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Mahrokhian SH, Tostanoski LH, Vidal SJ, Barouch DH. COVID-19 vaccines: Immune correlates and clinical outcomes. Hum Vaccin Immunother 2024; 20:2324549. [PMID: 38517241 PMCID: PMC10962618 DOI: 10.1080/21645515.2024.2324549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 02/24/2024] [Indexed: 03/23/2024] Open
Abstract
Severe disease due to COVID-19 has declined dramatically as a result of widespread vaccination and natural immunity in the population. With the emergence of SARS-CoV-2 variants that largely escape vaccine-elicited neutralizing antibody responses, the efficacy of the original vaccines has waned and has required vaccine updating and boosting. Nevertheless, hospitalizations and deaths due to COVID-19 have remained low. In this review, we summarize current knowledge of immune responses that contribute to population immunity and the mechanisms how vaccines attenuate COVID-19 disease severity.
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Affiliation(s)
- Shant H. Mahrokhian
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Lisa H. Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Samuel J. Vidal
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
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2
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Clark RD, Rabito F, Munyonho FT, Remcho TP, Kolls JK. Evaluation of anti-vector immune responses to adenovirus-mediated lung gene therapy and modulation by αCD20. Mol Ther Methods Clin Dev 2024; 32:101286. [PMID: 39070292 PMCID: PMC11283059 DOI: 10.1016/j.omtm.2024.101286] [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: 08/16/2023] [Accepted: 06/21/2024] [Indexed: 07/30/2024]
Abstract
Although the last decade has seen tremendous progress in drugs that treat cystic fibrosis (CF) due to mutations that lead to protein misfolding, there are approximately 8%-10% of subjects with mutations that result in no significant CFTR protein expression demonstrating the need for gene editing or gene replacement with inhaled mRNA or vector-based approaches. A limitation for vector-based approaches is the formation of neutralizing humoral responses. Given that αCD20 has been used to manage post-transplant lymphoproliferative disease in CF subjects with lung transplants, we studied the ability of αCD20 to module both T and B cell responses in the lung to one of the most immunogenic vectors, E1-deleted adenovirus serotype 5. We found that αCD20 significantly blocked luminal antibody responses and efficiently permitted re-dosing. αCD20 had more limited impact on the T cell compartment, but reduced tissue resident memory T cell responses in bronchoalveolar lavage fluid. Taken together, these pre-clinical studies suggest that αCD20 could be re-purposed for lung gene therapy protocols to permit re-dosing.
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Affiliation(s)
- Robert D.E. Clark
- Departments of Pediatrics & Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Felix Rabito
- Departments of Pediatrics & Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Ferris T. Munyonho
- Departments of Pediatrics & Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - T. Parks Remcho
- Departments of Pediatrics & Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jay K. Kolls
- Departments of Pediatrics & Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA
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Wang W, Jia H, Hua X, Song J. New insights gained from cellular landscape changes in myocarditis and inflammatory cardiomyopathy. Heart Fail Rev 2024; 29:883-907. [PMID: 38896377 DOI: 10.1007/s10741-024-10406-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/26/2024] [Indexed: 06/21/2024]
Abstract
Advances in the etiological classification of myocarditis and inflammatory cardiomyopathy (ICM) have reached a consensus. However, the mechanism of myocarditis/ICM remains unclear, which affects the development of treatment and the improvement of outcome. Cellular transcription and metabolic reprogramming, and the interactions between cardiomyocytes and non-cardiomyocytes, such as the immune cells, contribute to the process of myocarditis/ICM. Recent efforts have been made by multi-omics techniques, particularly in single-cell RNA sequencing, to gain a better understanding of the cellular landscape alteration occurring in disease during the progression. This article aims to provide a comprehensive overview of the latest studies in myocarditis/ICM, particularly as revealed by single-cell sequencing.
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Affiliation(s)
- Weiteng Wang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 167 Beilishi Road, Xicheng District, Beijing, 100037, China
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 10037, China
| | - Hao Jia
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 167 Beilishi Road, Xicheng District, Beijing, 100037, China
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 10037, China
| | - Xiumeng Hua
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 167 Beilishi Road, Xicheng District, Beijing, 100037, China
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 10037, China
| | - Jiangping Song
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 167 Beilishi Road, Xicheng District, Beijing, 100037, China.
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences, Shenzhen, 518057, China.
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 10037, China.
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Wen Z, Ablimit A. Aquaporin 1 aggravates lipopolysaccharide-induced macrophage polarization and pyroptosis. Sci Rep 2024; 14:18569. [PMID: 39127771 DOI: 10.1038/s41598-024-68899-2] [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: 01/08/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Acute respiratory infections (ARIs) are associated with high mortality and morbidity. Acute lung injury (ALI) is caused by the activation of immune cells during ARIs caused by viruses such as SARS-CoV-2. Aquaporin 1 (AQP1) is distributed in a variety of immune cells and is related to the occurrence of ALI, but the mechanism is not clear. A reference map of human single cells was used to identify macrophages in COVID-19 patients at the single-cell level. "FindMarkers" was used to analyze differentially expressed genes (DEGs), and "clusterProfiler" was used to analyze the functions of the DEGs. An M1 macrophage polarization model was established with lipopolysaccharide (LPS) in vitro, and the relationships among AQP1, pyroptosis and M1 polarization were examined by using an AQP1 inhibitor. Transcriptome sequencing and RT-qPCR were used to examine the molecular mechanism by which AQP1 regulates macrophage polarization and pyroptosis. Antigen presentation, M1 polarization, migration and phagocytosis are abnormal in SARS-CoV-2-infected macrophages, which is related to the high expression of AQP1. An M1 polarization model of macrophages was constructed in vitro, and an AQP1 inhibitor was used to examine whether AQP1 could promote M1 polarization and pyroptosis in response to LPS. Transcriptome and cell experiments showed that this effect was related to a decrease in chemokines caused by AQP1 deficiency. AQP1 participates in M1 polarization and pyroptosis in macrophages by increasing the levels of chemokines induced by LPS, which provides new insights for the diagnosis and treatment of ALI.
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Affiliation(s)
- Zhuman Wen
- Department of Histology and Embryology, Basic Medical College, Xinjiang Medical University, Urumqi, China
| | - Abduxukur Ablimit
- Department of Histology and Embryology, Basic Medical College, Xinjiang Medical University, Urumqi, China.
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Lee S, Lim KR, Chun KJ, Kim BS. Long-term impacts of COVID-19 in patients with prior heart failure in Korea: A nationwide cohort study using the common data model. Medicine (Baltimore) 2024; 103:e39236. [PMID: 39093748 PMCID: PMC11296475 DOI: 10.1097/md.0000000000039236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Limited data are available on the long-term prognosis and monitoring period after coronavirus disease 2019 (COVID-19) infection in the population with prior heart failure (HF). We aimed to exam the association of COVID-19 with clinical prognosis in populations with prior HF and evaluate prognosis within 30 days and 30 days to 1 year after infection. Based on insurance benefit claims sent to the Health Insurance Review and Assessment Service of Korea from January 2018 to April 2022, 9,822,577 patients were selected and converted to the Observational Medical Outcomes Partnership-common data model by the Big Data Department of Health Insurance Review and Assessment Service of Korea. In the dataset, 1,565,274 patients exhibited diagnosis of HF based on the International Statistical Classification of Diseases and Related Health Problems 10 codes. They were divided into 2 groups according to COVID-19 infection, and propensity-score-matching analysis was performed. The clinical outcome was all-cause mortality. Among the 1,565,274 patients with an HF diagnosis, 1,152,975 patients were classified into the HF with the COVID-19 group and 412,299 patients in the HF without COVID-19 group. We created 200,780 matched pairs by propensity-score-matching analysis. Within 30 days of COVID-19, the HF with COVID-19 group had a higher risk of all-cause death compared with the HF without COVID-19 group (hazard ratio [HR]: 2.19, 95% confidence interval [CI]: 2.04-2.36, P < .01). Thirty days to 1 year after COVID-19 infection, the HF with COVID-19 group exhibited a higher risk of all-cause death (HR: 2.04, 95% CI: 1.83-2.27, P < .01). In populations with prior HF, COVID-19 is associated with a higher risk of all-cause mortality within 30 days and this risk remains augmented up to 1 year after the acute phase of COVID-19. Our findings suggest that greater attention may be crucial in populations with prior HF for a prolonged period after COVID-19 infection.
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Affiliation(s)
- Seunghwa Lee
- Division of Cardiology, Department of Medicine, Wiltse Memorial Hospital, Suwon, Gyeonggi-do, South Korea
| | - Kyoung Ree Lim
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul, South Korea
| | - Kwang Jin Chun
- Division of Cardiology, Department of Internal Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, South Korea
| | - Bum Sung Kim
- Division of Cardiology, Department of Medicine, Konkuk University Medical Center, Seoul, South Korea
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Du Q, Liang R, Wu M, Yang M, Xie Y, Liu Q, Tang K, Lin X, Yuan S, Shen J. Alisol B 23-acetate broadly inhibits coronavirus through blocking virus entry and suppresses proinflammatory T cells responses for the treatment of COVID-19. J Adv Res 2024; 62:273-290. [PMID: 37802148 DOI: 10.1016/j.jare.2023.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/11/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023] Open
Abstract
INTRODUCTION Emerging severe acute respiratory syndrome (SARS) coronavirus (CoV)-2 causes a global health disaster and pandemic. Seeking effective anti-pan-CoVs drugs benefit critical illness patients of coronavirus disease 2019 (COVID-19) but also may play a role in emerging CoVs of the future. OBJECTIVES This study tested the hypothesis that alisol B 23-acetate could be a viral entry inhibitor and would have proinflammatory inhibition for COVID-19 treatment. METHODS SARS-CoV-2 and its variants infected several cell lines were applied to evaluate the anti-CoVs activities of alisol B 23-aceate in vitro. The effects of alisol B 23-acetate on in vivo models were assessed by using SARS-CoV-2 and its variants challenged hamster and human angiotensin-converting enzyme 2 (ACE2) transgenic mice. The target of alisol B 23-acetate to ACE2 was analyzed using hydrogen/deuterium exchange (HDX) mass spectrometry (MS). RESULTS Alisol B 23-acetate had inhibitory effects on different species of coronavirus. By using HDX-MS, we found that alisol B 23-acetate had inhibition potency toward ACE2. In vivo experiments showed that alisol B 23-acetate treatment remarkably decreased viral copy, reduced CD4+ T lymphocytes and CD11b+ macrophages infiltration and ameliorated lung damages in the hamster model. In Omicron variant infected human ACE2 transgenic mice, alisol B 23-acetate effectively alleviated viral load in nasal turbinate and reduced proinflammatory cytokines interleukin 17 (IL17) and interferon γ (IFNγ) in peripheral blood. The prophylactic treatment of alisol B 23-acetate by intranasal administration significantly attenuated Omicron viral load in the hamster lung tissues. Moreover, alisol B 23-acetate treatment remarkably inhibited proinflammatory responses through mitigating the secretions of IFNγ and IL17 in the cultured human and mice lymphocytes in vitro. CONCLUSION Alisol B 23-acetate could be a promising therapeutic agent for COVID-19 treatment and its underlying mechanisms might be attributed to viral entry inhibition and anti-inflammatory activities.
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Affiliation(s)
- Qiaohui Du
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region; State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Ronghui Liang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Meiling Wu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Minxiao Yang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Yubin Xie
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Qing Liu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Kaiming Tang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Xiang Lin
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China.
| | - Jiangang Shen
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 3 Sassoon Road, Pokfulam, Hong Kong, Hong Kong Special Administrative Region; State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong Special Administrative Region.
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7
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Murthy A, Rodriguez LR, Dimopoulos T, Bui S, Iyer S, Chavez K, Tomer Y, Abraham V, Cooper C, Renner DM, Katzen JB, Bentley ID, Ghadiali SN, Englert JA, Weiss SR, Beers MF. Activation of alveolar epithelial ER stress by β-coronavirus infection disrupts surfactant homeostasis in mice: implications for COVID-19 respiratory failure. Am J Physiol Lung Cell Mol Physiol 2024; 327:L232-L249. [PMID: 38860845 DOI: 10.1152/ajplung.00324.2023] [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: 10/19/2023] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
COVID-19 syndrome is characterized by acute lung injury, hypoxemic respiratory failure, and high mortality. Alveolar type 2 (AT2) cells are essential for gas exchange, repair, and regeneration of distal lung epithelium. We have shown that the causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and other members of the β-coronavirus genus induce an endoplasmic reticulum (ER) stress response in vitro; however, the consequences for host AT2 cell function in vivo are less understood. To study this, two murine models of coronavirus infection were used-mouse hepatitis virus-1 (MHV-1) in A/J mice and a mouse-adapted SARS-CoV-2 strain. MHV-1-infected mice exhibited dose-dependent weight loss with histological evidence of distal lung injury accompanied by elevated bronchoalveolar lavage fluid (BALF) cell counts and total protein. AT2 cells showed evidence of both viral infection and increased BIP/GRP78 expression, consistent with activation of the unfolded protein response (UPR). The AT2 UPR included increased inositol-requiring enzyme 1α (IRE1α) signaling and a biphasic response in PKR-like ER kinase (PERK) signaling accompanied by marked reductions in AT2 and BALF surfactant protein (SP-B and SP-C) content, increases in surfactant surface tension, and emergence of a reprogrammed epithelial cell population (Krt8+ and Cldn4+). The loss of a homeostatic AT2 cell state was attenuated by treatment with the IRE1α inhibitor OPK-711. As a proof-of-concept, C57BL6 mice infected with mouse-adapted SARS-CoV-2 demonstrated similar lung injury and evidence of disrupted surfactant homeostasis. We conclude that lung injury from β-coronavirus infection results from an aberrant host response, activating multiple AT2 UPR stress pathways, altering surfactant metabolism/function, and changing AT2 cell state, offering a mechanistic link between SARS-CoV-2 infection, AT2 cell biology, and acute respiratory failure.NEW & NOTEWORTHY COVID-19 syndrome is characterized by hypoxemic respiratory failure and high mortality. In this report, we use two murine models to show that β-coronavirus infection produces acute lung injury, which results from an aberrant host response, activating multiple epithelial endoplasmic reticular stress pathways, disrupting pulmonary surfactant metabolism and function, and forcing emergence of an aberrant epithelial transition state. Our results offer a mechanistic link between SARS-CoV-2 infection, AT2 cell biology, and respiratory failure.
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Affiliation(s)
- Aditi Murthy
- Pulmonary and Critical Care Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
- PENN-CHOP Lung Biology Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Luis R Rodriguez
- Pulmonary and Critical Care Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
- PENN-CHOP Lung Biology Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Thalia Dimopoulos
- Pulmonary and Critical Care Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Sarah Bui
- Pulmonary and Critical Care Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
- PENN-CHOP Lung Biology Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Swati Iyer
- Pulmonary and Critical Care Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Katrina Chavez
- Pulmonary and Critical Care Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Yaniv Tomer
- Pulmonary and Critical Care Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Valsamma Abraham
- Pulmonary and Critical Care Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Charlotte Cooper
- Pulmonary and Critical Care Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - David M Renner
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
- Penn Center for Research on Coronaviruses and Emerging Pathogens, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Jeremy B Katzen
- Pulmonary and Critical Care Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
- PENN-CHOP Lung Biology Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Ian D Bentley
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
| | - Samir N Ghadiali
- Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
- Department of Biomedical Engineering, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
| | - Joshua A Englert
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
- Penn Center for Research on Coronaviruses and Emerging Pathogens, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Michael F Beers
- Pulmonary and Critical Care Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
- PENN-CHOP Lung Biology Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
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Chen S, Zhang L, Song Y, Xie K, Wang Y, Liang Y. A Comprehensive Analysis of NRP1 in Malignancies Provide Therapeutic Implication for Treating Cancer Patients Infected with SARS-CoV-2. Biochem Genet 2024; 62:2399-2417. [PMID: 37938510 DOI: 10.1007/s10528-023-10518-2] [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: 03/03/2023] [Accepted: 09/05/2023] [Indexed: 11/09/2023]
Abstract
COVID-19 (Coronavirus disease 2019) is caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2), which can lead to pneumonia, cytokine storms, and lymphopenia. Patients with cancer are more susceptible to SARS-CoV-2 infection and severe COVID-19 due to immunosuppression. Recent studies have indicated that NRP1 (Neuropilin 1) may act as a novel mediator of SARS-CoV-2 entry into the host cell. As no systematic review has been performed investigating the characteristics of NRP1 in pan-carcinoma, we comprehensively analyzed NRP1 in patients with pan-cancer. Using a bioinformatics approach, we aimed to systematically examine NRP1 expression profiles in both pan-carcinoma and healthy tissues. We found that lung and genitourinary cancers have a relatively higher NRP-1 expression than other cancer patients, suggesting that these patients may be more susceptible to SARS-CoV-2. Our analysis further revealed that NRP1 expression was downregulated in Vero E6 cells, whole blood, lung organoids, testis tissue, and alveolospheres infected with SARS-CoV-2. Notably, NRP1 was associated with immune cell infiltration, immune checkpoint genes, and immune-related genes in most patients with cancer. These findings suggest that, in patients with specific types of cancer, especially lung and genitourinary, high expression of NRP1 contributes to greater susceptibility to SARS-CoV-2 infection and an increased risk of damage due to cytokine storms. Overall, NRP1 appears to play a critical role in regulating immunological properties and metabolism in many tumor types. Specific inhibitors of the NRP1 antigen (pegaptanib, EG00229, or MNRP1685A) combined with other anti-SARS-CoV-2 strategies may aid in treating patients with lung and genitourinary cancers following SARS-CoV-2 infection.
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Affiliation(s)
- Shuzhao Chen
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Limei Zhang
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yiling Song
- Department of Clinical Laboratory, SunYat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Kunying Xie
- Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Yun Wang
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Yang Liang
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China.
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9
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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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10
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Yan A, Zhang R, Feng C, Feng J. Coronavirus disease 2019-related myocarditis genes contribute to ECMO prognosis. BMC Cardiovasc Disord 2024; 24:375. [PMID: 39026189 PMCID: PMC11264513 DOI: 10.1186/s12872-024-04032-5] [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: 02/20/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Acute myocardial injury, cytokine storms, hypoxemia and pathogen-mediated damage were the major causes responsible for mortality induced by coronavirus disease 2019 (COVID-19)-related myocarditis. These need ECMO treatment. We investigated differentially expressed genes (DEGs) in patients with COVID-19-related myocarditis and ECMO prognosis. METHODS GSE150392 and GSE93101 were analyzed to identify DEGs. A Venn diagram was used to obtain the same transcripts between myocarditis-related and ECMO-related DEGs. Enrichment pathway analysis was performed and hub genes were identified. Pivotal miRNAs, transcription factors, and chemicals with the screened gene interactions were identified. The GSE167028 dataset and single-cell sequencing data were used to validate the screened genes. RESULTS Using a Venn diagram, 229 overlapping DEGs were identified between myocarditis-related and ECMO-related DEGs, which were mainly involved in T cell activation, contractile actin filament bundle, actomyosin, cyclic nucleotide phosphodiesterase activity, and cytokine-cytokine receptor interaction. 15 hub genes and 15 neighboring DEGs were screened, which were mainly involved in the positive regulation of T cell activation, integrin complex, integrin binding, the PI3K-Akt signaling pathway, and the TNF signaling pathway. Data in GSE167028 and single-cell sequencing data were used to validate the screened genes, and this demonstrated that the screened genes CCL2, APOE, ITGB8, LAMC2, COL6A3 and TNC were mainly expressed in fibroblast cells; IL6, ITGA1, PTK2, ITGB5, IL15, LAMA4, CAV1, SNCA, BDNF, ACTA2, CD70, MYL9, DPP4, ENO2 and VEGFC were expressed in cardiomyocytes; IL6, PTK2, ITGB5, IL15, APOE, JUN, SNCA, CD83, DPP4 and ENO2 were expressed in macrophages; and IL6, ITGA1, PTK2, ITGB5, IL15, VCAM1, LAMA4, CAV1, ACTA2, MYL9, CD83, DPP4, ENO2, VEGFC and IL32 were expressed in vascular endothelial cells. CONCLUSION The screened hub genes, IL6, ITGA1, PTK2, ITGB3, ITGB5, CCL2, IL15, VCAM1, GZMB, APOE, ITGB8, LAMA4, LAMC2, COL6A3 and TNFRSF9, were validated using GEO dataset and single-cell sequencing data, which may be therapeutic targets patients with myocarditis to prevent MI progression and adverse cardiovascular events.
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Affiliation(s)
- An Yan
- Tianjin Chest Hospital, Taierzhuang North Road 261, Jinnan District, Tianjin, China
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Taierzhuang North Road 261, Jinnan District, Tianjin, China
| | - Ruiying Zhang
- Tianjin Chest Hospital, Taierzhuang North Road 261, Jinnan District, Tianjin, China
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Taierzhuang North Road 261, Jinnan District, Tianjin, China
| | - Chao Feng
- Tianjin Chest Hospital, Taierzhuang North Road 261, Jinnan District, Tianjin, China
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Taierzhuang North Road 261, Jinnan District, Tianjin, China
| | - Jinping Feng
- Tianjin Chest Hospital, Taierzhuang North Road 261, Jinnan District, Tianjin, China.
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Taierzhuang North Road 261, Jinnan District, Tianjin, China.
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11
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Xian SP, Li ZY, Li W, Yang PF, Huang SH, Liu Y, Tang L, Lai J, Zeng FM, He JZ, Liu Y. Spatial immune landscapes of SARS-CoV-2 gastrointestinal infection: macrophages contribute to local tissue inflammation and gastrointestinal symptoms. Front Cell Dev Biol 2024; 12:1375354. [PMID: 39100091 PMCID: PMC11295004 DOI: 10.3389/fcell.2024.1375354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 07/02/2024] [Indexed: 08/06/2024] Open
Abstract
Background In some patients, persistent gastrointestinal symptoms like abdominal pain, nausea, and diarrhea occur as part of long COVID-19 syndrome following acute respiratory symptoms caused by SARS-CoV-2. However, the characteristics of immune cells in the gastrointestinal tract of COVID-19 patients and their association with these symptoms remain unclear. Methodology Data were collected from 95 COVID-19 patients. Among this cohort, 11 patients who exhibited gastrointestinal symptoms and underwent gastroscopy were selected. Using imaging mass cytometry, the gastrointestinal tissues of these patients were thoroughly analyzed to identify immune cell subgroups and investigate their spatial distribution. Results Significant acute inflammatory responses were found in the gastrointestinal tissues, particularly in the duodenum, of COVID-19 patients. These alterations included an increase in the levels of CD68+ macrophages and CD3+CD4+ T-cells, which was more pronounced in tissues with nucleocapsid protein (NP). The amount of CD68+ macrophages positively correlates with the number of CD3+CD4+ T-cells (R = 0.783, p < 0.001), additionally, spatial neighborhood analysis uncovered decreased interactions between CD68+ macrophages and multiple immune cells were noted in NP-positive tissues. Furthermore, weighted gene coexpression network analysis was employed to extract gene signatures related to clinical features and immune responses from the RNA-seq data derived from gastrointestinal tissues from COVID-19 patients, and we validated that the MEgreen module shown positive correlation with clinical parameter (i.e., Total bilirubin, ALT, AST) and macrophages (R = 0.84, p = 0.001), but negatively correlated with CD4+ T cells (R = -0.62, p = 0.004). By contrast, the MEblue module was inversely associated with macrophages and positively related with CD4+ T cells. Gene function enrichment analyses revealed that the MEgreen module is closely associated with biological processes such as immune response activation, signal transduction, and chemotaxis regulation, indicating its role in the gastrointestinal inflammatory response. Conclusion The findings of this study highlight the role of specific immune cell groups in the gastrointestinal inflammatory response in COVID-19 patients. Gene coexpression network analysis further emphasized the importance of the gene modules in gastrointestinal immune responses, providing potential molecular targets for the treatment of COVID-19-related gastrointestinal symptoms.
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Affiliation(s)
- Shi-Ping Xian
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Zhan-Yu Li
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Wei Li
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Peng-Fei Yang
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Shen-Hao Huang
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Ye Liu
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Lei Tang
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Jun Lai
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Fa-Min Zeng
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Jian-Zhong He
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Yang Liu
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Department of Ophthalmology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
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12
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Loeb K, Lemaille C, Frederick C, Wallace HL, Kindrachuk J. Harnessing high-throughput OMICS in emerging zoonotic virus preparedness and response activities. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167337. [PMID: 38986821 DOI: 10.1016/j.bbadis.2024.167337] [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: 05/06/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Emerging and re-emerging viruses pose unpredictable and significant challenges to global health. Emerging zoonotic infectious diseases, which are transmitted between humans and non-human animals, have been estimated to be responsible for nearly two-thirds of emerging infectious disease events and emergence events attributed to these pathogens have been increasing in frequency with the potential for high global health and economic burdens. In this review we will focus on the application of highthroughput OMICS approaches to emerging zoonotic virus investigtations. We highlight the key contributions of transcriptome and proteome investigations to emerging zoonotic virus preparedness and response activities with a focus on SARS-CoV-2, avian influenza virus subtype H5N1, and Orthoebolavirus investigations.
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Affiliation(s)
- Kristi Loeb
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Candice Lemaille
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Christina Frederick
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Hannah L Wallace
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Jason Kindrachuk
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada; Manitoba Centre for Proteomics and Systems Biology, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada; Department of Internal Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada.
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13
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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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14
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Baldassarro VA, Alastra G, Cescatti M, Quadalti C, Lorenzini L, Giardino L, Calzà L. SARS-CoV-2-related peptides induce endothelial-to-mesenchymal transition in endothelial capillary cells derived from different body districts: focus on membrane (M) protein. Cell Tissue Res 2024:10.1007/s00441-024-03900-y. [PMID: 38953987 DOI: 10.1007/s00441-024-03900-y] [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: 03/04/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19, may lead to multiple organ dysfunctions and long-term complications. The induction of microvascular dysfunction is regarded as a main player in these pathological processes. To investigate the possible impact of SARS-CoV-2-induced endothelial-to-mesenchymal transition (EndMT) on fibrosis in "long-COVID" syndrome, we used primary cultures of human microvascular cells derived from the lungs, as the main infection target, compared to cells derived from different organs (dermis, heart, kidney, liver, brain) and to the HUVEC cell line. To mimic the virus action, we used mixed SARS-CoV-2 peptide fragments (PepTivator®) of spike (S), nucleocapsid (N), and membrane (M) proteins. TGFβ2 and cytokine mix (IL-1β, IL-6, TNFα) were used as positive controls. The percentage of cells positive to mesenchymal and endothelial markers was quantified by high content screening. We demonstrated that S+N+M mix induces irreversible EndMT in all analyzed endothelial cells via the TGFβ pathway, as demonstrated by ApoA1 treatment. We then tested the contribution of single peptides in lung and brain cells, demonstrating that EndMT is triggered by M peptide. This was confirmed by transfection experiment, inducing the endogenous expression of the glycoprotein M in lung-derived cells. In conclusion, we demonstrated that SARS-CoV-2 peptides induce EndMT in microvascular endothelial cells from multiple body districts. The different peptides play different roles in the induction and maintenance of the virus-mediated effects, which are organ-specific. These results corroborate the hypothesis of the SARS-CoV-2-mediated microvascular damage underlying the multiple organ dysfunctions and the long-COVID syndrome.
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Affiliation(s)
- Vito Antonio Baldassarro
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, Ozzano dell'Emilia, Bologna, Italy
- Interdepartmental Centre for Industrial Research in Health Sciences and Technology ICIR-HST, University of Bologna, Bologna, Italy
| | - Giuseppe Alastra
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, Ozzano dell'Emilia, Bologna, Italy
| | | | - Corinne Quadalti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Luca Lorenzini
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, Ozzano dell'Emilia, Bologna, Italy
- Interdepartmental Centre for Industrial Research in Health Sciences and Technology ICIR-HST, University of Bologna, Bologna, Italy
| | - Luciana Giardino
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, Ozzano dell'Emilia, Bologna, Italy
- Interdepartmental Centre for Industrial Research in Health Sciences and Technology ICIR-HST, University of Bologna, Bologna, Italy
| | - Laura Calzà
- Interdepartmental Centre for Industrial Research in Health Sciences and Technology ICIR-HST, University of Bologna, Bologna, Italy.
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy.
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15
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Song L, Li K, Chen H, Xie L. Cell Cross-Talk in Alveolar Microenvironment: From Lung Injury to Fibrosis. Am J Respir Cell Mol Biol 2024; 71:30-42. [PMID: 38579159 PMCID: PMC11225874 DOI: 10.1165/rcmb.2023-0426tr] [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: 12/05/2023] [Accepted: 04/05/2024] [Indexed: 04/07/2024] Open
Abstract
Alveoli are complex microenvironments composed of various cell types, including epithelial, fibroblast, endothelial, and immune cells, which work together to maintain a delicate balance in the lung environment, ensuring proper growth, development, and an effective response to lung injuries. However, prolonged inflammation or aging can disrupt normal interactions among these cells, leading to impaired repair processes and a substantial decline in lung function. Therefore, it is essential to understand the key mechanisms underlying the interactions among the major cell types within the alveolar microenvironment. We explored the key mechanisms underlying the interactions among the major cell types within the alveolar microenvironment. These interactions occur through the secretion of signaling factors and play crucial roles in the response to injury, repair mechanisms, and the development of fibrosis in the lungs. Specifically, we focused on the regulation of alveolar type 2 cells by fibroblasts, endothelial cells, and macrophages. In addition, we explored the diverse phenotypes of fibroblasts at different stages of life and in response to lung injury, highlighting their impact on matrix production and immune functions. Furthermore, we summarize the various phenotypes of macrophages in lung injury and fibrosis as well as their intricate interplay with other cell types. This interplay can either contribute to the restoration of immune homeostasis in the alveoli or impede the repair process. Through a comprehensive exploration of these cell interactions, we aim to reveal new insights into the molecular mechanisms that drive lung injury toward fibrosis and identify potential targets for therapeutic intervention.
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Affiliation(s)
- Licheng Song
- College of Pulmonary and Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, China; and
| | - Kuan Li
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, Tianjin, China
| | - Huaiyong Chen
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe Hospital, Tianjin University, Tianjin, China
| | - Lixin Xie
- College of Pulmonary and Critical Care Medicine, 8th Medical Center of Chinese PLA General Hospital, Beijing, China; and
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16
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Machkovech HM, Hahn AM, Garonzik Wang J, Grubaugh ND, Halfmann PJ, Johnson MC, Lemieux JE, O'Connor DH, Piantadosi A, Wei W, Friedrich TC. Persistent SARS-CoV-2 infection: significance and implications. THE LANCET. INFECTIOUS DISEASES 2024; 24:e453-e462. [PMID: 38340735 DOI: 10.1016/s1473-3099(23)00815-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 02/12/2024]
Abstract
SARS-CoV-2 causes persistent infections in a subset of individuals, which is a major clinical and public health problem that should be prioritised for further investigation for several reasons. First, persistent SARS-CoV-2 infection often goes unrecognised, and therefore might affect a substantial number of people, particularly immunocompromised individuals. Second, the formation of tissue reservoirs (including in non-respiratory tissues) might underlie the pathophysiology of the persistent SARS-CoV-2 infection and require new strategies for diagnosis and treatment. Finally, persistent SARS-CoV-2 replication, particularly in the setting of suboptimal immune responses, is a possible source of new, divergent virus variants that escape pre-existing immunity on the individual and population levels. Defining optimal diagnostic and treatment strategies for patients with persistent virus replication and monitoring viral evolution are therefore urgent medical and public health priorities.
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Affiliation(s)
- Heather M Machkovech
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | | | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, USA
| | - Jacob E Lemieux
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Wanting Wei
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
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17
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Currey J, Ellsworth C, Khatun MS, Wang C, Chen Z, Liu S, Midkiff C, Xiao M, Ren M, Liu F, Elgazzaz M, Fox S, Maness NJ, Rappaport J, Lazartigues E, Blair R, Kolls JK, Mauvais-Jarvis F, Qin X. Upregulation of inflammatory genes and pathways links obesity to severe COVID-19. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167322. [PMID: 38942338 DOI: 10.1016/j.bbadis.2024.167322] [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: 11/28/2023] [Revised: 06/15/2024] [Accepted: 06/19/2024] [Indexed: 06/30/2024]
Abstract
Obesity is a risk factor for developing severe COVID-19. However, the mechanism underlying obesity-accelerated COVID-19 remains unclear. Here, we report results from a study in which 2-3-month-old K18-hACE2 (K18) mice were fed a western high-fat diet (WD) or normal chow (NC) over 3 months before intranasal infection with a sublethal dose of SARS-CoV2 WA1 (a strain ancestral to the Wuhan variant). After infection, the WD-fed K18 mice lost significantly more body weight and had more severe lung inflammation than normal chow (NC)-fed mice. Bulk RNA-seq analysis of lungs and adipose tissue revealed a diverse landscape of various immune cells, inflammatory markers, and pathways upregulated in the infected WD-fed K18 mice when compared with the infected NC-fed control mice. The transcript levels of IL-6, an important marker of COVID-19 disease severity, were upregulated in the lung at 6-9 days post-infection in the WD-fed mice when compared to NC-fed mice. Transcriptome analysis of the lung and adipose tissue obtained from deceased COVID-19 patients found that the obese patients had an increase in the expression of genes and the activation of pathways associated with inflammation as compared to normal-weight patients (n = 2). The K18 mouse model and human COVID-19 patient data support a link between inflammation and an obesity-accelerated COVID-19 disease phenotype. These results also indicate that obesity-accelerated severe COVID-19 caused by SARS-CoV-2 WA1 infection in the K18 mouse model would be a suitable model for dissecting the cellular and molecular mechanisms underlying pathogenesis.
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Affiliation(s)
- Joshua Currey
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Calder Ellsworth
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Mst Shamima Khatun
- Departments of Medicine and Pediatrics, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA; Department of Pulmonary Critical Care and Environmental Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Chenxiao Wang
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Zheng Chen
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Shumei Liu
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Cecily Midkiff
- Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Mark Xiao
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Mi Ren
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Fengming Liu
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Mona Elgazzaz
- Southeast Louisiana VA Medical Center, New Orleans, LA 70119, USA
| | - Sharon Fox
- Southeast Louisiana VA Medical Center, New Orleans, LA 70119, USA
| | - Nicholas J Maness
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jay Rappaport
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Eric Lazartigues
- Southeast Louisiana VA Medical Center, New Orleans, LA 70119, USA
| | - Robert Blair
- Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Jay K Kolls
- Departments of Medicine and Pediatrics, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA; Department of Pulmonary Critical Care and Environmental Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Franck Mauvais-Jarvis
- Department of Medicine, Section of Endocrinology and Metabolism, Tulane University School of Medicine, New Orleans, LA 70112, USA; Southeast Louisiana VA Medical Center, New Orleans, LA 70119, USA
| | - Xuebin Qin
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA.
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18
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Patrick R, Janbandhu V, Tallapragada V, Tan SSM, McKinna EE, Contreras O, Ghazanfar S, Humphreys DT, Murray NJ, Tran YTH, Hume RD, Chong JJH, Harvey RP. Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis in diverse pathologies. SCIENCE ADVANCES 2024; 10:eadk8501. [PMID: 38905342 PMCID: PMC11192082 DOI: 10.1126/sciadv.adk8501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
Single-cell technology has allowed researchers to probe tissue complexity and dynamics at unprecedented depth in health and disease. However, the generation of high-dimensionality single-cell atlases and virtual three-dimensional tissues requires integrated reference maps that harmonize disparate experimental designs, analytical pipelines, and taxonomies. Here, we present a comprehensive single-cell transcriptome integration map of cardiac fibrosis, which underpins pathophysiology in most cardiovascular diseases. Our findings reveal similarity between cardiac fibroblast (CF) identities and dynamics in ischemic versus pressure overload models of cardiomyopathy. We also describe timelines for commitment of activated CFs to proliferation and myofibrogenesis, profibrotic and antifibrotic polarization of myofibroblasts and matrifibrocytes, and CF conservation across mouse and human healthy and diseased hearts. These insights have the potential to inform knowledge-based therapies.
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Affiliation(s)
- Ralph Patrick
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Vaibhao Janbandhu
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia
| | | | - Shannon S. M. Tan
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Emily E. McKinna
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
| | - Osvaldo Contreras
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Shila Ghazanfar
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW 2006, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW 2006, Australia
| | - David T. Humphreys
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Nicholas J. Murray
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Yen T. H. Tran
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Robert D. Hume
- Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
- School of Medical Science, The University of Sydney, Camperdown, NSW 2006, Australia
- Centre for Heart Failure and Diseases of the Aorta, The Baird Institute, Sydney, NSW 2042, Australia
| | - James J. H. Chong
- Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
- Department of Cardiology, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Richard P. Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, NSW 2052, Australia
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19
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Murphy SL, Balzer NR, Ranheim T, Sagen EL, Huse C, Bjerkeli V, Michelsen AE, Finbråten AK, Heggelund L, Dyrhol-Riise AM, Tveita A, Holten AR, Trøseid M, Ueland T, Ulas T, Aukrust P, Barratt-Due A, Halvorsen B, Dahl TB. Extracellular matrix remodelling pathway in peripheral blood mononuclear cells from severe COVID-19 patients: an explorative study. Front Immunol 2024; 15:1379570. [PMID: 38957465 PMCID: PMC11217192 DOI: 10.3389/fimmu.2024.1379570] [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: 01/31/2024] [Accepted: 06/03/2024] [Indexed: 07/04/2024] Open
Abstract
There is a reciprocal relationship between extracellular matrix (ECM) remodelling and inflammation that could be operating in the progression of severe COVID-19. To explore the immune-driven ECM remodelling in COVID-19, we in this explorative study analysed these interactions in hospitalised COVID-19 patients. RNA sequencing and flow analysis were performed on peripheral blood mononuclear cells. Inflammatory mediators in plasma were measured by ELISA and MSD, and clinical information from hospitalised COVID-19 patients (N=15) at admission was included in the analysis. Further, we reanalysed two publicly available datasets: (1) lung tissue RNA-sequencing dataset (N=5) and (2) proteomics dataset from PBCM. ECM remodelling pathways were enriched in PBMC from COVID-19 patients compared to healthy controls. Patients treated at the intensive care unit (ICU) expressed distinct ECM remodelling gene profiles compared to patients in the hospital ward. Several markers were strongly correlated to immune cell subsets, and the dysregulation in the ICU patients was positively associated with plasma levels of inflammatory cytokines and negatively associated with B-cell activating factors. Finally, our analysis of publicly accessible datasets revealed (i) an augmented ECM remodelling signature in inflamed lung tissue compared to non-inflamed tissue and (ii) proteomics analysis of PBMC from severe COVID-19 patients demonstrated an up-regulation in an ECM remodelling pathway. Our results may suggest the presence of an interaction between ECM remodelling, inflammation, and immune cells, potentially initiating or perpetuating pulmonary pathology in severe COVID-19.
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Affiliation(s)
- Sarah Louise Murphy
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Nora Reka Balzer
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Trine Ranheim
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Ellen Lund Sagen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Camilla Huse
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medicine, Division of Cardiovascular Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Vigdis Bjerkeli
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Annika E. Michelsen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Lars Heggelund
- Department of Internal Medicine, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Anne Ma Dyrhol-Riise
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Infectious Diseases, Oslo University Hospital Ullevål, Oslo, Norway
| | - Anders Tveita
- Department of Internal Medicine, Bærum Hospital, Vestre Viken Hospital Trust, Gjettum, Norway
- Division of Laboratory Medicine, Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Aleksander Rygh Holten
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Acute Medicine, Oslo University Hospital, Oslo, Norway
| | - Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Thor Ueland
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Thrombosis Research Center (TREC), Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Thomas Ulas
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Andreas Barratt-Due
- Division of Laboratory Medicine, Department of Immunology, Oslo University Hospital, Oslo, Norway
- Department of Anesthesia and Intensive Care Medicine, Oslo University Hospital, Oslo, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medicine, Division of Cardiovascular Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Tuva Børresdatter Dahl
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
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20
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Gonzalez-Orozco M, Tseng HC, Hage A, Xia H, Behera P, Afreen K, Peñaflor-Tellez Y, Giraldo MI, Huante M, Puebla-Clark L, van Tol S, Odle A, Crown M, Teruel N, Shelite TR, Menachery V, Endsley M, Endsley JJ, Najmanovich RJ, Bashton M, Stephens R, Shi PY, Xie X, Freiberg AN, Rajsbaum R. TRIM7 ubiquitinates SARS-CoV-2 membrane protein to limit apoptosis and viral replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599107. [PMID: 38948778 PMCID: PMC11212893 DOI: 10.1101/2024.06.17.599107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
SARS-CoV-2 is a highly transmissible virus that causes COVID-19 disease. Mechanisms of viral pathogenesis include excessive inflammation and viral-induced cell death, resulting in tissue damage. We identified the host E3-ubiquitin ligase TRIM7 as an inhibitor of apoptosis and SARS-CoV-2 replication via ubiquitination of the viral membrane (M) protein. Trim7 -/- mice exhibited increased pathology and virus titers associated with epithelial apoptosis and dysregulated immune responses. Mechanistically, TRIM7 ubiquitinates M on K14, which protects cells from cell death. Longitudinal SARS-CoV-2 sequence analysis from infected patients revealed that mutations on M-K14 appeared in circulating variants during the pandemic. The relevance of these mutations was tested in a mouse model. A recombinant M-K14/K15R virus showed reduced viral replication, consistent with the role of K15 in virus assembly, and increased levels of apoptosis associated with the loss of ubiquitination on K14. TRIM7 antiviral activity requires caspase-6 inhibition, linking apoptosis with viral replication and pathology.
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Affiliation(s)
- Maria Gonzalez-Orozco
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Hsiang-chi Tseng
- Center for Virus-Host-Innate-Immunity, RBHS Institute for Infectious and Inflammatory Diseases, and Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ
| | - Adam Hage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX
| | - Padmanava Behera
- Center for Virus-Host-Innate-Immunity, RBHS Institute for Infectious and Inflammatory Diseases, and Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ
| | - Kazi Afreen
- Center for Virus-Host-Innate-Immunity, RBHS Institute for Infectious and Inflammatory Diseases, and Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ
| | - Yoatzin Peñaflor-Tellez
- Center for Virus-Host-Innate-Immunity, RBHS Institute for Infectious and Inflammatory Diseases, and Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ
| | - Maria I. Giraldo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Matthew Huante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Lucinda Puebla-Clark
- Department of Internal Medicine, Division of Infectious Diseases, University of Texas Medical Branch, Galveston, TX
| | - Sarah van Tol
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Abby Odle
- Center for Virus-Host-Innate-Immunity, RBHS Institute for Infectious and Inflammatory Diseases, and Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ
| | - Matthew Crown
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, UK
| | - Natalia Teruel
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Thomas R Shelite
- Department of Internal Medicine, Division of Infectious Diseases, University of Texas Medical Branch, Galveston, TX
| | - Vineet Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Mark Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Janice J. Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Rafael J. Najmanovich
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Matthew Bashton
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, UK
| | - Robin Stephens
- Department of Internal Medicine, Division of Infectious Diseases, University of Texas Medical Branch, Galveston, TX
- Center for Immunity and Inflammation and Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX
| | | | - Ricardo Rajsbaum
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
- Center for Virus-Host-Innate-Immunity, RBHS Institute for Infectious and Inflammatory Diseases, and Department of Medicine, New Jersey Medical School, Rutgers University, Newark, NJ
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21
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Song S, Zeng L, Xu J, Shi L, Lu L, Ling Y, Zhang L. Proteomic lung analysis revealed hyper-activation of neutrophil extracellular trap formation in cases of fatal COVID-19. Heliyon 2024; 10:e31878. [PMID: 38882332 PMCID: PMC11177151 DOI: 10.1016/j.heliyon.2024.e31878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/18/2024] Open
Abstract
The molecular pathology of lung injury in patients with Corona Virus Disease 2019 (COVID-19) remain unclear. In this study, we performed a proteomic study of lung tissues from seven patients with COVID-19, and eight without. Lung parenchymal tissues with COVID-19 were obtained from autopsy samples, while control samples were obtained from paracancerous tissues. Proteins were extracted using phenol extraction. A tandem mass tag-based quantitative proteomic approach combined with bioinformatic analysis was used to detect proteomic changes in the SARS-CoV-2-infected lung tissues. A total of 6,602, and 6,549 proteins were identified in replicates 1 and 2, respectively. Of these, 307, and 278, respectively, were identified as differentially expressed proteins (DEPs). In total, 216 DEPs were identified in this study. These proteins were enriched in 189 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The downregulated proteins are mainly involved in focal adhesion (n = 5), and the PI3K-Akt signaling pathway (n = 4). The upregulated proteins were related to neutrophil extracellular trap (NET) formation (n = 16), and the phagosome pathway (n = 11). The upregulated proteins in these two pathways interact with one another. Further immunohistochemistry verified NET enrichment in the tissues with COVID-19 compared to the controls. Our results systematically outlined the proteomic profiles of the lung's response to SARS-CoV-2 infection and indicated that NET formation was hyper-activated. These results will hopefully provide new evidence for understanding the mechanism behind fatal COVID-19.
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Affiliation(s)
- Shu Song
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Liyan Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
- Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Jingjing Xu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lei Shi
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lingqing Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yun Ling
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
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22
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fan G, Yang W, Wang D, Xu F, Wang Y, Si C, Zhai Z, Li Z, Wu R, Cao B, Yang W. Prolonged lymphopenia and prognoses among inpatients with different respiratory virus infections: A retrospective cohort study. Heliyon 2024; 10:e31733. [PMID: 38867947 PMCID: PMC11167307 DOI: 10.1016/j.heliyon.2024.e31733] [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: 04/11/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/14/2024] Open
Abstract
Background Lymphopenia is common in respiratory viral infection. However, no studies elucidated the impact of prolonged lymphopenia on worse outcome in the way of quantitative risk. Methods Adult patients with laboratory-confirmed respiratory virus infection (influenza, SARS-CoV-2, and other viruses) between January 1st, 2016, and February 1st, 2023 were enrolled in this retrospective cohort study. Serial data of laboratory examination during hospitalization were acquired. The primary outcome was in-hospital all-cause death, and all information was obtained from the electronic medical records system. Legendre orthogonal polynomials (LOP), restricted cubic splines, and multivariable logistic regression were performed. Results Finally, 2388 inpatients were involved in this study, including 436 patients with influenza, 1397 with SARS-CoV-2, and 319 with other respiratory virus infections. After being adjusted for age, corticosteroids, chronic kidney disease, chronic respiratory disease, cardiovascular disease, lymphopenia on admission and length of hospital stay, prolonged lymphopenia was significantly associated with death in influenza (OR 7.20, 95 % CI 2.27-22.77, p = 0. 0008 for lasting for 3-7 days; OR 17.80, 95 % CI 5.21-60.82, p < 0.0001 for lasting for more than 7 days) and SARS-CoV-2 (OR 3.07, 95 % CI 1.89-5.01, p < 0.0001 for lasting for 3-7 days; OR 6.28, 95 % CI 3.53-11.18, p < 0.0001 for lasting for more than 7 days), compared with a transient lymphopenia of 1-2 days, while no significant association was found in other respiratory viruses. Prolonged lymphopenia was also associated with multi-organ damage in influenza and SARS-CoV-2 infections. Conclusions Prolonged lymphopenia was significantly associated with worse clinical prognoses in influenza and SARS-CoV-2 infections, but not in other respiratory virus infections.
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Affiliation(s)
- Guohui fan
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, State Key Laboratory of Respiratory Health and Multimorbidity, Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, PR China
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Department of Clinical Research and Data Management, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, PR China
| | - Wuyue Yang
- Beijing Institute of Mathematical Sciences and Applications, Beijing, 101408, PR China
| | - Dingyi Wang
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Department of Clinical Research and Data Management, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, PR China
| | - Feiya Xu
- Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, PR China
| | - Yeming Wang
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, PR China
| | - Chaozeng Si
- Information Center, China-Japan Friendship Hospital, Beijing, PR China
| | - Zhenguo Zhai
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, PR China
| | - Zhongjie Li
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, State Key Laboratory of Respiratory Health and Multimorbidity, Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, PR China
| | - Rongling Wu
- Beijing Institute of Mathematical Sciences and Applications, Beijing, 101408, PR China
| | - Bin Cao
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, PR China
| | - Weizhong Yang
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, State Key Laboratory of Respiratory Health and Multimorbidity, Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, PR China
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23
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Curion F, Theis FJ. Machine learning integrative approaches to advance computational immunology. Genome Med 2024; 16:80. [PMID: 38862979 PMCID: PMC11165829 DOI: 10.1186/s13073-024-01350-3] [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: 06/29/2023] [Accepted: 05/23/2024] [Indexed: 06/13/2024] Open
Abstract
The study of immunology, traditionally reliant on proteomics to evaluate individual immune cells, has been revolutionized by single-cell RNA sequencing. Computational immunologists play a crucial role in analysing these datasets, moving beyond traditional protein marker identification to encompass a more detailed view of cellular phenotypes and their functional roles. Recent technological advancements allow the simultaneous measurements of multiple cellular components-transcriptome, proteome, chromatin, epigenetic modifications and metabolites-within single cells, including in spatial contexts within tissues. This has led to the generation of complex multiscale datasets that can include multimodal measurements from the same cells or a mix of paired and unpaired modalities. Modern machine learning (ML) techniques allow for the integration of multiple "omics" data without the need for extensive independent modelling of each modality. This review focuses on recent advancements in ML integrative approaches applied to immunological studies. We highlight the importance of these methods in creating a unified representation of multiscale data collections, particularly for single-cell and spatial profiling technologies. Finally, we discuss the challenges of these holistic approaches and how they will be instrumental in the development of a common coordinate framework for multiscale studies, thereby accelerating research and enabling discoveries in the computational immunology field.
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Affiliation(s)
- Fabiola Curion
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.
- School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
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24
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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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25
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Wu TTH, Travaglini KJ, Rustagi A, Xu D, Zhang Y, Andronov L, Jang S, Gillich A, Dehghannasiri R, Martínez-Colón GJ, Beck A, Liu DD, Wilk AJ, Morri M, Trope WL, Bierman R, Weissman IL, Shrager JB, Quake SR, Kuo CS, Salzman J, Moerner W, Kim PS, Blish CA, Krasnow MA. Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung. J Exp Med 2024; 221:e20232192. [PMID: 38597954 PMCID: PMC11009983 DOI: 10.1084/jem.20232192] [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: 11/28/2023] [Revised: 02/09/2024] [Accepted: 03/04/2024] [Indexed: 04/11/2024] Open
Abstract
Early stages of deadly respiratory diseases including COVID-19 are challenging to elucidate in humans. Here, we define cellular tropism and transcriptomic effects of SARS-CoV-2 virus by productively infecting healthy human lung tissue and using scRNA-seq to reconstruct the transcriptional program in "infection pseudotime" for individual lung cell types. SARS-CoV-2 predominantly infected activated interstitial macrophages (IMs), which can accumulate thousands of viral RNA molecules, taking over 60% of the cell transcriptome and forming dense viral RNA bodies while inducing host profibrotic (TGFB1, SPP1) and inflammatory (early interferon response, CCL2/7/8/13, CXCL10, and IL6/10) programs and destroying host cell architecture. Infected alveolar macrophages (AMs) showed none of these extreme responses. Spike-dependent viral entry into AMs used ACE2 and Sialoadhesin/CD169, whereas IM entry used DC-SIGN/CD209. These results identify activated IMs as a prominent site of viral takeover, the focus of inflammation and fibrosis, and suggest targeting CD209 to prevent early pathology in COVID-19 pneumonia. This approach can be generalized to any human lung infection and to evaluate therapeutics.
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Affiliation(s)
- Timothy Ting-Hsuan Wu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Kyle J. Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Yue Zhang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Leonid Andronov
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - SoRi Jang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Astrid Gillich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Roozbeh Dehghannasiri
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Giovanny J. Martínez-Colón
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aimee Beck
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Dan Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron J. Wilk
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Winston L. Trope
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Rob Bierman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph B. Shrager
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Stephen R. Quake
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Christin S. Kuo
- Department of Pediatrics, Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Salzman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - W.E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Catherine A. Blish
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark A. Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
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26
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Wu K, Zhang Y, Mao D, Iberg CA, Yin-Declue H, Sun K, Keeler SP, Wikfors HA, Young D, Yantis J, Austin SR, Byers DE, Brody SL, Crouch EC, Romero AG, Holtzman MJ. MAPK13 controls structural remodeling and disease after epithelial injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596863. [PMID: 38895360 PMCID: PMC11185504 DOI: 10.1101/2024.05.31.596863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
All living organisms are charged with repair after injury particularly at epithelial barrier sites, but in some cases this response leads instead to structural remodeling and long-term disease. Identifying the molecular and cellular control of this divergence is key to disease modification. In that regard, stress kinase control of epithelial stem cells is a rational entry point for study. Here we examine the potential for mitogen-activated protein kinase 13 (MAPK13) regulation of epithelial stem cells using models of respiratory viral injury and post-viral lung disease. We show that Mapk13 gene-knockout mice handle acute infectious illness as expected but are protected against structural remodeling manifest as basal-epithelial stem cell (basal-ESC) hyperplasia-metaplasia, immune activation, and mucinous differentiation. In corresponding cell models, Mapk13-deficiency directly attenuates basal-ESC growth and organoid formation. Extension to human studies shows marked induction/activation of basal-cell MAPK13 in clinical samples of comparable remodeling found in asthma and COPD. Here again, MAPK13 gene-knockdown inhibits human basal-ESC growth in culture. Together, the data identify MAPK13 as a control for structural remodeling and disease after epithelial injury and as a suitable target for down-regulation as a disease-modifying strategy.
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Affiliation(s)
- Kangyun Wu
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Yong Zhang
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Dailing Mao
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Courtney A. Iberg
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Huiqing Yin-Declue
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Kelly Sun
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Shamus P. Keeler
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Hallie A. Wikfors
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Deanna Young
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Jennifer Yantis
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Stephen R. Austin
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Derek E Byers
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Steven L. Brody
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Erika C. Crouch
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Arthur G. Romero
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Michael J. Holtzman
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110
- NuPeak Therapeutics Inc., St. Louis, MO 63105
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27
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Biasetti L, Zervogiannis N, Shaw K, Trewhitt H, Serpell L, Bailey D, Wright E, Hall CN. Risk factors for severe COVID-19 disease increase SARS-CoV-2 infectivity of endothelial cells and pericytes. Open Biol 2024; 14:230349. [PMID: 38862017 DOI: 10.1098/rsob.230349] [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: 09/25/2023] [Accepted: 04/15/2024] [Indexed: 06/13/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) was initially considered a primarily respiratory disease but is now known to affect other organs including the heart and brain. A major route by which COVID-19 impacts different organs is via the vascular system. We studied the impact of apolipoprotein E (APOE) genotype and inflammation on vascular infectivity by pseudo-typed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses in mouse and human cultured endothelial cells and pericytes. Possessing the APOE4 allele or having existing systemic inflammation is known to enhance the severity of COVID-19. Using targeted replacement human APOE3 and APOE4 mice and inflammation induced by bacterial lipopolysaccharide (LPS), we investigated infection by SARS-CoV-2. Here, we show that infectivity was higher in murine cerebrovascular pericytes compared to endothelial cells and higher in cultures expressing APOE4. Furthermore, increasing the inflammatory state of the cells by prior incubation with LPS increased infectivity into human and mouse pericytes and human endothelial cells. Our findings provide insights into the mechanisms underlying severe COVID-19 infection, highlighting how risk factors such as APOE4 genotype and prior inflammation may exacerbate disease severity by augmenting the virus's ability to infect vascular cells.
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Affiliation(s)
- Luca Biasetti
- Sussex Neuroscience, School of Psychology, University of Sussex , East Sussex BN1 9QG, UK
| | - Nikos Zervogiannis
- Sussex Neuroscience, School of Psychology, University of Sussex , East Sussex BN1 9QG, UK
| | - Kira Shaw
- Sussex Neuroscience, School of Psychology, University of Sussex , East Sussex BN1 9QG, UK
| | - Harry Trewhitt
- Sussex Neuroscience, School of Psychology, University of Sussex , East Sussex BN1 9QG, UK
| | - Louise Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex , East Sussex BN1 9QG, UK
| | | | - Edward Wright
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex , , East Sussex BN1 9QG, UK
| | - Catherine N Hall
- Sussex Neuroscience, School of Psychology, University of Sussex , East Sussex BN1 9QG, UK
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28
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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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29
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Nussbaum YI, Hossain KSMT, Kaifi J, Warren WC, Shyu CR, Mitchem JB. Identifying gene expression programs in single-cell RNA-seq data using linear correlation explanation. J Biomed Inform 2024; 154:104644. [PMID: 38631462 DOI: 10.1016/j.jbi.2024.104644] [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: 10/05/2023] [Revised: 02/29/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
OBJECTIVE Gene expression analysis through single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of gene regulation in diverse cell types, tissues, and organisms. While existing methods primarily focus on identifying cell type-specific gene expression programs (GEPs), the characterization of GEPs associated with biological processes and stimuli responses remains limited. In this study, we aim to infer biologically meaningful GEPs that are associated with both cellular phenotypes and activity programs directly from scRNA-seq data. METHODS We applied linear CorEx, a machine-learning-based approach, to infer GEPs by grouping genes based on total correlation optimization function in simulated and real-world scRNA-seq datasets. Additionally, we utilized a transfer learning approach to project CorEx-inferred GEPs to other scRNA-seq datasets. RESULTS By leveraging total correlation optimization, linear CorEx groups genes and demonstrates superior performance in identifying cell types and activity programs compared to similar methods using simulated data. Furthermore, we apply this same approach to real-world scRNA-seq data from the mouse dentate gyrus and embryonic colon development, uncovering biologically relevant GEPs related to cell types, developmental ages, and cell cycle programs. We also demonstrate the potential for transfer learning by evaluating similar datasets, showcasing the cross-species sensitivity of linear CorEx. CONCLUSION Our findings validate linear CorEx as a valuable tool for comprehensively analyzing complex signals in scRNA-seq data, leading to deeper insights into gene expression dynamics, cellular heterogeneity, and regulatory mechanisms.
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Affiliation(s)
- Yulia I Nussbaum
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA
| | - K S M Tozammel Hossain
- Department of Information Science, University of North Texas, 3940 N Elm St, Denton, TX 76203, USA
| | - Jussuf Kaifi
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA; Department of Surgery, University of Missouri Hospital, 1 Hospital Dr., Columbia, MO 65212, USA; Harry S. Truman Memorial Veterans' Hospital, 800 Hospital Dr., Columbia, MO 65201, USA; Siteman Cancer Center, Washington University School of Medicine, 4921 Parkview Pl, St. Louis, MO 63110, USA
| | - Wesley C Warren
- Department of Surgery, University of Missouri Hospital, 1 Hospital Dr., Columbia, MO 65212, USA; Bond Life Sciences Center, University of Missouri, 1201 Rollin St., Columbia, MO 65211, USA
| | - Chi-Ren Shyu
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65201, USA
| | - Jonathan B Mitchem
- VA Northeast Ohio Healthcare System, 10701 East Boulevard, Cleveland, OH 44106, USA; Department of Colon and Rectal Surgery, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA; Department of Inflammation and Immunity, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA.
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30
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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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Bloomquist R, Mondal AK, Vashisht A, Sahajpal N, Jones K, Vashisht V, Singh H, Farmaha J, Kolhe R. Gene Regulatory Network Analysis of Post-Mortem Lungs Unveils Novel Insights into COVID-19 Pathogenesis. Viruses 2024; 16:853. [PMID: 38932146 PMCID: PMC11209433 DOI: 10.3390/v16060853] [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: 05/02/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
The novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as one of the most significant global health crises in recent history. The clinical characteristics of COVID-19 patients have revealed the possibility of immune activity changes contributing to disease severity. Nevertheless, limited information is available regarding the immune response in human lung tissue, which is the primary site of infection. In this study, we conducted an extensive analysis of lung tissue to screen for differentially expressed miRNAs and mRNAs in five individuals who died due to COVID-19 and underwent a rapid autopsy, as well as seven control individuals who died of other causes unrelated to COVID-19. To analyze the host response gene expression, miRNA microarray and Nanostring's nCounter XT gene expression assay were performed. Our study identified 37 downregulated and 77 upregulated miRNAs in COVID-19 lung biopsy samples compared to the controls. A total of 653 mRNA transcripts were differentially expressed between the two sample types, with most transcripts (472) being downregulated in COVID-19-positive specimens. Hierarchical and PCA K-means clustering analysis showed distinct clustering between COVID-19 and control samples. Enrichment and network analyses revealed differentially expressed genes important for innate immunity and inflammatory response in COVID-19 lung biopsies. The interferon-signaling pathway was highly upregulated in COVID-19 specimens while genes involved in interleukin-17 signaling were downregulated. These findings shed light on the mechanisms of host cellular responses to COVID-19 infection in lung tissues and could help identify new targets for the prevention and treatment of COVID-19 infection.
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Affiliation(s)
- Ryan Bloomquist
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
- School of Medicine, University of South Carolina, Columbia, SC 29209, USA
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Ashutosh Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | | | - Kimya Jones
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Vishakha Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Harmanpreet Singh
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Jaspreet Farmaha
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
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Luo D, Bai M, Zhang W, Wang J. The possible mechanism and research progress of ACE2 involved in cardiovascular injury caused by COVID-19: a review. Front Cardiovasc Med 2024; 11:1409723. [PMID: 38863899 PMCID: PMC11165996 DOI: 10.3389/fcvm.2024.1409723] [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: 03/30/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
ACE2 is the earliest receptor discovered to mediate the entry of SARS-CoV-2. In addition to the receptor, it also participates in complex pathological and physiological processes, including regulating the RAS system, apelin, KKS system, and immune system. In addition to affecting the respiratory system, viral infections also interact with cardiovascular diseases. SARS-CoV-2 can directly invade the cardiovascular system through ACE2; Similarly, cardiovascular diseases such as hypertension and coronary heart disease can affect ACE2 levels and exacerbate the disease, and ACE2 dysregulation may also be a potential mechanism for long-term acute sequelae of COVID-19. Since the SARS CoV-2 epidemic, many large population studies have tried to clarify the current focus of debate, that is, whether we should give COVID-19 patients ACEI and ARB drug treatment, but there is still no conclusive conclusion. We also discussed potential disease treatment options for ACE2 at present. Finally, we discussed the researchers' latest findings on ACE2 and their prospects for future research.
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Affiliation(s)
| | | | | | - Junnan Wang
- Department of Cardiology, Second Hospital of Jilin University, Changchun, Jilin, China
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33
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Zhang G, He S, Lin L, Gan P. Infection with COVID-19 Complicated by Sinus Arrest. Case Rep Infect Dis 2024; 2024:5361758. [PMID: 38784432 PMCID: PMC11115995 DOI: 10.1155/2024/5361758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 04/24/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
As a respiratory tract-transmitted disease, coronavirus disease 2019 (COVID-19) exerts a profound immune injury effect, leading not only to pulmonary impairment but also to cardiac complications. We present a case of a 79-year-old woman, who had previously contracted COVID-19 and subsequently developed sinus arrest (SA) following her second infection. The longest asystole time detected by Holter monitoring was 7.2 seconds. Although the patient met criteria for permanent pacemaker implantation, her family declined this intervention and conservative management was pursued instead. However, after a period of observation, the patient's SA resolved. The present case study describes a patient who experienced SA upon reinfection with COVID-19, which was not present during the initial infection. It emphasizes the impact of COVID-19 on cardiac health, particularly its potential to induce arrhythmias. In addition, it is worth noting that the arrhythmia induced by a COVID-19 infection may show reversibility, suggesting that a permanent pacemaker might not be the priority option if further pacing therapy is being considered.
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Affiliation(s)
- Guojun Zhang
- Department of Infectious Disease, The First People's Hospital of Fuyang Hangzhou, Fuyang District, Hangzhou, Zhejiang, China
| | - Shuai He
- Department of Hand and Foot Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai District, Taizhou, Zhejiang, China
| | - Lu Lin
- Department of Intensive Care Rehabilitation, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Luqiao District, Taizhou, Zhejiang, China
| | - Pengcheng Gan
- Department of Intensive Care Rehabilitation, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Luqiao District, Taizhou, Zhejiang, China
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34
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Ospina OE, Soupir AC, Manjarres-Betancur R, Gonzalez-Calderon G, Yu X, Fridley BL. Differential gene expression analysis of spatial transcriptomic experiments using spatial mixed models. Sci Rep 2024; 14:10967. [PMID: 38744956 PMCID: PMC11094014 DOI: 10.1038/s41598-024-61758-0] [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: 02/01/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
Spatial transcriptomics (ST) assays represent a revolution in how the architecture of tissues is studied by allowing for the exploration of cells in their spatial context. A common element in the analysis is delineating tissue domains or "niches" followed by detecting differentially expressed genes to infer the biological identity of the tissue domains or cell types. However, many studies approach differential expression analysis by using statistical approaches often applied in the analysis of non-spatial scRNA data (e.g., two-sample t-tests, Wilcoxon's rank sum test), hence neglecting the spatial dependency observed in ST data. In this study, we show that applying linear mixed models with spatial correlation structures using spatial random effects effectively accounts for the spatial autocorrelation and reduces inflation of type-I error rate observed in non-spatial based differential expression testing. We also show that spatial linear models with an exponential correlation structure provide a better fit to the ST data as compared to non-spatial models, particularly for spatially resolved technologies that quantify expression at finer scales (i.e., single-cell resolution).
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Affiliation(s)
- Oscar E Ospina
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alex C Soupir
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | | | - Xiaoqing Yu
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Brooke L Fridley
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
- Biostatistics and Epidemiology Core, Division of Health Services & Outcomes Research, Children's Mercy, Kansas City, MO, USA.
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35
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Stanley HB, Pereda-Campos V, Mantel M, Rouby C, Daudé C, Aguera PE, Fornoni L, Hummel T, Weise S, Mignot C, Konstantinidis I, Garefis K, Ferdenzi C, Pierron D, Bensafi M. Identification of the needs of individuals affected by COVID-19. COMMUNICATIONS MEDICINE 2024; 4:83. [PMID: 38724573 PMCID: PMC11082167 DOI: 10.1038/s43856-024-00510-1] [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: 05/30/2023] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The optimal management of COVID-19 symptoms and their sequelae remains an important area of clinical research. Policy makers have little scientific data regarding the effects on the daily life of affected individuals and the identification of their needs. Such data are needed to inform effective care policy. METHODS We studied 639 people with COVID-19 resident in France via an online questionnaire. They reported their symptoms, effects on daily life, and resulting needs, with particular focus on olfaction. RESULTS The results indicate that a majority of participants viewed their symptoms as disabling, with symptoms affecting their physical and mental health, social and professional lives. 60% of the individuals reported having unmet medical, psychological and socio-professional support needs. Finally, affected individuals were concerned about the risk and invasiveness of possible treatments as shown by a preference for non-invasive intervention over surgery to cure anosmia. CONCLUSIONS It is important that policy makers take these needs into consideration in order to assist affected individuals to regain a normal quality of life.
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Affiliation(s)
- Halina B Stanley
- Université Claude Bernard Lyon 1, CNRS, INSERM, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, NEUROPOP, F-69500, Bron, France.
| | - Veronica Pereda-Campos
- Équipe de Médecine Evolutive Faculté de chirurgie dentaire-UMR5288, CNRS/Université Paul-Sabatier Toulouse III, Toulouse, 31400, France
| | - Marylou Mantel
- Université Claude Bernard Lyon 1, CNRS, INSERM, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, NEUROPOP, F-69500, Bron, France
- Équipe de Médecine Evolutive Faculté de chirurgie dentaire-UMR5288, CNRS/Université Paul-Sabatier Toulouse III, Toulouse, 31400, France
| | - Catherine Rouby
- Université Claude Bernard Lyon 1, CNRS, INSERM, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, NEUROPOP, F-69500, Bron, France
| | - Christelle Daudé
- Université Claude Bernard Lyon 1, CNRS, INSERM, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, NEUROPOP, F-69500, Bron, France
| | - Pierre-Emmanuel Aguera
- Université Claude Bernard Lyon 1, CNRS, INSERM, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, NEUROPOP, F-69500, Bron, France
| | - Lesly Fornoni
- Université Claude Bernard Lyon 1, CNRS, INSERM, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, NEUROPOP, F-69500, Bron, France
| | - Thomas Hummel
- Smell & Taste Clinic, Department of Otorhinlaryngology, Technische Universität Dresden, Dresden, Germany
| | - Susanne Weise
- Smell & Taste Clinic, Department of Otorhinlaryngology, Technische Universität Dresden, Dresden, Germany
| | - Coralie Mignot
- Smell & Taste Clinic, Department of Otorhinlaryngology, Technische Universität Dresden, Dresden, Germany
| | - Iordanis Konstantinidis
- 2nd Academic ORL Department, Papageorgiou Hospital, Aristotle University, Thessaloniki, Greece
| | - Konstantinos Garefis
- 2nd Academic ORL Department, Papageorgiou Hospital, Aristotle University, Thessaloniki, Greece
| | - Camille Ferdenzi
- Université Claude Bernard Lyon 1, CNRS, INSERM, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, NEUROPOP, F-69500, Bron, France
| | - Denis Pierron
- Équipe de Médecine Evolutive Faculté de chirurgie dentaire-UMR5288, CNRS/Université Paul-Sabatier Toulouse III, Toulouse, 31400, France
| | - Moustafa Bensafi
- Université Claude Bernard Lyon 1, CNRS, INSERM, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, NEUROPOP, F-69500, Bron, France.
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36
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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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Koganesawa M, Dwyer D, Alhallak K, Nagai J, Zaleski K, Samuchiwal S, Hiroaki H, Nishida A, Hirsch TI, Brennan PJ, Puder M, Balestrieri B. Pla2g5 contributes to viral-like-induced lung inflammation through macrophage proliferation and LA/Ffar1 lung cell recruitment. Immunology 2024; 172:144-162. [PMID: 38361249 PMCID: PMC11057362 DOI: 10.1111/imm.13766] [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: 09/26/2023] [Accepted: 02/01/2024] [Indexed: 02/17/2024] Open
Abstract
Macrophages expressing group V phospholipase A2 (Pla2g5) release the free fatty acid (FFA) linoleic acid (LA), potentiating lung type 2 inflammation. Although Pla2g5 and LA increase in viral infections, their role remains obscure. We generated Pla2g5flox/flox mice, deleted Pla2g5 by using the Cx3cr1cre transgene, and activated bone marrow-derived macrophages (BM-Macs) with poly:IC, a synthetic double-stranded RNA that triggers a viral-like immune response, known Pla2g5-dependent stimuli (IL-4, LPS + IFNγ, IL-33 + IL-4 + GM-CSF) and poly:IC + LA followed by lipidomic and transcriptomic analysis. Poly:IC-activated Pla2g5flox/flox;Cx3cr1cre/+ BM-Macs had downregulation of major bioactive lipids and critical enzymes producing those bioactive lipids. In addition, AKT phosphorylation was lower in poly:IC-stimulated Pla2g5flox/flox;Cx3cr1cre/+ BM-Macs, which was not restored by adding LA to poly:IC-stimulated BM-Macs. Consistently, Pla2g5flox/flox;Cx3cr1cre/+ mice had diminished poly:IC-induced lung inflammation, including inflammatory macrophage proliferation, while challenging Pla2g5flox/flox;Cx3cr1cre/+ mice with poly:IC + LA partially restored lung inflammation and inflammatory macrophage proliferation. Finally, mice lacking FFA receptor-1 (Ffar1)-null mice had reduced poly:IC-induced lung cell recruitment and tissue macrophage proliferation, not corrected by LA. Thus, Pla2g5 contributes to poly:IC-induced lung inflammation by regulating inflammatory macrophage proliferation and LA/Ffar1-mediated lung cell recruitment and tissue macrophage proliferation.
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Affiliation(s)
- Masaya Koganesawa
- Division of Allergy and Clinical Immunology, Vinik Center for Translational Immunology Research, Brigham and Women’s Hospital, Boston, MA
| | - Daniel Dwyer
- Division of Allergy and Clinical Immunology, Vinik Center for Translational Immunology Research, Brigham and Women’s Hospital, Boston, MA
| | - Kinan Alhallak
- Division of Allergy and Clinical Immunology, Vinik Center for Translational Immunology Research, Brigham and Women’s Hospital, Boston, MA
| | - Jun Nagai
- Division of Allergy and Clinical Immunology, Vinik Center for Translational Immunology Research, Brigham and Women’s Hospital, Boston, MA
| | - Kendall Zaleski
- Division of Allergy and Clinical Immunology, Vinik Center for Translational Immunology Research, Brigham and Women’s Hospital, Boston, MA
| | - Sachin Samuchiwal
- Division of Allergy and Clinical Immunology, Vinik Center for Translational Immunology Research, Brigham and Women’s Hospital, Boston, MA
| | - Hayashi Hiroaki
- Division of Allergy and Clinical Immunology, Vinik Center for Translational Immunology Research, Brigham and Women’s Hospital, Boston, MA
| | - Airi Nishida
- Division of Allergy and Clinical Immunology, Vinik Center for Translational Immunology Research, Brigham and Women’s Hospital, Boston, MA
| | - Thomas I. Hirsch
- Department of Surgery and Vascular Biology Program Boston Children’s Hospital, Boston, MA
| | - Patrick J. Brennan
- Division of Allergy and Clinical Immunology, Vinik Center for Translational Immunology Research, Brigham and Women’s Hospital, Boston, MA
| | - Mark Puder
- Department of Surgery and Vascular Biology Program Boston Children’s Hospital, Boston, MA
| | - Barbara Balestrieri
- Division of Allergy and Clinical Immunology, Vinik Center for Translational Immunology Research, Brigham and Women’s Hospital, Boston, MA
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38
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Ji X, Ji HL. Metabolic signatures of acute respiratory distress syndrome: COVID versus non-COVID. Am J Physiol Lung Cell Mol Physiol 2024; 326:L596-L603. [PMID: 38469648 DOI: 10.1152/ajplung.00266.2023] [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: 09/27/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/13/2024] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a fatal pulmonary disorder characterized by severe hypoxia and inflammation. ARDS is commonly triggered by systemic and pulmonary infections, with bacteria and viruses. Notable pathogens include Pseudomonas aeruginosa, Streptococcus aureus, Enterobacter species, coronaviruses, influenza viruses, and herpesviruses. COVID-19 ARDS represents the latest etiological phenotype of the disease. The pathogenesis of ARDS caused by bacteria and viruses exhibits variations in host immune responses and lung mesenchymal injury. We postulate that the systemic and pulmonary metabolomics profiles of ARDS induced by COVID-19 pathogens may exhibit distinctions compared with those induced by other infectious agents. This review aims to compare metabolic signatures in blood and lung specimens specifically within the context of ARDS. Both prevalent and phenotype-specific metabolomic signatures, including but not limited to glycolysis, ketone body production, lipid oxidation, and dysregulation of the kynurenine pathways, were thoroughly examined in this review. The distinctions in metabolic signatures between COVID-19 and non-COVID ARDS have the potential to reveal new biomarkers, elucidate pathogenic mechanisms, identify druggable targets, and facilitate differential diagnosis in the future.
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Affiliation(s)
- Xiangming Ji
- Department of Nutrition, Georgia State University, Atlanta, Georgia, United States
| | - Hong-Long Ji
- Burn and Shock Trauma Research Institute, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, Illinois, United States
- Department of Surgery, Stritch School of Medicine, Loyola University Chicago Health Sciences Division, Maywood, Illinois, United States
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39
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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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Yu S, Xu J, Yu C, Zhang X, Cheng Y, Lin D, Yan C, Guo M, Li J, He P, Cheng W. Persistence of SARS-CoV-2 colonization and high expression of inflammatory factors in cardiac tissue 6 months after COVID-19 recovery: a prospective cohort study. Cardiovasc Diagn Ther 2024; 14:251-263. [PMID: 38716313 PMCID: PMC11070996 DOI: 10.21037/cdt-23-381] [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: 09/19/2023] [Accepted: 02/02/2024] [Indexed: 07/09/2024]
Abstract
Background The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in myocardial autopsy tissues has been observed in certain individuals with coronavirus disease 2019 (COVID-19). However, the duration of cardiac involvement remains uncertain among recovered COVID-19 patients. Our study aims to evaluate the long-term persistence of SARS-CoV-2 within cardiac tissue. Methods We prospectively and consecutively evaluated the patients undergoing mitral valve replacement (MVR) and left atrial (LA) volume reduction surgery from May 25 to June 10, 2023 at our center, who had been approximately 6 months of recovery after Omicron wave. Patients tested positive for SARS-CoV-2 upon admission were excluded. The surgical LA tissue was collected in RNA preservation solution and stored at -80 ℃ immediately. Then SARS-CoV-2, interleukin-6 (IL-6) and interleukin-1β (IL-1β) RNA expression in LA tissues were assessed through thrice-repeated reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analyses. Categorical variables were assessed using the Chi-square or Fisher's exact tests, and continuous variables was analyzed using the Mann-Whitney U test. Results Nine of 41 patients were enrolled, all of whom tested negative for SARS-CoV-2 upon admission (two antigen and PCR tests). In four of nine patients, SARS-CoV-2 RNA was detected in their LA tissue, indicating viral colonization. Among the four positive cases, the IL-6 and IL-1β relative expression levels in the LA tissue of one patient were increased approximately 55- and 110-fold, respectively, compared to those of SARS-CoV-2 (-) patients. Increased expression of IL-6 and IL-1β were observed in the myocardium of this patient. Another patient demonstrated a remarkable 7-fold increase in both IL-6 and IL-1β expression, surpassing that of SARS-CoV-2 (-) patients. Additionally, no other cardiac inflammation-related diseases or conditions were presented in these two patients. The IL-6 and IL-1β expression levels of the remaining two patients were not significantly different from those of SARS-CoV-2 (-) patients. The relative expression levels of IL-6 and IL-1β in cardiac tissues of all SARS-CoV-2 (-) patients were relatively low. Interestingly, despite abnormally elevated levels of IL-6 and IL-1β within their cardiac tissue, two patients did not show a significant increase in serum IL-6 and IL-1β levels when compared to other patients. Conclusions Our research suggests that certain COVID-19-recovered patients have persistent colonization of SARS-CoV-2 in their cardiac tissue, accompanied by a local increase in inflammatory factors.
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Affiliation(s)
| | | | | | - Xianpu Zhang
- Department of Cardiac Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yongbo Cheng
- Department of Cardiac Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Deqing Lin
- Department of Cardiac Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Chaojun Yan
- Department of Cardiac Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Mei Guo
- Department of Cardiac Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
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41
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Chen L, Li M, Wu Z, Liu S, Huang Y. A nomogram to predict severe COVID-19 patients with increased pulmonary lesions in early days. Front Med (Lausanne) 2024; 11:1343661. [PMID: 38737763 PMCID: PMC11082326 DOI: 10.3389/fmed.2024.1343661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/25/2024] [Indexed: 05/14/2024] Open
Abstract
Objectives This study aimed to predict severe coronavirus disease 2019 (COVID-19) progression in patients with increased pneumonia lesions in the early days. A simplified nomogram was developed utilizing artificial intelligence (AI)-based quantified computed tomography (CT). Methods From 17 December 2019 to 20 February 2020, a total of 246 patients were confirmed COVID-19 infected in Jingzhou Central Hospital, Hubei Province, China. Of these patients, 93 were mildly ill and had follow-up examinations in 7 days, and 61 of them had enlarged lesions on CT scans. We collected the neutrophil-to-lymphocyte ratio (NLR) and three quantitative CT features from two examinations within 7 days. The three quantitative CT features of pneumonia lesions, including ground-glass opacity volume (GV), semi-consolidation volume (SV), and consolidation volume (CV), were automatically calculated using AI. Additionally, the variation volumes of the lesions were also computed. Finally, a nomogram was developed using a multivariable logistic regression model. To simplify the model, we classified all the lesion volumes based on quartiles and curve fitting results. Results Among the 93 patients, 61 patients showed enlarged lesions on CT within 7 days, of whom 19 (31.1%) developed any severe illness. The multivariable logistic regression model included age, NLR on the second time, an increase in lesion volume, and changes in SV and CV in 7 days. The personalized prediction nomogram demonstrated strong discrimination in the sample, with an area under curve (AUC) and the receiver operating characteristic curve (ROC) of 0.961 and a 95% confidence interval (CI) of 0.917-1.000. Decision curve analysis illustrated that a nomogram based on quantitative AI was clinically useful. Conclusion The integration of CT quantitative changes, NLR, and age in this model exhibits promising performance in predicting the progression to severe illness in COVID-19 patients with early-stage pneumonia lesions. This comprehensive approach holds the potential to assist clinical decision-making.
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Affiliation(s)
- Lina Chen
- Department of Radiology, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei Province, China
| | - Min Li
- Department of Radiology, Jingzhou Hospital of Traditional Chinese Medicine, Jingzhou, Hubei Province, China
| | - Zhenghong Wu
- Department of Radiology, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei Province, China
| | - Sibin Liu
- Department of Radiology, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei Province, China
| | - Yuanyi Huang
- Department of Radiology, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei Province, China
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Hurwitz SJ, De R, LeCher JC, Downs-Bowen JA, Goh SL, Zandi K, McBrayer T, Amblard F, Patel D, Kohler JJ, Bhasin M, Dobosh BS, Sukhatme V, Tirouvanziam RM, Schinazi RF. Why Certain Repurposed Drugs Are Unlikely to Be Effective Antivirals to Treat SARS-CoV-2 Infections. Viruses 2024; 16:651. [PMID: 38675992 PMCID: PMC11053489 DOI: 10.3390/v16040651] [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: 03/08/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Most repurposed drugs have proved ineffective for treating COVID-19. We evaluated median effective and toxic concentrations (EC50, CC50) of 49 drugs, mostly from previous clinical trials, in Vero cells. Ratios of reported unbound peak plasma concentrations, (Cmax)/EC50, were used to predict the potential in vivo efficacy. The 20 drugs with the highest ratios were retested in human Calu-3 and Caco-2 cells, and their CC50 was determined in an expanded panel of cell lines. Many of the 20 drugs with the highest ratios were inactive in human Calu-3 and Caco-2 cells. Antivirals effective in controlled clinical trials had unbound Cmax/EC50 ≥ 6.8 in Calu-3 or Caco-2 cells. EC50 of nucleoside analogs were cell dependent. This approach and earlier availability of more relevant cultures could have reduced the number of unwarranted clinical trials.
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Affiliation(s)
- Selwyn J. Hurwitz
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Ramyani De
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Julia C. LeCher
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Jessica A. Downs-Bowen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Shu Ling Goh
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Keivan Zandi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Tamara McBrayer
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Franck Amblard
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Dharmeshkumar Patel
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - James J. Kohler
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
| | - Manoj Bhasin
- Center for Cystic Fibrosis & Airways Disease Research, Division of Pulmonary, Allergy & Immunology, Cystic Fibrosis and Sleep, Emory University and Children’s Healthcare of Atlanta, 2015 Uppergate Drive, Atlanta, GA 30322, USA; (M.B.); (B.S.D.); (R.M.T.)
| | - Brian S. Dobosh
- Center for Cystic Fibrosis & Airways Disease Research, Division of Pulmonary, Allergy & Immunology, Cystic Fibrosis and Sleep, Emory University and Children’s Healthcare of Atlanta, 2015 Uppergate Drive, Atlanta, GA 30322, USA; (M.B.); (B.S.D.); (R.M.T.)
| | - Vikas Sukhatme
- Morningside Center for Innovative and Affordable Medicine, Departments of Medicine and Hematology and Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Rabindra M. Tirouvanziam
- Center for Cystic Fibrosis & Airways Disease Research, Division of Pulmonary, Allergy & Immunology, Cystic Fibrosis and Sleep, Emory University and Children’s Healthcare of Atlanta, 2015 Uppergate Drive, Atlanta, GA 30322, USA; (M.B.); (B.S.D.); (R.M.T.)
| | - Raymond F. Schinazi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, Atlanta, GA 30322, USA; (S.J.H.); (R.D.); (J.C.L.); (J.A.D.-B.); (S.L.G.); (K.Z.); (T.M.); (F.A.); (D.P.); (J.J.K.)
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Chau CW, To A, Au-Yeung RKH, Tang K, Xiang Y, Ruan D, Zhang L, Wong H, Zhang S, Au MT, Chung S, Song E, Choi DH, Liu P, Yuan S, Wen C, Sugimura R. SARS-CoV-2 infection activates inflammatory macrophages in vascular immune organoids. Sci Rep 2024; 14:8781. [PMID: 38627497 PMCID: PMC11021416 DOI: 10.1038/s41598-024-59405-9] [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: 12/07/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
SARS-CoV-2 provokes devastating tissue damage by cytokine release syndrome and leads to multi-organ failure. Modeling the process of immune cell activation and subsequent tissue damage is a significant task. Organoids from human tissues advanced our understanding of SARS-CoV-2 infection mechanisms though, they are missing crucial components: immune cells and endothelial cells. This study aims to generate organoids with these components. We established vascular immune organoids from human pluripotent stem cells and examined the effect of SARS-CoV-2 infection. We demonstrated that infections activated inflammatory macrophages. Notably, the upregulation of interferon signaling supports macrophages' role in cytokine release syndrome. We propose vascular immune organoids are a useful platform to model and discover factors that ameliorate SARS-CoV-2-mediated cytokine release syndrome.
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Affiliation(s)
- Chiu Wang Chau
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Alex To
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Rex K H Au-Yeung
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kaiming Tang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yang Xiang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Degong Ruan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Lanlan Zhang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Hera Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Shihui Zhang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Man Ting Au
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | | | | | | | - Pentao Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
- Centre for Translational Stem Cell Biology, Sha Tin, Hong Kong
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Chunyi Wen
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong.
| | - Ryohichi Sugimura
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
- Centre for Translational Stem Cell Biology, Sha Tin, Hong Kong.
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Sun YK, Wang C, Lin PQ, Hu L, Ye J, Gao ZG, Lin R, Li HM, Shu Q, Huang LS, Tan LH. Severe pediatric COVID-19: a review from the clinical and immunopathophysiological perspectives. World J Pediatr 2024; 20:307-324. [PMID: 38321331 PMCID: PMC11052880 DOI: 10.1007/s12519-023-00790-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/14/2023] [Indexed: 02/08/2024]
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) tends to have mild presentations in children. However, severe and critical cases do arise in the pediatric population with debilitating systemic impacts and can be fatal at times, meriting further attention from clinicians. Meanwhile, the intricate interactions between the pathogen virulence factors and host defense mechanisms are believed to play indispensable roles in severe COVID-19 pathophysiology but remain incompletely understood. DATA SOURCES A comprehensive literature review was conducted for pertinent publications by reviewers independently using the PubMed, Embase, and Wanfang databases. Searched keywords included "COVID-19 in children", "severe pediatric COVID-19", and "critical illness in children with COVID-19". RESULTS Risks of developing severe COVID-19 in children escalate with increasing numbers of co-morbidities and an unvaccinated status. Acute respiratory distress stress and necrotizing pneumonia are prominent pulmonary manifestations, while various forms of cardiovascular and neurological involvement may also be seen. Multiple immunological processes are implicated in the host response to COVID-19 including the type I interferon and inflammasome pathways, whose dysregulation in severe and critical diseases translates into adverse clinical manifestations. Multisystem inflammatory syndrome in children (MIS-C), a potentially life-threatening immune-mediated condition chronologically associated with COVID-19 exposure, denotes another scientific and clinical conundrum that exemplifies the complexity of pediatric immunity. Despite the considerable dissimilarities between the pediatric and adult immune systems, clinical trials dedicated to children are lacking and current management recommendations are largely adapted from adult guidelines. CONCLUSIONS Severe pediatric COVID-19 can affect multiple organ systems. The dysregulated immune pathways in severe COVID-19 shape the disease course, epitomize the vast functional diversity of the pediatric immune system and highlight the immunophenotypical differences between children and adults. Consequently, further research may be warranted to adequately address them in pediatric-specific clinical practice guidelines.
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Affiliation(s)
- Yi-Kan Sun
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, China
| | - Can Wang
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Pei-Quan Lin
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Lei Hu
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Jing Ye
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Zhi-Gang Gao
- Department of General Surgery, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Ru Lin
- Department of Cardiopulmonary and Extracorporeal Life Support, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Hao-Min Li
- Clinical Data Center, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Qiang Shu
- Department of Cardiac Surgery, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Li-Su Huang
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China.
- Department of Infectious Diseases, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China.
| | - Lin-Hua Tan
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China.
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Noguera-Castells A, Parra J, Davalos V, García-Prieto CA, Veselinova Y, Pérez-Miés B, Caniego-Casas T, Palacios J, Saenz-Sardà X, Englund E, Musulen E, Esteller M. Epigenetic Fingerprint of the SARS-CoV-2 Infection in the Lung of Lethal COVID-19. Chest 2024; 165:820-824. [PMID: 37914026 DOI: 10.1016/j.chest.2023.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/22/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Affiliation(s)
- Aleix Noguera-Castells
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Vic, Barcelona, Catalonia, Spain; Department of Biosciences, Faculty of Science, Technology and Engineering, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Barcelona, Catalonia, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Jerónimo Parra
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Vic, Barcelona, Catalonia, Spain
| | - Veronica Davalos
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Vic, Barcelona, Catalonia, Spain
| | - Carlos A García-Prieto
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Vic, Barcelona, Catalonia, Spain; Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Catalonia, Spain
| | - Yoana Veselinova
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Vic, Barcelona, Catalonia, Spain
| | - Belén Pérez-Miés
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain; Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Department of Medicine and Medical Specialties, University of Alcalá, Alcalá de Henares (Madrid), Spain
| | - Tamara Caniego-Casas
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain; Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - José Palacios
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain; Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Department of Medicine and Medical Specialties, University of Alcalá, Alcalá de Henares (Madrid), Spain
| | - Xavier Saenz-Sardà
- Division of Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Elisabet Englund
- Division of Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Eva Musulen
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Vic, Barcelona, Catalonia, Spain; Department of Pathology, Hospital Universitari General de Catalunya Grupo-QuirónSalud, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Vic, Barcelona, Catalonia, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.
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Zheng C, Wang Y, Cheng Y, Wang X, Wei H, King I, Li Y. scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics. Brief Bioinform 2024; 25:bbae112. [PMID: 38555470 PMCID: PMC10981759 DOI: 10.1093/bib/bbae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/05/2024] [Accepted: 02/20/2024] [Indexed: 04/02/2024] Open
Abstract
Single-cell RNA sequencing has achieved massive success in biological research fields. Discovering novel cell types from single-cell transcriptomics has been demonstrated to be essential in the field of biomedicine, yet is time-consuming and needs prior knowledge. With the unprecedented boom in cell atlases, auto-annotation tools have become more prevalent due to their speed, accuracy and user-friendly features. However, existing tools have mostly focused on general cell-type annotation and have not adequately addressed the challenge of discovering novel rare cell types. In this work, we introduce scNovel, a powerful deep learning-based neural network that specifically focuses on novel rare cell discovery. By testing our model on diverse datasets with different scales, protocols and degrees of imbalance, we demonstrate that scNovel significantly outperforms previous state-of-the-art novel cell detection models, reaching the most AUROC performance(the only one method whose averaged AUROC results are above 94%, up to 16.26% more comparing to the second-best method). We validate scNovel's performance on a million-scale dataset to illustrate the scalability of scNovel further. Applying scNovel on a clinical COVID-19 dataset, three potential novel subtypes of Macrophages are identified, where the COVID-related differential genes are also detected to have consistent expression patterns through deeper analysis. We believe that our proposed pipeline will be an important tool for high-throughput clinical data in a wide range of applications.
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Affiliation(s)
- Chuanyang Zheng
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, China
| | - Yixuan Wang
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, China
| | - Yuqi Cheng
- College of Computing, Georgia Institute of Technology, Atlanta, GA, USA
| | - Xuesong Wang
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, China
| | - Hongxin Wei
- MLR Lab, Southern University of Science and Technology
| | - Irwin King
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, China
| | - Yu Li
- Department of Computer Science and Engineering, CUHK, Hong Kong SAR, China
- The CUHK Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China
- Institute for Medical Enginering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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47
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Grant RA, Poor TA, Sichizya L, Diaz E, Bailey JI, Soni S, Senkow KJ, Pérez-Leonor XG, Abdala-Valencia H, Lu Z, Donnelly HK, Simons LM, Ozer EA, Tighe RM, Lomasney JW, Wunderink RG, Singer BD, Misharin AV, Budinger GS. Prolonged exposure to lung-derived cytokines is associated with activation of microglia in patients with COVID-19. JCI Insight 2024; 9:e178859. [PMID: 38502186 PMCID: PMC11141878 DOI: 10.1172/jci.insight.178859] [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: 12/27/2023] [Accepted: 03/13/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUNDSurvivors of pneumonia, including SARS-CoV-2 pneumonia, are at increased risk for cognitive dysfunction and dementia. In rodent models, cognitive dysfunction following pneumonia has been linked to the systemic release of lung-derived pro-inflammatory cytokines. Microglia are poised to respond to inflammatory signals from the circulation, and their dysfunction has been linked to cognitive impairment in murine models of dementia and in humans.METHODSWe measured levels of 55 cytokines and chemokines in bronchoalveolar lavage fluid and plasma from 341 patients with respiratory failure and 13 healthy controls, including 93 unvaccinated patients with COVID-19 and 203 patients with other causes of pneumonia. We used flow cytometry to sort neuroimmune cells from postmortem brain tissue from 5 patients who died from COVID-19 and 3 patients who died from other causes for single-cell RNA-sequencing.RESULTSMicroglia from patients with COVID-19 exhibited a transcriptomic signature suggestive of their activation by circulating pro-inflammatory cytokines. Peak levels of pro-inflammatory cytokines were similar in patients with pneumonia irrespective of etiology, but cumulative cytokine exposure was higher in patients with COVID-19. Treatment with corticosteroids reduced expression of COVID-19-specific cytokines.CONCLUSIONProlonged lung inflammation results in sustained elevations in circulating cytokines in patients with SARS-CoV-2 pneumonia compared with those with pneumonia secondary to other pathogens. Microglia from patients with COVID-19 exhibit transcriptional responses to inflammatory cytokines. These findings support data from rodent models causally linking systemic inflammation with cognitive dysfunction in pneumonia and support further investigation into the role of microglia in pneumonia-related cognitive dysfunction.FUNDINGSCRIPT U19AI135964, UL1TR001422, P01AG049665, P01HL154998, R01HL149883, R01LM013337, R01HL153122, R01HL147290, R01HL147575, R01HL158139, R01ES034350, R01ES027574, I01CX001777, U01TR003528, R21AG075423, T32AG020506, F31AG071225, T32HL076139.
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Affiliation(s)
- Rogan A. Grant
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Taylor A. Poor
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Lango Sichizya
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Estefani Diaz
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Joseph I. Bailey
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Sahil Soni
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Karolina J. Senkow
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | | | | | - Ziyan Lu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Helen K. Donnelly
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Lacy M. Simons
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Pathogen Genomics and Microbial Evolution, Robert J. Havey, MD Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Pathogen Genomics and Microbial Evolution, Robert J. Havey, MD Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Robert M. Tighe
- Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University School of Medicine, Duke University, Durham, North Carolina, USA
| | | | | | - Benjamin D. Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
- Department of Biochemistry and Molecular Genetics, and Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | | | - G.R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
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48
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Li Y, Qin S, Dong L, Qiao S, Wang X, Yu D, Gao P, Hou Y, Quan S, Li Y, Fan F, Zhao X, Ma Y, Gao GF. Long-term effects of Omicron BA.2 breakthrough infection on immunity-metabolism balance: a 6-month prospective study. Nat Commun 2024; 15:2444. [PMID: 38503738 PMCID: PMC10951309 DOI: 10.1038/s41467-024-46692-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: 07/28/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024] Open
Abstract
There have been reports of long coronavirus disease (long COVID) and breakthrough infections (BTIs); however, the mechanisms and pathological features of long COVID after Omicron BTIs remain unclear. Assessing long-term effects of COVID-19 and immune recovery after Omicron BTIs is crucial for understanding the disease and managing new-generation vaccines. Here, we followed up mild BA.2 BTI convalescents for six-month with routine blood tests, proteomic analysis and single-cell RNA sequencing (scRNA-seq). We found that major organs exhibited ephemeral dysfunction and recovered to normal in approximately six-month after BA.2 BTI. We also observed durable and potent levels of neutralizing antibodies against major circulating sub-variants, indicating that hybrid humoral immunity stays active. However, platelets may take longer to recover based on proteomic analyses, which also shows coagulation disorder and an imbalance between anti-pathogen immunity and metabolism six-month after BA.2 BTI. The immunity-metabolism imbalance was then confirmed with retrospective analysis of abnormal levels of hormones, low blood glucose level and coagulation profile. The long-term malfunctional coagulation and imbalance in the material metabolism and immunity may contribute to the development of long COVID and act as useful indicator for assessing recovery and the long-term impacts after Omicron sub-variant BTIs.
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Affiliation(s)
- Yanhua Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Shijie Qin
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, 518026, China
| | - Lei Dong
- Department of Clinical Laboratory, Air Force Medical Center, 100142, Beijing, China
| | - Shitong Qiao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 101408, Beijing, China
| | - Xiao Wang
- School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Dongshan Yu
- Department of Infectious Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, 330008, China
| | - Pengyue Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yali Hou
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, 030032, China
| | - Shouzhen Quan
- Department of Clinical Laboratory, Air Force Medical Center, 100142, Beijing, China
| | - Ying Li
- Department of Clinical Laboratory, Air Force Medical Center, 100142, Beijing, China
| | - Fengyan Fan
- Department of Clinical Laboratory, Air Force Medical Center, 100142, Beijing, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 101408, Beijing, China.
- Beijing Life Science Academy, 102209, Beijing, China.
| | - Yueyun Ma
- Department of Clinical Laboratory, Air Force Medical Center, 100142, Beijing, China.
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 101408, Beijing, China.
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, 030032, China.
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49
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Kenney D, O’Connell AK, Tseng AE, Turcinovic J, Sheehan ML, Nitido AD, Montanaro P, Gertje HP, Ericsson M, Connor JH, Vrbanac V, Crossland NA, Harly C, Balazs AB, Douam F. Resolution of SARS-CoV-2 infection in human lung tissues is driven by extravascular CD163+ monocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583965. [PMID: 38496468 PMCID: PMC10942442 DOI: 10.1101/2024.03.08.583965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The lung-resident immune mechanisms driving resolution of SARS-CoV-2 infection in humans remain elusive. Using mice co-engrafted with a genetically matched human immune system and fetal lung xenograft (fLX), we mapped the immunological events defining resolution of SARS-CoV-2 infection in human lung tissues. Viral infection is rapidly cleared from fLX following a peak of viral replication. Acute replication results in the emergence of cell subsets enriched in viral RNA, including extravascular inflammatory monocytes (iMO) and macrophage-like T-cells, which dissipate upon infection resolution. iMO display robust antiviral responses, are transcriptomically unique among myeloid lineages, and their emergence associates with the recruitment of circulating CD4+ monocytes. Consistently, mice depleted for human CD4+ cells but not CD3+ T-cells failed to robustly clear infectious viruses and displayed signatures of chronic infection. Our findings uncover the transient differentiation of extravascular iMO from CD4+ monocytes as a major hallmark of SARS-CoV-2 infection resolution and open avenues for unravelling viral and host adaptations defining persistently active SARS-CoV-2 infection.
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Affiliation(s)
- Devin Kenney
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K. O’Connell
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian 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
| | - Anna E. Tseng
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian 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
| | - Jacquelyn Turcinovic
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Meagan L. Sheehan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Adam D. Nitido
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Paige Montanaro
- 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
| | - Hans P. Gertje
- 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
| | - Maria Ericsson
- Electron Microscopy Core Facility, Harvard Medical School, Boston, MA, USA
| | - John H. Connor
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | | | - Nicholas A. Crossland
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian 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
| | - Christelle Harly
- Université de Nantes, INSERM, CNRS, CRCINA, Nantes, France
- LabEx IGO ‘Immunotherapy, Graft, Oncology’, Nantes, France
- These authors contributed equally to the work
| | - Alejandro B. Balazs
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Florian Douam
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- These authors contributed equally to the work
- Lead contact
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50
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Conte C, Cipponeri E, Roden M. Diabetes Mellitus, Energy Metabolism, and COVID-19. Endocr Rev 2024; 45:281-308. [PMID: 37934800 PMCID: PMC10911957 DOI: 10.1210/endrev/bnad032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/30/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
Obesity, diabetes mellitus (mostly type 2), and COVID-19 show mutual interactions because they are not only risk factors for both acute and chronic COVID-19 manifestations, but also because COVID-19 alters energy metabolism. Such metabolic alterations can lead to dysglycemia and long-lasting effects. Thus, the COVID-19 pandemic has the potential for a further rise of the diabetes pandemic. This review outlines how preexisting metabolic alterations spanning from excess visceral adipose tissue to hyperglycemia and overt diabetes may exacerbate COVID-19 severity. We also summarize the different effects of SARS-CoV-2 infection on the key organs and tissues orchestrating energy metabolism, including adipose tissue, liver, skeletal muscle, and pancreas. Last, we provide an integrative view of the metabolic derangements that occur during COVID-19. Altogether, this review allows for better understanding of the metabolic derangements occurring when a fire starts from a small flame, and thereby help reducing the impact of the COVID-19 pandemic.
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Affiliation(s)
- Caterina Conte
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome 00166, Italy
- Department of Endocrinology, Nutrition and Metabolic Diseases, IRCCS MultiMedica, Milan 20099, Italy
| | - Elisa Cipponeri
- Department of Endocrinology, Nutrition and Metabolic Diseases, IRCCS MultiMedica, Milan 20099, Italy
| | - Michael Roden
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- German Center for Diabetes Research, Partner Düsseldorf, Neuherberg 85764, Germany
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