue Henri Koch 29, Esch-sur-Alzette L-4354, Luxembourg
- Faculty
of Science, Technology and Medicine, University
of Luxembourg, 2 Avenue
de l’Université, Esch-sur-Alzette L-4365, Luxembourg
| | - Natalia V. Ortiz Zacarías
- Leiden
Academic Centre for Drug Research (LACDR), Division of Chemistry, Leiden University, Leiden 2333 CC, Netherlands
| | - Sherif Nasser
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, the German University in Cairo, New Cairo City 11835, Cairo, Egypt
| | - Stephan Scholl
- Institute
for Chemical and Thermal Process Engineering (ICTV), Technische Universität Braunschweig, Langer Kamp 7, Braunschweig 38106, Germany
| | - Darius P. Zlotos
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, the German University in Cairo, New Cairo City 11835, Cairo, Egypt
| | - Yasmine M. Mandour
- School
of Life and Medical Sciences, University
of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo 11578, Egypt
| | - Laura H. Heitman
- Leiden
Academic Centre for Drug Research (LACDR), Division of Chemistry, Leiden University, Leiden 2333 CC, Netherlands
- Oncode
Institute, Leiden University, Leiden 2333 CC, Netherlands
| | - Martyna Szpakowska
- Immuno-Pharmacology
and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Rue Henri Koch 29, Esch-sur-Alzette L-4354, Luxembourg
| | - Andy Chevigné
- Immuno-Pharmacology
and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Rue Henri Koch 29, Esch-sur-Alzette L-4354, Luxembourg
| | - Matthias Schiedel
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen 91058, Germany
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, Braunschweig 38106, Germany
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26
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Shouman S, El-Kholy N, Hussien AE, El-Derby AM, Magdy S, Abou-Shanab AM, Elmehrath AO, Abdelwaly A, Helal M, El-Badri N. SARS-CoV-2-associated lymphopenia: possible mechanisms and the role of CD147. Cell Commun Signal 2024; 22:349. [PMID: 38965547 PMCID: PMC11223399 DOI: 10.1186/s12964-024-01718-3] [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: 02/24/2024] [Accepted: 06/15/2024] [Indexed: 07/06/2024] Open
Abstract
T lymphocytes play a primary role in the adaptive antiviral immunity. Both lymphocytosis and lymphopenia were found to be associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While lymphocytosis indicates an active anti-viral response, lymphopenia is a sign of poor prognosis. T-cells, in essence, rarely express ACE2 receptors, making the cause of cell depletion enigmatic. Moreover, emerging strains posed an immunological challenge, potentially alarming for the next pandemic. Herein, we review how possible indirect and direct key mechanisms could contribute to SARS-CoV-2-associated-lymphopenia. The fundamental mechanism is the inflammatory cytokine storm elicited by viral infection, which alters the host cell metabolism into a more acidic state. This "hyperlactic acidemia" together with the cytokine storm suppresses T-cell proliferation and triggers intrinsic/extrinsic apoptosis. SARS-CoV-2 infection also results in a shift from steady-state hematopoiesis to stress hematopoiesis. Even with low ACE2 expression, the presence of cholesterol-rich lipid rafts on activated T-cells may enhance viral entry and syncytia formation. Finally, direct viral infection of lymphocytes may indicate the participation of other receptors or auxiliary proteins on T-cells, that can work alone or in concert with other mechanisms. Therefore, we address the role of CD147-a novel route-for SARS-CoV-2 and its new variants. CD147 is not only expressed on T-cells, but it also interacts with other co-partners to orchestrate various biological processes. Given these features, CD147 is an appealing candidate for viral pathogenicity. Understanding the molecular and cellular mechanisms behind SARS-CoV-2-associated-lymphopenia will aid in the discovery of potential therapeutic targets to improve the resilience of our immune system against this rapidly evolving virus.
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Affiliation(s)
- Shaimaa Shouman
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, 12587, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
| | - Nada El-Kholy
- Department of Drug Discovery, H. Lee Moffit Cancer Center& Research Institute, Tampa, FL, 33612, USA
- Cancer Chemical Biology Ph.D. Program, University of South Florida, Tampa, FL, 33620, USA
| | - Alaa E Hussien
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, 12587, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
| | - Azza M El-Derby
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, 12587, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
| | - Shireen Magdy
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, 12587, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
| | - Ahmed M Abou-Shanab
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, 12587, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
| | | | - Ahmad Abdelwaly
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - Mohamed Helal
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt
- Medicinal Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia, 41522, Egypt
| | - Nagwa El-Badri
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, 12587, Egypt.
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, 12587, Egypt.
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27
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Gu L, Chen H, Sun M, Chen Y, Shi Q, Chang J, Wei J, Ma W, Bao X, Wang R. Unraveling dynamic immunological landscapes in intracerebral hemorrhage: insights from single-cell and spatial transcriptomic profiling. MedComm (Beijing) 2024; 5:e635. [PMID: 38988493 PMCID: PMC11233862 DOI: 10.1002/mco2.635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 07/12/2024] Open
Abstract
Intracerebral hemorrhage (ICH) poses a formidable challenge in stroke management, with limited therapeutic options, particularly in the realm of immune-targeted interventions. Clinical trials targeting immune responses post-ICH have encountered setbacks, potentially attributable to the substantial cellular heterogeneity and intricate intercellular networks within the brain. Here, we present a pioneering investigation utilizing single-cell RNA sequencing and spatial transcriptome profiling at hyperacute (1 h), acute (24 h), and subacute (7 days) intervals post-ICH, aimed at unraveling the dynamic immunological landscape and spatial distributions within the cerebral tissue. Our comprehensive analysis revealed distinct cell differentiation patterns among myeloid and lymphocyte populations, along with delineated spatial distributions across various brain regions. Notably, we identified a subset of lymphocytes characterized by the expression of Spp1 and Lyz2, termed macrophage-associated lymphocytes, which exhibited close interactions with myeloid cells. Specifically, we observed prominent interactions between Lgmn+Macro-T cells and microglia through the spp1-cd44 pathway during the acute phase post-ICH in the choroid plexus. These findings represent a significant advancement in our understanding of immune cell dynamics at single-cell resolution across distinct post-ICH time points, thereby laying the groundwork for exploring critical temporal windows and informing the development of targeted therapeutic strategies.
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Affiliation(s)
- Lingui Gu
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Hualin Chen
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Mingjiang Sun
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical UniversityBeijingChina
| | - Yihao Chen
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Qinglei Shi
- Research Institute of Big Data, Chinese University of Hong Kong (Shenzhen) School of MedicineShenzhenChina
| | - Jianbo Chang
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Junji Wei
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Wenbin Ma
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xinjie Bao
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- State Key Laboratory of Common Mechanism Research for Major DiseasesBeijingChina
| | - Renzhi Wang
- Department of NeurosurgeryPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- School of MedicineThe Chinese University of Hong KongShenzhenGuangdongChina
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28
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Toya S, Struyf S, Huerta L, Morris P, Gavioli E, Minnella EM, Cesta MC, Allegretti M, Proost P. A narrative review of chemokine receptors CXCR1 and CXCR2 and their role in acute respiratory distress syndrome. Eur Respir Rev 2024; 33:230172. [PMID: 39048127 PMCID: PMC11267298 DOI: 10.1183/16000617.0172-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 05/15/2024] [Indexed: 07/27/2024] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a severe form of acute respiratory failure characterised by extensive inflammatory injury to the alveolocapillary barrier leading to alveolar oedema, impaired gas exchange and, ultimately, hypoxaemia necessitating the use of supplemental oxygen combined with some degree of positive airway pressure. Although much heterogeneity exists regarding the aetiology, localisation and endotypic characterisation of ARDS, what remains largely undisputed is the role of the innate immune system, and in particular of neutrophils, in precipitating and propagating lung injury. Activated neutrophils, recruited to the lung through chemokine gradients, promote injury by releasing oxidants, proteases and neutrophil extracellular traps, which ultimately cause platelet aggregation, microvascular thrombosis and cellular death. Among various neutrophilic chemoattractants, interleukin-8/C-X-C motif ligand 8 and related chemokines, collectively called ELR+ chemokines, acting on neutrophils through the G protein-coupled receptors CXCR1 and CXCR2, are pivotal in orchestrating the neutrophil activation status and chemotaxis in the inflamed lung. This allows efficient elimination of infectious agents while at the same time minimising collateral damage to host tissue. Therefore, understanding how CXCR1 and CXCR2 receptors are regulated is important if we hope to effectively target them for therapeutic use in ARDS. In the following narrative review, we provide an overview of the role of ELR+ chemokines in acute lung injury (ALI) and ARDS, we summarise the relevant regulatory pathways of their cognisant receptors CXCR1/2 and highlight current preclinical and clinical evidence on the therapeutic role of CXCR1 and CXCR2 inhibition in animal models of ALI, as well as in ARDS patients.
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Affiliation(s)
| | - Sofie Struyf
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Leuven, Belgium
| | - Luis Huerta
- Keck School of Medicine of USC, Department of Medicine, Pulmonary and Critical Care Medicine, Los Angeles, CA, USA
| | - Peter Morris
- The University of Alabama at Birmingham, Department of Medicine, Pulmonary, Allergy, and Critical Care Medicine, Birmingham, AL, USA
| | | | | | | | | | - Paul Proost
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Leuven, Belgium
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29
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Gutierrez-Chavez C, Aperrigue-Lira S, Ortiz-Saavedra B, Paz I. Chemokine receptors in COVID-19 infection. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 388:53-94. [PMID: 39260938 DOI: 10.1016/bs.ircmb.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Chemokine receptors play diverse roles in the immune response against pathogens by recruiting innate and adaptive immune cells to sites of infection. However, their involvement could also be detrimental, causing tissue damage and exacerbating respiratory diseases by triggering histological alterations such as fibrosis and remodeling. This chapter reviews the role of chemokine receptors in the immune defense against SARS-CoV-2 infection. In COVID-19, CXCR3 is expressed mainly in T cells, and its upregulation is related to an increase in SARS-CoV-2-specific antibodies but also to COVID-19 severity. CCR5 is a key player in T-cell recruitment, and its suppression leads to reduced inflammation and viremia levels. Conversely, CXCR6 is implicated in the aberrant migration of memory T cells within airways. On the other hand, increased CCR4+ cells in the blood and decreased CCR4+ cells in lung cells are associated with severe COVID-19. Additionally, CCR2 is associated with an increase in macrophage recruitment to lung tissues. Elevated levels of CXCR1 and CXCR2, which are predominantly expressed in neutrophils, are associated with the severity of the disease, and finally, the expression of CX3CR1 in cytotoxic T lymphocytes affects the retention of these cells in lung tissues, thereby impacting the severity of COVID-19. Despite the efforts of many clinical trials to find effective therapies for COVID-19 using chemokine receptor inhibitors, no conclusive results have been found due to the small number of patients, redundancy, and co-expression of chemokine receptors by immune cells, which explains the difficulty in finding a single therapeutic target or effective treatment.
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Affiliation(s)
| | - Shalom Aperrigue-Lira
- Universidad Nacional de San Agustín de Arequipa, Arequipa, Peru; Grupo de Investigación en Inmunología-GII, UNSA, Arequipa, Peru
| | - Brando Ortiz-Saavedra
- Universidad Nacional de San Agustín de Arequipa, Arequipa, Peru; Grupo de Investigación en Inmunología-GII, UNSA, Arequipa, Peru
| | - Irmia Paz
- Universidad Nacional de San Agustín de Arequipa, Arequipa, Peru.
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30
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Peidli S, Nouailles G, Wyler E, Adler JM, Kunder S, Voß A, Kazmierski J, Pott F, Pennitz P, Postmus D, Teixeira Alves LG, Goffinet C, Gruber AD, Blüthgen N, Witzenrath M, Trimpert J, Landthaler M, Praktiknjo SD. Single-cell-resolved interspecies comparison shows a shared inflammatory axis and a dominant neutrophil-endothelial program in severe COVID-19. Cell Rep 2024; 43:114328. [PMID: 38861386 DOI: 10.1016/j.celrep.2024.114328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/21/2024] [Accepted: 05/22/2024] [Indexed: 06/13/2024] Open
Abstract
A key issue for research on COVID-19 pathogenesis is the lack of biopsies from patients and of samples at the onset of infection. To overcome these hurdles, hamsters were shown to be useful models for studying this disease. Here, we further leverage the model to molecularly survey the disease progression from time-resolved single-cell RNA sequencing data collected from healthy and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected Syrian and Roborovski hamster lungs. We compare our data to human COVID-19 studies, including bronchoalveolar lavage, nasal swab, and postmortem lung tissue, and identify a shared axis of inflammation dominated by macrophages, neutrophils, and endothelial cells, which we show to be transient in Syrian and terminal in Roborovski hamsters. Our data suggest that, following SARS-CoV-2 infection, commitment to a type 1- or type 3-biased immunity determines moderate versus severe COVID-19 outcomes, respectively.
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Affiliation(s)
- Stefan Peidli
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Berlin, Germany; Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Julia M Adler
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Sandra Kunder
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Anne Voß
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Julia Kazmierski
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Fabian Pott
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Pennitz
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany
| | - Dylan Postmus
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Luiz Gustavo Teixeira Alves
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Christine Goffinet
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Achim D Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Nils Blüthgen
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Berlin, Germany; Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany; German Center for Lung Research (DZL), Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Markus Landthaler
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany; Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Samantha D Praktiknjo
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
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31
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Gonçalves SM, Pereira I, Feys S, Cunha C, Chamilos G, Hoenigl M, Wauters J, van de Veerdonk FL, Carvalho A. Integrating genetic and immune factors to uncover pathogenetic mechanisms of viral-associated pulmonary aspergillosis. mBio 2024; 15:e0198223. [PMID: 38651925 PMCID: PMC11237550 DOI: 10.1128/mbio.01982-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Invasive pulmonary aspergillosis is a severe fungal infection primarily affecting immunocompromised patients. Individuals with severe viral infections have recently been identified as vulnerable to developing invasive fungal infections. Both influenza-associated pulmonary aspergillosis (IAPA) and COVID-19-associated pulmonary aspergillosis (CAPA) are linked to high mortality rates, emphasizing the urgent need for an improved understanding of disease pathogenesis to unveil new molecular targets with diagnostic and therapeutic potential. The recent establishment of animal models replicating the co-infection context has offered crucial insights into the mechanisms that underlie susceptibility to disease. However, the development and progression of human viral-fungal co-infections exhibit a significant degree of interindividual variability, even among patients with similar clinical conditions. This observation implies a significant role for host genetics, but information regarding the genetic basis for viral-fungal co-infections is currently limited. In this review, we discuss how genetic factors known to affect either antiviral or antifungal immunity could potentially reveal pathogenetic mechanisms that predispose to IAPA or CAPA and influence the overall disease course. These insights are anticipated to foster further research in both pre-clinical models and human patients, aiming to elucidate the complex pathophysiology of viral-associated pulmonary aspergillosis and contributing to the identification of new diagnostic and therapeutic targets to improve the management of these co-infections.
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Affiliation(s)
- Samuel M Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Inês Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Simon Feys
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Georgios Chamilos
- Laboratory of Clinical Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
| | - Martin Hoenigl
- Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - Joost Wauters
- Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Frank L van de Veerdonk
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
- Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
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32
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Ziegler CGK, Owings AH, Galeas-Pena M, Kazer SW, Miao VN, Navia AW, Tang Y, Bromley JD, Lotfy P, Sloan M, Laird H, Williams HB, George M, Drake RS, Pride Y, Abraham GE, Senitko M, Robinson TO, Diamond G, Lionakis MS, Shalek AK, Ordovas-Montanes J, Horwitz BH, Glover SC. An enhanced IL17 and muted type I interferon nasal epithelial cell state characterizes severe COVID-19 with fungal coinfection. Microbiol Spectr 2024; 12:e0351623. [PMID: 38687064 PMCID: PMC11237666 DOI: 10.1128/spectrum.03516-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Recent case reports and epidemiological data suggest that fungal infections represent an underappreciated complication among people with severe COVID-19. However, the frequency of fungal colonization in patients with COVID-19 and associations with specific immune responses in the airways remain incompletely defined. We previously generated a single-cell RNA-sequencing data set characterizing the upper respiratory microenvironment during COVID-19 and mapped the relationship between disease severity and the local behavior of nasal epithelial cells and infiltrating immune cells. Our previous study, in agreement with findings from related human cohorts, demonstrated that a profound deficiency in host immunity, particularly in type I and type III interferon signaling in the upper respiratory tract, is associated with rapid progression to severe disease and worse clinical outcomes. We have now performed further analysis of this cohort and identified a subset of participants with severe COVID-19 and concurrent detection of Candida species-derived transcripts within samples collected from the nasopharynx and trachea. Here, we present the clinical characteristics of these individuals. Using matched single-cell transcriptomic profiles of these individuals' respiratory mucosa, we identify epithelial immune signatures suggestive of IL17 stimulation and anti-fungal immunity. Further, we observe a significant expression of anti-fungal inflammatory cascades in the nasal and tracheal epithelium of all participants who went on to develop severe COVID-19, even among participants without detectable genetic material from fungal pathogens. Together, our data suggest that IL17 stimulation-in part driven by Candida colonization-and blunted interferon signaling represent a common feature of severe COVID-19 infection. IMPORTANCE In this paper, we present an analysis suggesting that symptomatic and asymptomatic fungal coinfections can impact patient disease progression during COVID-19 hospitalization. By looking into the presence of other pathogens and their effect on the host immune response during COVID-19 hospitalizations, we aim to offer insight into an underestimated scenario, furthering our current knowledge of determinants of severity that could be considered for future diagnostic and intervention strategies.
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Affiliation(s)
- Carly G. K. Ziegler
- Program in Health Sciences & Technology, Harvard Medical School & MIT, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Anna H. Owings
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Michelle Galeas-Pena
- Department of Medicine, Section of Gastroenterology and Hepatology, Tulane University School of Medicine, New Orleans, Los Angeles, USA
| | - Samuel W. Kazer
- Program in Immunology, Harvard Medical School, Boston, Massachusetts, USA
- Division of Emergency Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Vincent N. Miao
- Program in Health Sciences & Technology, Harvard Medical School & MIT, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Andrew W. Navia
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ying Tang
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Joshua D. Bromley
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Microbiology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Peter Lotfy
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Meredith Sloan
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Hannah Laird
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Haley B. Williams
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Micayla George
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Riley S. Drake
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yilianys Pride
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - George E. Abraham
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Michal Senitko
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Tanya O. Robinson
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Gill Diamond
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
| | - Michail S. Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, Maryland, USA
| | - Alex K. Shalek
- Program in Health Sciences & Technology, Harvard Medical School & MIT, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Program in Immunology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Jose Ordovas-Montanes
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Program in Immunology, Harvard Medical School, Boston, Massachusetts, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Bruce H. Horwitz
- Program in Immunology, Harvard Medical School, Boston, Massachusetts, USA
- Division of Emergency Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Sarah C. Glover
- Division of Digestive Diseases, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, Department of Cell & Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
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33
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Loske J, Völler M, Lukassen S, Stahl M, Thürmann L, Seegebarth A, Röhmel J, Wisniewski S, Messingschlager M, Lorenz S, Klages S, Eils R, Lehmann I, Mall MA, Graeber SY, Trump S. Pharmacological Improvement of Cystic Fibrosis Transmembrane Conductance Regulator Function Rescues Airway Epithelial Homeostasis and Host Defense in Children with Cystic Fibrosis. Am J Respir Crit Care Med 2024; 209:1338-1350. [PMID: 38259174 PMCID: PMC11146576 DOI: 10.1164/rccm.202310-1836oc] [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: 10/21/2023] [Accepted: 01/19/2024] [Indexed: 01/24/2024] Open
Abstract
Rationale: Pharmacological improvement of cystic fibrosis transmembrane conductance regulator (CFTR) function with elexacaftor/tezacaftor/ivacaftor (ETI) provides unprecedented improvements in lung function and other clinical outcomes in patients with cystic fibrosis (CF). However, ETI effects on impaired mucosal homeostasis and host defense at the molecular and cellular levels in the airways of patients with CF remain unknown. Objectives: To investigate effects of ETI on the transcriptome of nasal epithelial and immune cells from children with CF at the single-cell level. Methods: Nasal swabs from 13 children with CF and at least one F508del allele aged 6 to 11 years were collected at baseline and 3 months after initiation of ETI, subjected to single-cell RNA sequencing, and compared with swabs from 12 age-matched healthy children. Measurements and Main Results: Proportions of CFTR-positive cells were decreased in epithelial basal, club, and goblet cells, but not in ionocytes, from children with CF at baseline and were restored by ETI therapy to nearly healthy levels. Single-cell transcriptomics revealed an impaired IFN signaling and reduced expression of major histocompatibility complex classes I and II encoding genes in epithelial cells of children with CF at baseline, which was partially restored by ETI. In addition, ETI therapy markedly reduced the inflammatory phenotype of immune cells, particularly of neutrophils and macrophages. Conclusions: Pharmacological improvement of CFTR function improves innate mucosal immunity and reduces immune cell inflammatory responses in the upper airways of children with CF at the single-cell level, highlighting the potential to restore epithelial homeostasis and host defense in CF airways by early initiation of ETI therapy.
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Affiliation(s)
- Jennifer Loske
- Center of Digital Health, Molecular Epidemiology Unit, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Biology and
| | - Mirjam Völler
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sören Lukassen
- Center of Digital Health, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Mirjam Stahl
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner Site, Berlin, Germany
| | - Loreen Thürmann
- Center of Digital Health, Molecular Epidemiology Unit, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Anke Seegebarth
- Center of Digital Health, Molecular Epidemiology Unit, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Jobst Röhmel
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner Site, Berlin, Germany
| | - Sebastian Wisniewski
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marey Messingschlager
- Center of Digital Health, Molecular Epidemiology Unit, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Biology and
| | - Stephan Lorenz
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Roland Eils
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
- Center of Digital Health, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner Site, Berlin, Germany
- Health Data Science Unit, BioQuant, Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Irina Lehmann
- Center of Digital Health, Molecular Epidemiology Unit, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner Site, Berlin, Germany
| | - Marcus A. Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner Site, Berlin, Germany
| | - Simon Y. Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research, Associated Partner Site, Berlin, Germany
| | - Saskia Trump
- Center of Digital Health, Molecular Epidemiology Unit, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
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Abdelgied M, Zhou S, Uhl K, Jager T, Lawson C, Chesla D, Murphy E, Li K, Girgis RE, Li X. Increased Expression of ATP12A in Small Airway Epithelia of Post-COVID-19 Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2024; 70:527-530. [PMID: 38819123 PMCID: PMC11160418 DOI: 10.1165/rcmb.2023-0419le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024] Open
Affiliation(s)
- Mohamed Abdelgied
- Department of Pediatrics and Human DevelopmentMichigan State UniversityGrand Rapids, Michigan
| | - Shan Zhou
- The Cleveland Clinic Florida Research & Innovation CenterPort St. Lucie, Florida
| | - Katie Uhl
- Department of Pediatrics and Human DevelopmentMichigan State UniversityGrand Rapids, Michigan
| | - Tara Jager
- Richard DeVos Heart and Lung Transplant ProgramCorewell Health GrandRapids, Michigan
| | - Cameron Lawson
- Richard DeVos Heart and Lung Transplant ProgramCorewell Health GrandRapids, Michigan
| | - David Chesla
- Research and Development DepartmentCorewell HealthGrand Rapids, Michigan
| | - Edward Murphy
- Richard DeVos Heart and Lung Transplant ProgramCorewell Health GrandRapids, Michigan
| | - Kun Li
- The Cleveland Clinic Florida Research & Innovation CenterPort St. Lucie, Florida
| | - Reda E. Girgis
- Richard DeVos Heart and Lung Transplant ProgramCorewell Health GrandRapids, Michigan
| | - Xiaopeng Li
- Department of Pediatrics and Human DevelopmentMichigan State UniversityGrand Rapids, Michigan
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35
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Borczuk AC. Pathology of COVID-19 Lung Disease. Surg Pathol Clin 2024; 17:203-214. [PMID: 38692805 DOI: 10.1016/j.path.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
The pathology of severe COVID-19 lung injury is predominantly diffuse alveolar damage, with other reported patterns including acute fibrinous organizing pneumonia, organizing pneumonia, and bronchiolitis. Lung injury was caused by primary viral injury, exaggerated immune responses, and superinfection with bacteria and fungi. Although fatality rates have decreased from the early phases of the pandemic, persistent pulmonary dysfunction occurs and its pathogenesis remains to be fully elucidated.
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Affiliation(s)
- Alain C Borczuk
- Department of Pathology, Northwell Health, 2200 Northern Boulevard Suite 104, Greenvale, NY 11548, USA.
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36
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Almanzar G, Koosha K, Vogt T, Stein A, Ziegler L, Asam C, Weps M, Schwägerl V, Richter L, Hepp N, Fuchs A, Wagenhäuser I, Reusch J, Krone M, Geldmacher C, Protzer U, Steininger P, Überla K, Wagner R, Liese J, Prelog M. Hybrid immunity by two COVID-19 mRNA vaccinations and one breakthrough infection provides a robust and balanced cellular immune response as basic immunity against severe acute respiratory syndrome coronavirus 2. J Med Virol 2024; 96:e29739. [PMID: 38899449 DOI: 10.1002/jmv.29739] [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: 01/09/2024] [Revised: 04/22/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
This longitudinal prospective controlled multicenter study aimed to monitor immunity generated by three exposures caused by breakthrough infections (BTI) after COVID-19-vaccination considering pre-existing cell-mediated immunity to common-corona-viruses (CoV) which may impact cellular reactivity against SARS-CoV-2. Anti-SARS-CoV-2-spike-IgG antibodies (anti-S-IgG) and cellular reactivity against Spike-(S)- and nucleocapsid-(N)-proteins were determined in fully-vaccinated (F) individuals who either experienced BTI (F+BTI) or had booster vaccination (F+Booster) compared to partially vaccinated (P+BTI) and unvaccinated (U) from 1 to 24 weeks post PCR-confirmed infection. High avidity anti-S-IgG were found in F+BTI compared to U, the latter exhibiting increased long-lasting pro-inflammatory cytokines to S-stimulation. CoV was associated with higher cellular reactivity in U, whereas no association was seen in F. The study illustrates the induction of significant S-specific cellular responses in F+BTI building-up basic immunity by three exposures. Only U seem to benefit from pre-existing CoV immunity but demonstrated inflammatory immune responses compared to F+BTI who immunologically benefit from enhanced humoral and cellular immunity after BTI. This study demonstrates that individuals with hybrid immunity from COVID-19-vaccination and BTI acquire a stable humoral and cellular immune response that is maintained for at least 6 months. Our findings corroborate recommendations by health authorities to build on basic immunity by three S-protein exposures.
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Affiliation(s)
- Giovanni Almanzar
- Department of Pediatrics, Pediatric Rheumatology/Special Immunology, University Hospital Würzburg, Würzburg, Germany
| | - Kimia Koosha
- Department of Pediatrics, Pediatric Rheumatology/Special Immunology, University Hospital Würzburg, Würzburg, Germany
| | - Tim Vogt
- Department of Pediatrics, Pediatric Rheumatology/Special Immunology, University Hospital Würzburg, Würzburg, Germany
| | - Astrid Stein
- Department of Pediatrics, Pediatric Rheumatology/Special Immunology, University Hospital Würzburg, Würzburg, Germany
| | - Lars Ziegler
- Department of Pediatrics, Pediatric Rheumatology/Special Immunology, University Hospital Würzburg, Würzburg, Germany
| | - Claudia Asam
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Manuela Weps
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Valeria Schwägerl
- Department of Pediatrics, Pediatric Rheumatology/Special Immunology, University Hospital Würzburg, Würzburg, Germany
| | - Lorena Richter
- Department of Pediatrics, Pediatric Rheumatology/Special Immunology, University Hospital Würzburg, Würzburg, Germany
| | - Nicola Hepp
- Department of Pediatrics, Pediatric Rheumatology/Special Immunology, University Hospital Würzburg, Würzburg, Germany
| | - Andre Fuchs
- Internal Medicine III-Gastroenterology and Infectious Diseases, University Hospital of Augsburg, Augsburg, Germany
| | - Isabell Wagenhäuser
- Institute for Hygiene and Microbiology, Julius-Maximilian-Universität Würzburg, Würzburg, Germany
| | - Julia Reusch
- Institute for Hygiene and Microbiology, Julius-Maximilian-Universität Würzburg, Würzburg, Germany
| | - Manuel Krone
- Institute for Hygiene and Microbiology, Julius-Maximilian-Universität Würzburg, Würzburg, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Ulrike Protzer
- School of Medicine, Institute of Virology, Technical University of Munich, Munich, Germany
- German Center for Infection Research, Institute of Virology, Helmholtz Munich, Munich Partner Site, Munich, Germany
| | - Philipp Steininger
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Klaus Überla
- Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ralf Wagner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Johannes Liese
- Department of Pediatrics, Pediatric Rheumatology/Special Immunology, University Hospital Würzburg, Würzburg, Germany
| | - Martina Prelog
- Department of Pediatrics, Pediatric Rheumatology/Special Immunology, University Hospital Würzburg, Würzburg, Germany
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Mukhatayev Z, Adilbayeva A, Kunz J. CTHRC1: An Emerging Hallmark of Pathogenic Fibroblasts in Lung Fibrosis. Cells 2024; 13:946. [PMID: 38891078 PMCID: PMC11171484 DOI: 10.3390/cells13110946] [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: 02/29/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Pulmonary fibrosis is a chronic, progressive, irreversible lung disease characterized by fibrotic scarring in the lung parenchyma. This condition involves the excessive accumulation of extracellular matrix (ECM) due to the aberrant activation of myofibroblasts in the alveolar environment. Transforming growth factor beta (TGF-β) signaling is a crucial driver of fibrogenesis because it promotes excessive ECM deposition, thereby leading to scar formation and lung damage. A primary target of TGF-β signaling in fibrosis is Collagen Triple Helix Repeat Containing 1 (CTHRC1), a secreted glycoprotein that plays a pivotal role in ECM deposition and wound repair. TGF-β transcriptionally regulates CTHRC1 in response to tissue injury and controls the wound healing response through functional activity. CTHRC1 may also play an essential role in re-establishing and maintaining tissue homeostasis after wound closure by modulating both the TGF-β and canonical Wnt signaling pathways. This dual function suggests that CTHRC1 regulates tissue remodeling and homeostasis. However, deregulated CTHRC1 expression in pathogenic fibroblasts has recently emerged as a hallmark of fibrosis in multiple organs and tissues. This review highlights recent studies suggesting that CTHRC1 can serve as a diagnostic and prognostic biomarker for fibrosis in idiopathic pulmonary fibrosis, systemic sclerosis, and post-COVID-19 lung fibrosis. Notably, CTHRC1 expression is responsive to antifibrotic drugs that target the TGF-β pathway, such as pirfenidone and bexotegrast, indicating its potential as a biomarker of treatment success. These findings suggest that CTHRC1 may present new opportunities for diagnosing and treating patients with lung fibrosis.
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Affiliation(s)
| | | | - Jeannette Kunz
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, 5/1 Kerey and Zhanibek Khans St., 020000 Astana, Kazakhstan; (Z.M.); (A.A.)
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38
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Kircheis R. In Silico Analyses Indicate a Lower Potency for Dimerization of TLR4/MD-2 as the Reason for the Lower Pathogenicity of Omicron Compared to Wild-Type Virus and Earlier SARS-CoV-2 Variants. Int J Mol Sci 2024; 25:5451. [PMID: 38791489 PMCID: PMC11121871 DOI: 10.3390/ijms25105451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The SARS-CoV-2 Omicron variants have replaced all earlier variants, due to increased infectivity and effective evasion from infection- and vaccination-induced neutralizing antibodies. Compared to earlier variants of concern (VoCs), the Omicron variants show high TMPRSS2-independent replication in the upper airway organs, but lower replication in the lungs and lower mortality rates. The shift in cellular tropism and towards lower pathogenicity of Omicron was hypothesized to correlate with a lower toll-like receptor (TLR) activation, although the underlying molecular mechanisms remained undefined. In silico analyses presented here indicate that the Omicron spike protein has a lower potency to induce dimerization of TLR4/MD-2 compared to wild type virus despite a comparable binding activity to TLR4. A model illustrating the molecular consequences of the different potencies of the Omicron spike protein vs. wild-type spike protein for TLR4 activation is presented. Further analyses indicate a clear tendency for decreasing TLR4 dimerization potential during SARS-CoV-2 evolution via Alpha to Gamma to Delta to Omicron variants.
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39
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Hartmann JA, Cardoso MR, Talarico MCR, Kenney DJ, Leone MR, Reese DC, Turcinovic J, O'Connell AK, Gertje HP, Marino C, Ojeda PE, De Paula EV, Orsi FA, Velloso LA, Cafiero TR, Connor JH, Ploss A, Hoelzemer A, Carrington M, Barczak AK, Crossland NA, Douam F, Boucau J, Garcia-Beltran WF. Evasion of NKG2D-mediated cytotoxic immunity by sarbecoviruses. Cell 2024; 187:2393-2410.e14. [PMID: 38653235 PMCID: PMC11088510 DOI: 10.1016/j.cell.2024.03.026] [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: 07/25/2023] [Revised: 01/30/2024] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
Abstract
SARS-CoV-2 and other sarbecoviruses continue to threaten humanity, highlighting the need to characterize common mechanisms of viral immune evasion for pandemic preparedness. Cytotoxic lymphocytes are vital for antiviral immunity and express NKG2D, an activating receptor conserved among mammals that recognizes infection-induced stress ligands (e.g., MIC-A/B). We found that SARS-CoV-2 evades NKG2D recognition by surface downregulation of MIC-A/B via shedding, observed in human lung tissue and COVID-19 patient serum. Systematic testing of SARS-CoV-2 proteins revealed that ORF6, an accessory protein uniquely conserved among sarbecoviruses, was responsible for MIC-A/B downregulation via shedding. Further investigation demonstrated that natural killer (NK) cells efficiently killed SARS-CoV-2-infected cells and limited viral spread. However, inhibition of MIC-A/B shedding with a monoclonal antibody, 7C6, further enhanced NK-cell activity toward SARS-CoV-2-infected cells. Our findings unveil a strategy employed by SARS-CoV-2 to evade cytotoxic immunity, identify the culprit immunevasin shared among sarbecoviruses, and suggest a potential novel antiviral immunotherapy.
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Affiliation(s)
- Jordan A Hartmann
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | | | | | - Devin J Kenney
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Madison R Leone
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Dagny C Reese
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Jacquelyn Turcinovic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K O'Connell
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Hans P Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Caitlin Marino
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Pedro E Ojeda
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Erich V De Paula
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil; Hematology and Hemotherapy Center, University of Campinas, Campinas, SP, Brazil
| | - Fernanda A Orsi
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil; Hematology and Hemotherapy Center, University of Campinas, Campinas, SP, Brazil
| | - Licio Augusto Velloso
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil; Obesity and Comorbidities Research Center, University of Campinas, Campinas, SP, Brazil
| | - Thomas R Cafiero
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - John H Connor
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Angelique Hoelzemer
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany; Institute for Infection and Vaccine Development (IIRVD), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany; Research Department Virus Immunology, Leibniz Institute for Virology, Hamburg, Germany
| | - Mary Carrington
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Amy K Barczak
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nicholas A Crossland
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Florian Douam
- Department of Virology, Immunology, and Microbiology, Chobanian and Avedisian Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Julie Boucau
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
| | - Wilfredo F Garcia-Beltran
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
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Tu TH, Grunbaum A, Santinon F, Kazanova A, Rozza N, Kremer R, Mihalcioiu C, Rudd CE. Decreased progenitor TCF1 + T-cells correlate with COVID-19 disease severity. Commun Biol 2024; 7:526. [PMID: 38702425 PMCID: PMC11068881 DOI: 10.1038/s42003-024-05922-2] [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: 09/19/2023] [Accepted: 02/16/2024] [Indexed: 05/06/2024] Open
Abstract
COVID-19, caused by SARS-CoV-2, can lead to a severe inflammatory disease characterized by significant lymphopenia. However, the underlying cause for the depletion of T-cells in COVID-19 patients remains incompletely understood. In this study, we assessed the presence of different T-cell subsets in the progression of COVID-19 from mild to severe disease, with a focus on TCF1 expressing progenitor T-cells that are needed to replenish peripheral T-cells during infection. Our results showed a preferential decline in TCF1+ progenitor CD4 and CD8+ T-cells with disease severity. This decline was seen in various TCF1+ subsets including naive, memory and effector-memory cells, and surprisingly, was accompanied by a loss in cell division as seen by a marked decline in Ki67 expression. In addition, TCF1+ T-cells showed a reduction in pro-survival regulator, BcL2, and the appearance of a new population of TCF1 negative caspase-3 expressing cells in peripheral blood from patients with severe disease. The decline in TCF1+ T-cells was also seen in a subgroup of severe patients with vitamin D deficiency. Lastly, we found that sera from severe patients inhibited TCF1 transcription ex vivo which was attenuated by a blocking antibody against the cytokine, interleukin-12 (IL12). Collectively, our findings underscore the potential significance of TCF1+ progenitor T-cells in accounting for the loss of immunity in severe COVID-19 and outline an array of markers that could be used to identify disease progression.
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Affiliation(s)
- Thai Hien Tu
- Départment of Medicine, Universite de Montreal, Montreal, QC, H3T 1J4, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Division of Immunology-Oncology, Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, H1T 2M4, Canada
| | - Ami Grunbaum
- Division of Experimental Medicine, McGill University, Montreal, QC, H3A 0G4, Canada
- Department of Medicine, Research Institute of the McGill University Health Center, Montreal, H3A 0G4, Canada
- Division of Medical Biochemistry, McGill University Health Centre, Montréal, QC, Canada
| | - François Santinon
- Départment of Medicine, Universite de Montreal, Montreal, QC, H3T 1J4, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Division of Immunology-Oncology, Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, H1T 2M4, Canada
| | - Alexandra Kazanova
- Départment of Medicine, Universite de Montreal, Montreal, QC, H3T 1J4, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Division of Immunology-Oncology, Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, H1T 2M4, Canada
| | - Nicholas Rozza
- Division of Experimental Medicine, McGill University, Montreal, QC, H3A 0G4, Canada
- Department of Medicine, Research Institute of the McGill University Health Center, Montreal, H3A 0G4, Canada
| | - Richard Kremer
- Division of Experimental Medicine, McGill University, Montreal, QC, H3A 0G4, Canada
- Department of Medicine, Research Institute of the McGill University Health Center, Montreal, H3A 0G4, Canada
- Division of Medical Biochemistry, McGill University Health Centre, Montréal, QC, Canada
| | - Catalin Mihalcioiu
- Department of Medical Oncology, McGill University Health Center, Montreal, Quebec, Canada
| | - Christopher E Rudd
- Départment of Medicine, Universite de Montreal, Montreal, QC, H3T 1J4, Canada.
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, H3T 1J4, Canada.
- Division of Immunology-Oncology, Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, H1T 2M4, Canada.
- Division of Experimental Medicine, McGill University, Montreal, QC, H3A 0G4, Canada.
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Woodall MNJ, Cujba AM, Worlock KB, Case KM, Masonou T, Yoshida M, Polanski K, Huang N, Lindeboom RGH, Mamanova L, Bolt L, Richardson L, Cakir B, Ellis S, Palor M, Burgoyne T, Pinto A, Moulding D, McHugh TD, Saleh A, Kilich E, Mehta P, O'Callaghan C, Zhou J, Barclay W, De Coppi P, Butler CR, Cortina-Borja M, Vinette H, Roy S, Breuer J, Chambers RC, Heywood WE, Mills K, Hynds RE, Teichmann SA, Meyer KB, Nikolić MZ, Smith CM. Age-specific nasal epithelial responses to SARS-CoV-2 infection. Nat Microbiol 2024; 9:1293-1311. [PMID: 38622380 PMCID: PMC11087271 DOI: 10.1038/s41564-024-01658-1] [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: 03/24/2023] [Accepted: 03/04/2024] [Indexed: 04/17/2024]
Abstract
Children infected with SARS-CoV-2 rarely progress to respiratory failure. However, the risk of mortality in infected people over 85 years of age remains high. Here we investigate differences in the cellular landscape and function of paediatric (<12 years), adult (30-50 years) and older adult (>70 years) ex vivo cultured nasal epithelial cells in response to infection with SARS-CoV-2. We show that cell tropism of SARS-CoV-2, and expression of ACE2 and TMPRSS2 in nasal epithelial cell subtypes, differ between age groups. While ciliated cells are viral replication centres across all age groups, a distinct goblet inflammatory subtype emerges in infected paediatric cultures and shows high expression of interferon-stimulated genes and incomplete viral replication. In contrast, older adult cultures infected with SARS-CoV-2 show a proportional increase in basaloid-like cells, which facilitate viral spread and are associated with altered epithelial repair pathways. We confirm age-specific induction of these cell types by integrating data from in vivo COVID-19 studies and validate that our in vitro model recapitulates early epithelial responses to SARS-CoV-2 infection.
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Affiliation(s)
| | | | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Tereza Masonou
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Ni Huang
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Liam Bolt
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Samuel Ellis
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Machaela Palor
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Thomas Burgoyne
- UCL Institute of Ophthalmology, University College London, London, UK
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Andreia Pinto
- Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dale Moulding
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Timothy D McHugh
- UCL Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK
| | - Aarash Saleh
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Eliz Kilich
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Jie Zhou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Paolo De Coppi
- Great Ormond Street UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Colin R Butler
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
| | | | - Heloise Vinette
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Sunando Roy
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Judith Breuer
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Rachel C Chambers
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Wendy E Heywood
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Kevin Mills
- Great Ormond Street UCL Institute of Child Health, London, UK
| | - Robert E Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory/Dept Physics, University of Cambridge, Cambridge, UK.
| | | | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
- University College London Hospitals NHS Foundation Trust, London, UK.
| | - Claire M Smith
- Great Ormond Street UCL Institute of Child Health, London, UK.
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Meganck RM, Edwards CE, Mallory ML, Lee RE, Dang H, Bailey AB, Wykoff JA, Gallant SC, Zhu DR, Yount BL, Kato T, Shaffer KM, Nakano S, Cawley AM, Sontake V, Wang JR, Hagan RS, Miller MB, Tata PR, Randell SH, Tse LV, Ehre C, Okuda K, Boucher RC, Baric RS. SARS-CoV-2 variant of concern fitness and adaptation in primary human airway epithelia. Cell Rep 2024; 43:114076. [PMID: 38607917 PMCID: PMC11165423 DOI: 10.1016/j.celrep.2024.114076] [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: 09/15/2023] [Revised: 02/09/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 pandemic is characterized by the emergence of novel variants of concern (VOCs) that replace ancestral strains. Here, we dissect the complex selective pressures by evaluating variant fitness and adaptation in human respiratory tissues. We evaluate viral properties and host responses to reconstruct forces behind D614G through Omicron (BA.1) emergence. We observe differential replication in airway epithelia, differences in cellular tropism, and virus-induced cytotoxicity. D614G accumulates the most mutations after infection, supporting zoonosis and adaptation to the human airway. We perform head-to-head competitions and observe the highest fitness for Gamma and Delta. Under these conditions, RNA recombination favors variants encoding the B.1.617.1 lineage 3' end. Based on viral growth kinetics, Alpha, Gamma, and Delta exhibit increased fitness compared to D614G. In contrast, the global success of Omicron likely derives from increased transmission and antigenic variation. Our data provide molecular evidence to support epidemiological observations of VOC emergence.
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Affiliation(s)
- Rita M Meganck
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Rhianna E Lee
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Alexis B Bailey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Jason A Wykoff
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Samuel C Gallant
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Deanna R Zhu
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Takafumi Kato
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Kendall M Shaffer
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Satoko Nakano
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Anne Marie Cawley
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | | | - Jeremy R Wang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Robert S Hagan
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; Division of Pulmonary Diseases and Critical Care Medicine, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Melissa B Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | | | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Longping V Tse
- Department of Molecular Microbiology & Immunology, Saint Louis University, St. Louis, MO 63104, USA
| | - Camille Ehre
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Kenichi Okuda
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA.
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Megasari NLA, Khairunisa SQ, Arizandy RY, Wijaksana IKE, Wungu CDK. Cytokine profiles of mild-to-moderate SARS-CoV-2 infected and recovered pre-vaccinated individuals residing in Indonesia. PeerJ 2024; 12:e17257. [PMID: 38646483 PMCID: PMC11032655 DOI: 10.7717/peerj.17257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/27/2024] [Indexed: 04/23/2024] Open
Abstract
Background Accumulating evidence suggests the involvement of cytokine-mediated inflammation, in clinical severity and death related to SARS-CoV-2 infection, especially among pre-vaccinated individuals. An increased risk of death was also described among SARS-CoV-2 recovered individuals, which might be correlated with prolonged inflammatory responses. Despite being among the countries with the highest cumulative deaths due to COVID-19, evidence regarding cytokine profiles among SARS-CoV-2 infected and recovered pre-vaccinated individuals in Indonesia is scarce. Thus, this study aimed to describe the cytokines profiles of pre-vaccinated individuals residing in Indonesia, with mild-to-moderate SARS-CoV-2 infection and those who recovered. Methods Sixty-one sera from 24 hospitalized patients with mild-to-moderate SARS-CoV-2 infection, 24 individuals recovered from asymptomatic-to-moderate SARS-CoV-2 infection, and 13 healthy controls unexposed to SARS-CoV-2 were used in this study. Quantification of serum cytokine levels, including IL-6, IL-8, IP-10, TNF-α, CCL-2, CCL-3, CCL-4, and CXCL-13, was performed using a Luminex multi-analyte-profiling (xMAP)-based assay. Results The levels of IL-8 along with CCL-2 and CCL-4, were significantly higher (p ≤ 0.01) in hospitalized patients with mild-to-moderate SARS-CoV-2 infection and recovered individuals compared to healthy controls. However, no significant difference was observed in these cytokine levels between infected and recovered individuals. On the other hand, there were no significant differences in several other cytokine levels, including IL-6, IL-10, TNF-α, CCL-3, and CXCL-13, among all groups. Conclusion IL-8, CCL-2, and CCL-4 were significantly elevated in pre-vaccinated Indonesian individuals with mild-to-moderate SARS-CoV-2 infection and those who recovered. The cytokine profiles described in this study might indicate inflammatory responses not only among SARS-CoV-2 infected, but also recovered individuals.
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Affiliation(s)
- Ni Luh Ayu Megasari
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
- Postgraduate School, Airlangga University, Surabaya, Indonesia
| | | | | | - I. Komang Evan Wijaksana
- Department of Periodontology, Faculty of Dental Medicine, Airlangga University, Surabaya, Indonesia
| | - Citrawati Dyah Kencono Wungu
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
- Department of Physiology and Medical Biochemistry, Faculty of Medicine, Airlangga University, Surabaya, Indonesia
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Oliveira VLS, Queiroz-Junior CM, Hoorelbeke D, Santos FRDS, Chaves IDM, Teixeira MM, Russo RDC, Proost P, Costa VV, Struyf S, Amaral FA. The glycosaminoglycan-binding chemokine fragment CXCL9(74-103) reduces inflammation and tissue damage in mouse models of coronavirus infection. Front Immunol 2024; 15:1378591. [PMID: 38686377 PMCID: PMC11056509 DOI: 10.3389/fimmu.2024.1378591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction Pulmonary diseases represent a significant burden to patients and the healthcare system and are one of the leading causes of mortality worldwide. Particularly, the COVID-19 pandemic has had a profound global impact, affecting public health, economies, and daily life. While the peak of the crisis has subsided, the global number of reported COVID-19 cases remains significantly high, according to medical agencies around the world. Furthermore, despite the success of vaccines in reducing the number of deaths caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there remains a gap in the treatment of the disease, especially in addressing uncontrolled inflammation. The massive recruitment of leukocytes to lung tissue and alveoli is a hallmark factor in COVID-19, being essential for effectively responding to the pulmonary insult but also linked to inflammation and lung damage. In this context, mice models are a crucial tool, offering valuable insights into both the pathogenesis of the disease and potential therapeutic approaches. Methods Here, we investigated the anti-inflammatory effect of the glycosaminoglycan (GAG)-binding chemokine fragment CXCL9(74-103), a molecule that potentially decreases neutrophil transmigration by competing with chemokines for GAG-binding sites, in two models of pneumonia caused by coronavirus infection. Results In a murine model of betacoronavirus MHV-3 infection, the treatment with CXCL9(74-103) decreased the accumulation of total leukocytes, mainly neutrophils, to the alveolar space and improved several parameters of lung dysfunction 3 days after infection. Additionally, this treatment also reduced the lung damage. In the SARS-CoV-2 model in K18-hACE2-mice, CXCL9(74-103) significantly improved the clinical manifestations of the disease, reducing pulmonary damage and decreasing viral titers in the lungs. Discussion These findings indicate that CXCL9(74-103) resulted in highly favorable outcomes in controlling pneumonia caused by coronavirus, as it effectively diminishes the clinical consequences of the infections and reduces both local and systemic inflammation.
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Affiliation(s)
- Vivian Louise Soares Oliveira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Departament of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Celso Martins Queiroz-Junior
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Delphine Hoorelbeke
- Departament of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Felipe Rocha da Silva Santos
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ian de Meira Chaves
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mauro Martins Teixeira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Remo de Castro Russo
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paul Proost
- Departament of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Vivian Vasconcelos Costa
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sofie Struyf
- Departament of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Flávio Almeida Amaral
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Wang Y, Thaler M, Salgado‐Benvindo C, Ly N, Leijs AA, Ninaber DK, Hansbro PM, Boedijono F, van Hemert MJ, Hiemstra PS, van der Does AM, Faiz A. SARS-CoV-2-infected human airway epithelial cell cultures uniquely lack interferon and immediate early gene responses caused by other coronaviruses. Clin Transl Immunology 2024; 13:e1503. [PMID: 38623540 PMCID: PMC11017760 DOI: 10.1002/cti2.1503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/22/2023] [Accepted: 03/24/2024] [Indexed: 04/17/2024] Open
Abstract
Objectives Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a member of a class of highly pathogenic coronaviruses. The large family of coronaviruses, however, also includes members that cause only mild symptoms, like human coronavirus-229E (HCoV-229E) or OC43 (HCoV-OC43). Unravelling how molecular (and cellular) pathophysiology differs between highly and low pathogenic coronaviruses is important for the development of therapeutic strategies. Methods Here, we analysed the transcriptome of primary human bronchial epithelial cells (PBEC), differentiated at the air-liquid interface (ALI) after infection with SARS-CoV-2, SARS-CoV, Middle East Respiratory Syndrome (MERS)-CoV and HCoV-229E using bulk RNA sequencing. Results ALI-PBEC were efficiently infected by all viruses, and SARS-CoV, MERS-CoV and HCoV-229E infection resulted in a largely similar transcriptional response. The response to SARS-CoV-2 infection differed markedly as it uniquely lacked the increase in expression of immediate early genes, including FOS, FOSB and NR4A1 that was observed with all other coronaviruses. This finding was further confirmed in publicly available experimental and clinical datasets. Interfering with NR4A1 signalling in Calu-3 lung epithelial cells resulted in a 100-fold reduction in extracellular RNA copies of SARS-CoV-2 and MERS-CoV, suggesting an involvement in virus replication. Furthermore, a lack in induction of interferon-related gene expression characterised the main difference between the highly pathogenic coronaviruses and low pathogenic viruses HCoV-229E and HCoV-OC43. Conclusion Our results demonstrate a previously unknown suppression of a host response gene set by SARS-CoV-2 and confirm a difference in interferon-related gene expression between highly pathogenic and low pathogenic coronaviruses.
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Affiliation(s)
- Ying Wang
- PulmoScience Lab, Department of PulmonologyLeiden University Medical CenterLeidenThe Netherlands
| | - Melissa Thaler
- Department of Medical MicrobiologyLeiden University Medical CenterLeidenThe Netherlands
| | | | - Nathan Ly
- Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life SciencesUniversity of Technology SydneySydneyNSWAustralia
| | - Anouk A Leijs
- Department of Medical MicrobiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Dennis K Ninaber
- PulmoScience Lab, Department of PulmonologyLeiden University Medical CenterLeidenThe Netherlands
| | - Philip M Hansbro
- Centre for InflammationCentenary Institute and University of Technology Sydney, Faculty of ScienceSydneyNSWAustralia
| | - Fia Boedijono
- Centre for InflammationCentenary Institute and University of Technology Sydney, Faculty of ScienceSydneyNSWAustralia
| | - Martijn J van Hemert
- Department of Medical MicrobiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Pieter S Hiemstra
- PulmoScience Lab, Department of PulmonologyLeiden University Medical CenterLeidenThe Netherlands
| | - Anne M van der Does
- PulmoScience Lab, Department of PulmonologyLeiden University Medical CenterLeidenThe Netherlands
| | - Alen Faiz
- Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life SciencesUniversity of Technology SydneySydneyNSWAustralia
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Gao F, Lin W, Wang X, Liao M, Zhang M, Qin N, Chen X, Xia L, Chen Q, Sha O. Identification of receptors and factors associated with human coronaviruses in the oral cavity using single-cell RNA sequencing. Heliyon 2024; 10:e28280. [PMID: 38560173 PMCID: PMC10981076 DOI: 10.1016/j.heliyon.2024.e28280] [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: 10/24/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) ravaged the world, and Coronavirus Disease 2019 (COVID-19) exhibited highly prevalent oral symptoms that had significantly impacted the lives of affected patients. However, the involvement of four human coronavirus (HCoVs), namely SARS-CoV-2, SARS-CoV, MERS-CoV, and HCoV-229E, in oral cavity infections remained poorly understood. We integrated single-cell RNA sequencing (scRNA-seq) data of seven human oral tissues through consistent normalization procedure, including minor salivary gland (MSG), parotid gland (PG), tongue, gingiva, buccal, periodontium and pulp. The Seurat, scDblFinder, Harmony, SingleR, Ucell and scCancer packages were comprehensively used for analysis. We identified specific cell clusters and generated expression profiles of SARS-CoV-2 and coronavirus-associated receptors and factors (SCARFs) in seven oral regions, providing direction for predicting the tropism of four HCoVs for oral tissues, as well as for dental clinical treatment. Based on our analysis, it appears that various SCARFs, including ACE2, ASGR1, KREMEN1, DPP4, ANPEP, CD209, CLEC4G/M, TMPRSS family proteins (including TMPRSS2, TMPRSS4, and TMPRSS11A), and FURIN, are expressed at low levels in the oral cavity. Conversely, BSG, CTSB, and CTSL exhibit enrichment in oral tissues. Our study also demonstrates widespread expression of restriction factors, particularly IFITM1-3 and LY6E, in oral cells. Additionally, some replication, assembly, and trafficking factors appear to exhibit broad oral tissues expression patterns. Overall, the oral cavity could potentially serve as a high-risk site for SARS-CoV-2 infection, while displaying a comparatively lower degree of susceptibility towards other HCoVs (including SARS-CoV, MERS-CoV and HCoV-229E). Specifically, MSG, tongue, and gingiva represent potential sites of vulnerability for four HCoVs infection, with the MSG exhibiting a particularly high susceptibility. However, the expression patterns of SCARFs in other oral sites demonstrate relatively intricate and may only be specifically associated with SARS-CoV-2 infection. Our study sheds light on the mechanisms of HCoVs infection in the oral cavity as well as gains insight into the characteristics and distribution of possible HCoVs target cells in oral tissues, providing potential therapeutic targets for HCoVs infection in the oral cavity.
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Affiliation(s)
- Feng Gao
- School of Dentistry, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
- Institute of Dental Research, Shenzhen University, Shenzhen, China
| | - Weiming Lin
- Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Xia Wang
- Shenzhen University Medical School, Shenzhen University, Shenzhen, China
- The Chinese University of Hong Kong Shenzhen, School of Medicine, Shenzhen, China
| | - Mingfeng Liao
- The Third People's Hospital of Shenzhen, Shenzhen, China
| | - Mingxia Zhang
- The Third People's Hospital of Shenzhen, Shenzhen, China
| | - Nianhong Qin
- Department of Stomatology, Shenzhen People's Hospital, Shenzhen, China
| | - Xianxiong Chen
- School of Dentistry, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Lixin Xia
- Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Qianming Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Clinical Research Center for Oral Diseases of Zhejiang Province, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Ou Sha
- School of Dentistry, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
- Institute of Dental Research, Shenzhen University, Shenzhen, China
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Losada A, Izquierdo-Useros N, Aviles P, Vergara-Alert J, Latino I, Segalés J, Gonzalez SF, Cuevas C, Raïch-Regué D, Muñoz-Alonso MJ, Perez-Zsolt D, Muñoz-Basagoiti J, Rodon J, Chang LA, Warang P, Singh G, Brustolin M, Cantero G, Roca N, Pérez M, Bustos-Morán E, White K, Schotsaert M, García-Sastre A. Plitidepsin as an Immunomodulator against Respiratory Viral Infections. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1307-1318. [PMID: 38416036 PMCID: PMC10984758 DOI: 10.4049/jimmunol.2300426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024]
Abstract
Plitidepsin is a host-targeted compound known for inducing a strong anti-SARS-CoV-2 activity, as well as for having the capacity of reducing lung inflammation. Because IL-6 is one of the main cytokines involved in acute respiratory distress syndrome, the effect of plitidepsin in IL-6 secretion in different in vitro and in vivo experimental models was studied. A strong plitidepsin-mediated reduction of IL-6 was found in human monocyte-derived macrophages exposed to nonproductive SARS-CoV-2. In resiquimod (a ligand of TLR7/8)-stimulated THP1 human monocytes, plitidepsin-mediated reductions of IL-6 mRNA and IL-6 levels were also noticed. Additionally, although resiquimod-induced binding to DNA of NF-κB family members was unaffected by plitidepsin, a decrease in the regulated transcription by NF-κB (a key transcription factor involved in the inflammatory cascade) was observed. Furthermore, the phosphorylation of p65 that is required for full transcriptional NF-κB activity was significantly reduced by plitidepsin. Moreover, decreases of IL-6 levels and other proinflammatory cytokines were also seen in either SARS-CoV-2 or H1N1 influenza virus-infected mice, which were treated at low enough plitidepsin doses to not induce antiviral effects. In summary, plitidepsin is a promising therapeutic agent for the treatment of viral infections, not only because of its host-targeted antiviral effect, but also for its immunomodulatory effect, both of which were evidenced in vitro and in vivo by the decrease of proinflammatory cytokines.
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Affiliation(s)
- Alejandro Losada
- Department of Research and Development, PharmaMar S.A., Colmenar Viejo, Madrid, Spain
| | - Nuria Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute, Can Ruti Campus, Badalona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo Aviles
- Department of Research and Development, PharmaMar S.A., Colmenar Viejo, Madrid, Spain
| | - Júlia Vergara-Alert
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Irene Latino
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Joaquim Segalés
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Santiago F Gonzalez
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Carmen Cuevas
- Department of Research and Development, PharmaMar S.A., Colmenar Viejo, Madrid, Spain
| | | | - María J Muñoz-Alonso
- Department of Research and Development, PharmaMar S.A., Colmenar Viejo, Madrid, Spain
| | | | | | - Jordi Rodon
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Lauren A Chang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Prajakta Warang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Marco Brustolin
- Unit of Entomology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Guillermo Cantero
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Núria Roca
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Mònica Pérez
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Eugenio Bustos-Morán
- Department of Research and Development, PharmaMar S.A., Colmenar Viejo, Madrid, Spain
| | - Kris White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY
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Li C, Wu K, Yang R, Liao M, Li J, Zhu Q, Zhang J, Zhang X. Comprehensive analysis of immunogenic cell death-related gene and construction of prediction model based on WGCNA and multiple machine learning in severe COVID-19. Sci Rep 2024; 14:8450. [PMID: 38600309 PMCID: PMC11006847 DOI: 10.1038/s41598-024-59117-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/08/2024] [Indexed: 04/12/2024] Open
Abstract
The death of coronavirus disease 2019 (COVID-19) is primarily due to from critically ill patients, especially from ARDS complications caused by SARS-CoV-2. Therefore, it is essential to contribute an in-depth understanding of the pathogenesis of the disease and to identify biomarkers for predicting critically ill patients at the molecular level. Immunogenic cell death (ICD), as a specific variant of regulatory cell death driven by stress, can induce adaptive immune responses against cell death antigens in the host. Studies have confirmed that both innate and adaptive immune pathways are involved in the pathogenesis of SARS-CoV-2 infection. However, the role of ICD in the pathogenesis of severe COVID-19 has rarely been explored. In this study, we systematically evaluated the role of ICD-related genes in COVID-19. We conducted consensus clustering, immune infiltration analysis, and functional enrichment analysis based on ICD differentially expressed genes. The results showed that immune infiltration characteristics were altered in severe and non-severe COVID-19. In addition, we used multiple machine learning methods to screen for five risk genes (KLF5, NSUN7, APH1B, GRB10 and CD4), which are used to predict COVID-19 severity. Finally, we constructed a nomogram to predict the risk of severe COVID-19 based on the classification and recognition model, and validated the model with external data sets. This study provides a valuable direction for the exploration of the pathogenesis and progress of COVID-19, and helps in the early identification of severe cases of COVID-19 to reduce mortality.
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Affiliation(s)
- Chunyu Li
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Ke Wu
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Rui Yang
- Department of Internal Medicine, Guiyang First People's Hospital, Guiyang, 550004, Guizhou, China
| | - Minghua Liao
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jun Li
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Qian Zhu
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jiayi Zhang
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xianming Zhang
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China.
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49
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Lv X, Zheng L, Zhang T, Wang W, Chen Y, Li J, Cai Z, Guo X, Song L. CLCA1 exacerbates lung inflammation via p38 MAPK pathway in acute respiratory distress syndrome. Exp Lung Res 2024; 50:85-95. [PMID: 38597420 DOI: 10.1080/01902148.2024.2334262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/19/2024] [Indexed: 04/11/2024]
Abstract
Recent research has revealed that airway epithelial calcium-activated chloride channel-1 (CLCA1) is implicated in the inflammation of multiple human respiratory diseases, but the specific role in acute respiratory distress syndrome (ARDS) remains unknown. To investigate the role of CLCA1 in ARDS, 80 participants, including 26 ARDS patients, 26 patients with community-acquired pneumonia (CAP) and 28 control subjects, were enrolled in this study. As the result shows, the level of CLCA1 was significantly increased in ARDS patients and positively correlated with neutrophil infiltration and the poor prognosis of ARDS. Then, the level of CLCA1 also elevated in the LPS-induced ARDS mouse model, and the administration of CLCA1 significantly regulated the phenotypes of ARDS in mice, such as lung injury score, BALF protein concentration, neutrophils infiltration and the secretions of inflammatory factors. Furthermore, administration of CLCA1 substantially altered the phosphorylation of p38 in the ARDS mouse model, whereas repressing the expression of CLCA1 or inhibiting the activation of p38 both alleviated the inflammatory response of ARDS. In summary, CLCA1 was notably correlated with ARDS and exacerbated the ARDS phenotypes through the p38 MAPK pathway.
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Affiliation(s)
- Xing Lv
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Long Zheng
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | | | - Weijia Wang
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yuanyuan Chen
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jing Li
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Zhigui Cai
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xingxing Guo
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Liqiang Song
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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50
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Zhou Z, Zeng X, Liao J, Dong X, Deng Y, Wang Y, Zhou M. Immune Characteristic Genes and Neutrophil Immune Transformation Studies in Severe COVID-19. Microorganisms 2024; 12:737. [PMID: 38674681 PMCID: PMC11052247 DOI: 10.3390/microorganisms12040737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/26/2024] [Accepted: 03/31/2024] [Indexed: 04/28/2024] Open
Abstract
As a disease causing a global pandemic, the progression of symptoms to severe disease in patients with COVID-19 often has adverse outcomes, but research on the immunopathology of COVID-19 severe disease remains limited. In this study, we used mRNA-seq data from the peripheral blood of COVID-19 patients to identify six COVID-19 severe immune characteristic genes (FPR1, FCGR2A, TLR4, S100A12, CXCL1, and L TF), and found neutrophils to be the critical immune cells in COVID-19 severe disease. Subsequently, using scRNA-seq data from bronchoalveolar lavage fluid from COVID-19 patients, neutrophil subtypes highly expressing the S100A family were found to be located at the end of cellular differentiation and tended to release neutrophil extracellular traps. Finally, it was also found that alveolar macrophages, macrophages, and monocytes with a high expression of COVID-19 severe disease immune characteristic genes may influence neutrophils through intercellular ligand-receptor pairs to promote neutrophil extracellular trap release. This study provides immune characteristic genes, critical immune pathways, and immune cells in COVID-19 severe disease, explores intracellular immune transitions of critical immune cells and pit-induced intercellular communication of immune transitions, and provides new biomarkers and potential drug targets for the treatment of patients with COVID-19 severe disease.
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Affiliation(s)
| | | | | | | | | | - Yinghui Wang
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (Z.Z.); (X.Z.); (J.L.); (X.D.); (Y.D.)
| | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (Z.Z.); (X.Z.); (J.L.); (X.D.); (Y.D.)
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