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Shafqat A, Masters MC, Tripathi U, Tchkonia T, Kirkland JL, Hashmi SK. Long COVID as a disease of accelerated biological aging: An opportunity to translate geroscience interventions. Ageing Res Rev 2024; 99:102400. [PMID: 38945306 DOI: 10.1016/j.arr.2024.102400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/12/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
It has been four years since long COVID-the protracted consequences that survivors of COVID-19 face-was first described. Yet, this entity continues to devastate the quality of life of an increasing number of COVID-19 survivors without any approved therapy and a paucity of clinical trials addressing its biological root causes. Notably, many of the symptoms of long COVID are typically seen with advancing age. Leveraging this similarity, we posit that Geroscience-which aims to target the biological drivers of aging to prevent age-associated conditions as a group-could offer promising therapeutic avenues for long COVID. Bearing this in mind, this review presents a translational framework for studying long COVID as a state of effectively accelerated biological aging, identifying research gaps and offering recommendations for future preclinical and clinical studies.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| | - Mary Clare Masters
- Division of Infectious Diseases, Northwestern University, Chicago, IL, USA
| | - Utkarsh Tripathi
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Tamara Tchkonia
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - James L Kirkland
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA; Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Shahrukh K Hashmi
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA; Research and Innovation Center, Department of Health, Abu Dhabi, UAE; College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
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2
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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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Bi Y, Li T, Zhang S, Yang Y, Dong M. Bioinformatics-based analysis of the dialog between COVID-19 and RSA. Heliyon 2024; 10:e30371. [PMID: 38737245 PMCID: PMC11088317 DOI: 10.1016/j.heliyon.2024.e30371] [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: 08/10/2023] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/14/2024] Open
Abstract
Pregnant women infected with SARS-CoV-2 in early pregnancy may face an increased risk of miscarriage due to immune imbalance at the maternal-fetal interface. However, the molecular mechanisms underlying the crosstalk between COVID-19 infection and recurrent spontaneous abortion (RSA) remain poorly understood. This study aimed to elucidate the transcriptomic molecular dialog between COVID-19 and RSA. Based on bioinformatics analysis, 307 common differentially expressed genes were found between COVID-19 (GSE171110) and RSA (GSE165004). Common DEGs were mainly enriched in ribosome-related and cell cycle-related signaling pathways. Using degree algorithm, the top 10 hub genes (RPS27A, RPL5, RPS8, RPL4, RPS2, RPL30, RPL23A, RPL31, RPL26, RPL37A) were selected from the common DEGs based on their scores. The results of the qPCR were in general agreement with the results of the raw letter analysis. The top 10 candidate drugs were also selected based on P-values. In this study, we provide molecular markers, signaling pathways, and small molecule compounds that may associate COVID-19. These findings may increase the accurate diagnosis and treatment of COVID-19 patients.
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Affiliation(s)
- Yin Bi
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, 530000, China
- The Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, 530000, China
| | - Ting Li
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, 530000, China
- The Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, 530000, China
| | - Shun Zhang
- Department of Reproductive Medical Center, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, China
| | - Yihua Yang
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, 530000, China
- The Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, 530000, China
| | - Mingyou Dong
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, China
- The Key Laboratory of Molecular Pathology (For Hepatobiliary Diseases) of Guangxi, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, China
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Filia A, Mitroulis I, Loukogiannaki C, Grigoriou M, Banos A, Sentis G, Giannouli S, Karali V, Athanasiadis E, Kokkinopoulos I, Boumpas DT. Single-cell transcriptomic analysis of hematopoietic progenitor cells from patients with systemic lupus erythematosus reveals interferon-inducible reprogramming in early progenitors. Front Immunol 2024; 15:1383358. [PMID: 38779657 PMCID: PMC11109438 DOI: 10.3389/fimmu.2024.1383358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Immune cells that contribute to the pathogenesis of systemic lupus erythematosus (SLE) derive from adult hematopoietic stem and progenitor cells (HSPCs) within the bone marrow (BM). For this reason, we reasoned that fundamental abnormalities in SLE can be traced to a BM-derived HSPC inflammatory signature. Methods BM samples from four SLE patients, six healthy controls, and two umbilical cord blood (CB) samples were used. CD34+ cells were isolated from BM and CB samples, and single-cell RNA-sequencing was performed. Results A total of 426 cells and 24,473 genes were used in the analysis. Clustering analysis resulted in seven distinct clusters of cell types. Mutually exclusive markers, which were characteristic of each cell type, were identified. We identified three HSPC subpopulations, one of which consisted of proliferating cells (MKI67 expressing cells), one T-like, one B-like, and two myeloid-like progenitor subpopulations. Differential expression analysis revealed i) cell cycle-associated signatures, in healthy BM of HSPC clusters 3 and 4 when compared with CB, and ii) interferon (IFN) signatures in SLE BM of HSPC clusters 3 and 4 and myeloid-like progenitor cluster 5 when compared with healthy controls. The IFN signature in SLE appeared to be deregulated following TF regulatory network analysis and differential alternative splicing analysis between SLE and healthy controls in HSPC subpopulations. Discussion This study revealed both quantitative-as evidenced by decreased numbers of non-proliferating early progenitors-and qualitative differences-characterized by an IFN signature in SLE, which is known to drive loss of function and depletion of HSPCs. Chronic IFN exposure affects early hematopoietic progenitors in SLE, which may account for the immune aberrancies and the cytopenias in SLE.
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Affiliation(s)
- Anastasia Filia
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Ioannis Mitroulis
- 1st Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Catherine Loukogiannaki
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Maria Grigoriou
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
- 1st Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Aggelos Banos
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - George Sentis
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Stavroula Giannouli
- 2nd Department of Internal Medicine, Ippokrateion Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Vassiliki Karali
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Emmanouil Athanasiadis
- Medical Image and Signal Processing Laboratory, Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | - Ioannis Kokkinopoulos
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Dimitrios T. Boumpas
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece
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Oliveira TT, Freitas JF, de Medeiros VPB, Xavier TJDS, Agnez-Lima LF. Integrated analysis of RNA-seq datasets reveals novel targets and regulators of COVID-19 severity. Life Sci Alliance 2024; 7:e202302358. [PMID: 38262689 PMCID: PMC10806258 DOI: 10.26508/lsa.202302358] [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: 09/06/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024] Open
Abstract
During the COVID-19 pandemic, RNA-seq datasets were produced to investigate the virus-host relationship. However, much of these data remains underexplored. To improve the search for molecular targets and biomarkers, we performed an integrated analysis of multiple RNA-seq datasets, expanding the cohort and including patients from different countries, encompassing severe and mild COVID-19 patients. Our analysis revealed that severe COVID-19 patients exhibit overexpression of genes coding for proteins of extracellular exosomes, endomembrane system, and neutrophil granules (e.g., S100A9, LY96, and RAB1B), which may play an essential role in the cellular response to infection. Concurrently, these patients exhibit down-regulation of genes encoding components of the T cell receptor complex and nucleolus, including TP53, IL2RB, and NCL Finally, SPI1 may emerge as a central transcriptional factor associated with the up-regulated genes, whereas TP53, MYC, and MAX were associated with the down-regulated genes during COVID-19. This study identified targets and transcriptional factors, lighting on the molecular pathophysiology of syndrome coronavirus 2 infection.
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Affiliation(s)
- Thais Teixeira Oliveira
- https://ror.org/04wn09761 Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | - Júlia Firme Freitas
- https://ror.org/04wn09761 Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | | | - Thiago Jesus da Silva Xavier
- https://ror.org/04wn09761 Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | - Lucymara Fassarella Agnez-Lima
- https://ror.org/04wn09761 Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
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Bonora BM, Marassi M, Fogar P, Zuin J, Cappellari R, Marinello S, Ferrari A, Cattelan A, Avogaro A, Basso D, Fadini GP. Circulating haematopoietic stem cells and long-term outcomes of COVID-19. Eur J Clin Invest 2024; 54:e14150. [PMID: 38088242 DOI: 10.1111/eci.14150] [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: 10/01/2023] [Revised: 11/19/2023] [Accepted: 11/30/2023] [Indexed: 03/13/2024]
Abstract
BACKGROUND AND AIMS An acute depletion of circulating haematopoietic stem/progenitor cells (HSPCs) occurs during COVID-19, especially among patients with a poorer disease course. We herein examined whether HSPCs levels at hospital admission for COVID-19 predict 1-year mortality and the long-COVID syndrome. MATERIALS AND METHODS Patients hospitalized for COVID-19 in an infectious disease ward were consecutively enrolled. Circulating HSPC levels were assessed by flow cytometry as cells expressing CD34 and/or CD133. Follow-up was performed for 12 months after hospitalization through the review of electronic medical records and demographic local registers. RESULTS The study included 100 patients, 36 of whom reported symptoms of long-COVID and 20 died during follow-up. The reduction of 1-SD of HSPCs was associated with a 3- to 5-fold increase in the risk of 1-year mortality. Age, admission hyperglycaemia, C-reactive protein peak, liver enzymes, the need of high-flow oxygen and/or invasive ventilation were predictors of mortality at univariate analysis. Among pre-existing comorbidities, coronary heart disease and chronic kidney disease, but not diabetes, were associated with 1-year mortality. In multivariate analyses, HSPCs remained significantly associated with 1-year mortality independently of confounders. The development of pneumonia an in-hospital treatment with glucocorticoids and convalescent plasma were associated with long-COVID symptoms at follow-up. HSPCs, diabetes and other comorbidities were not predictors of long-COVID. CONCLUSIONS In a cohort of patients hospitalized for COVID-19, lower HSPC levels at the time of admission were independent predictors of 1-year mortality. However, COVID-19 severity, but not HSPC level, was significantly associated with the development of long-COVID symptoms.
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Affiliation(s)
- Benedetta Maria Bonora
- Department of Medicine, University Hospital of Padova, Padua, Italy
- Veneto Institute of Molecular Medicine, Padua, Italy
| | - Marella Marassi
- Department of Medicine, University Hospital of Padova, Padua, Italy
| | - Paola Fogar
- Department of Medicine, University Hospital of Padova, Padua, Italy
| | - Jenny Zuin
- Department of Medicine, University Hospital of Padova, Padua, Italy
| | | | - Serena Marinello
- Department of Medicine, University Hospital of Padova, Padua, Italy
| | - Anna Ferrari
- Department of Medicine, University Hospital of Padova, Padua, Italy
| | | | - Angelo Avogaro
- Department of Medicine, University Hospital of Padova, Padua, Italy
| | - Daniela Basso
- Department of Medicine, University Hospital of Padova, Padua, Italy
| | - Gian Paolo Fadini
- Department of Medicine, University Hospital of Padova, Padua, Italy
- Veneto Institute of Molecular Medicine, Padua, Italy
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7
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Swann JW, Olson OC, Passegué E. Made to order: emergency myelopoiesis and demand-adapted innate immune cell production. Nat Rev Immunol 2024:10.1038/s41577-024-00998-7. [PMID: 38467802 DOI: 10.1038/s41577-024-00998-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 03/13/2024]
Abstract
Definitive haematopoiesis is the process by which haematopoietic stem cells, located in the bone marrow, generate all haematopoietic cell lineages in healthy adults. Although highly regulated to maintain a stable output of blood cells in health, the haematopoietic system is capable of extensive remodelling in response to external challenges, prioritizing the production of certain cell types at the expense of others. In this Review, we consider how acute insults, such as infections and cytotoxic drug-induced myeloablation, cause molecular, cellular and metabolic changes in haematopoietic stem and progenitor cells at multiple levels of the haematopoietic hierarchy to drive accelerated production of the mature myeloid cells needed to resolve the initiating insult. Moreover, we discuss how dysregulation or subversion of these emergency myelopoiesis mechanisms contributes to the progression of chronic inflammatory diseases and cancer.
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Affiliation(s)
- James W Swann
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Oakley C Olson
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Emmanuelle Passegué
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University, New York, NY, USA.
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8
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Healey AM, Fenner KN, O'Dell CT, Lawrence BP. Aryl hydrocarbon receptor activation alters immune cell populations in the lung and bone marrow during coronavirus infection. Am J Physiol Lung Cell Mol Physiol 2024; 326:L313-L329. [PMID: 38290163 PMCID: PMC11281796 DOI: 10.1152/ajplung.00236.2023] [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: 07/26/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/01/2024] Open
Abstract
Respiratory viral infections are one of the major causes of illness and death worldwide. Symptoms associated with respiratory infections can range from mild to severe, and there is limited understanding of why there is large variation in severity. Environmental exposures are a potential causative factor. The aryl hydrocarbon receptor (AHR) is an environment-sensing molecule expressed in all immune cells. Although there is considerable evidence that AHR signaling influences immune responses to other immune challenges, including respiratory pathogens, less is known about the impact of AHR signaling on immune responses during coronavirus (CoV) infection. In this study, we report that AHR activation significantly altered immune cells in the lungs and bone marrow of mice infected with a mouse CoV. AHR activation transiently reduced the frequency of multiple cells in the mononuclear phagocyte system, including monocytes, interstitial macrophages, and dendritic cells in the lung. In the bone marrow, AHR activation altered myelopoiesis, as evidenced by a reduction in granulocyte-monocyte progenitor cells and an increased frequency of myeloid-biased progenitor cells. Moreover, AHR activation significantly affected multiple stages of the megakaryocyte lineage. Overall, these findings indicate that AHR activation modulates multiple aspects of the immune response to a CoV infection. Given the significant burden of respiratory viruses on human health, understanding how environmental exposures shape immune responses to infection advances our knowledge of factors that contribute to variability in disease severity and provides insight into novel approaches to prevent or treat disease.NEW & NOTEWORTHY Our study reveals a multifaceted role for aryl hydrocarbon receptor (AHR) signaling in the immune response to coronavirus (CoV) infection. Sustained AHR activation during in vivo mouse CoV infection altered the frequency of mature immune cells in the lung and modulated emergency hematopoiesis, specifically myelopoiesis and megakaryopoiesis, in bone marrow. This provides new insight into immunoregulation by the AHR and extends our understanding of how environmental exposures can impact host responses to respiratory viral infections.
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Affiliation(s)
- Alicia M Healey
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States
| | - Kristina N Fenner
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States
| | - Colleen T O'Dell
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States
| | - B Paige Lawrence
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States
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9
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Jogi HR, Smaraki N, Nayak SS, Rajawat D, Kamothi DJ, Panigrahi M. Single cell RNA-seq: a novel tool to unravel virus-host interplay. Virusdisease 2024; 35:41-54. [PMID: 38817399 PMCID: PMC11133279 DOI: 10.1007/s13337-024-00859-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/12/2024] [Indexed: 06/01/2024] Open
Abstract
Over the last decade, single cell RNA sequencing (scRNA-seq) technology has caught the momentum of being a vital revolutionary tool to unfold cellular heterogeneity by high resolution assessment. It evades the inadequacies of conventional sequencing technology which was able to detect only average expression level among cell populations. In the era of twenty-first century, several epidemic and pandemic viruses have emerged. Being an intracellular entity, viruses totally rely on host. Complex virus-host dynamics result when the virus tend to obtain factors from host cell required for its replication and establishment of infection. As a prevailing tool, scRNA-seq is able to understand virus-host interplay by comprehensive transcriptome profiling. Because of technological and methodological advancement, this technology is capable to recognize viral genome and host cell response heterogeneity. Further development in analytical methods with multiomics approach and increased availability of accessible scRNA-seq datasets will improve the understanding of viral pathogenesis that can be helpful for development of novel antiviral therapeutic strategies.
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Affiliation(s)
- Harsh Rajeshbhai Jogi
- Division of Veterinary Microbiology, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Nabaneeta Smaraki
- Division of Veterinary Microbiology, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Divya Rajawat
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Dhaval J. Kamothi
- Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
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10
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Ferreira AV, Netea MG. Hematopoietic memory of severe COVID-19 infection. Cell Res 2024; 34:187-188. [PMID: 37864057 PMCID: PMC10907561 DOI: 10.1038/s41422-023-00885-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023] Open
Affiliation(s)
- Anaisa V Ferreira
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Immunology and Metabolism, Life and Medical Sciences Center, University of Bonn, Bonn, Germany.
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11
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May L, Chu CF, Zielinski CE. Single-Cell RNA Sequencing Reveals HIF1A as a Severity-Sensitive Immunological Scar in Circulating Monocytes of Convalescent Comorbidity-Free COVID-19 Patients. Cells 2024; 13:300. [PMID: 38391913 PMCID: PMC10886588 DOI: 10.3390/cells13040300] [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: 12/22/2023] [Revised: 01/20/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
COVID-19, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is characterized by a wide range of clinical symptoms and a poorly predictable disease course. Although in-depth transcriptomic investigations of peripheral blood samples from COVID-19 patients have been performed, the detailed molecular mechanisms underlying an asymptomatic, mild or severe disease course, particularly in patients without relevant comorbidities, remain poorly understood. While previous studies have mainly focused on the cellular and molecular dissection of ongoing COVID-19, we set out to characterize transcriptomic immune cell dysregulation at the single-cell level at different time points in patients without comorbidities after disease resolution to identify signatures of different disease severities in convalescence. With single-cell RNA sequencing, we reveal a role for hypoxia-inducible factor 1-alpha (HIF1A) as a severity-sensitive long-term immunological scar in circulating monocytes of convalescent COVID-19 patients. Additionally, we show that circulating complexes formed by monocytes with either T cells or NK cells represent a characteristic cellular marker in convalescent COVID-19 patients irrespective of their preceding symptom severity. Together, these results provide cellular and molecular correlates of recovery from COVID-19 and could help in immune monitoring and in the design of new treatment strategies.
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Affiliation(s)
- Lilly May
- Leibniz Institute for Natural Products Research and Infection Biology, Department of Infection Immunology, 07745 Jena, Germany; (L.M.); (C.-F.C.)
- Center for Translational Cancer Research (TranslaTUM) & Institute of Virology, Technical University of Munich, 81675 Munich, Germany
| | - Chang-Feng Chu
- Leibniz Institute for Natural Products Research and Infection Biology, Department of Infection Immunology, 07745 Jena, Germany; (L.M.); (C.-F.C.)
- Center for Translational Cancer Research (TranslaTUM) & Institute of Virology, Technical University of Munich, 81675 Munich, Germany
| | - Christina E. Zielinski
- Leibniz Institute for Natural Products Research and Infection Biology, Department of Infection Immunology, 07745 Jena, Germany; (L.M.); (C.-F.C.)
- Center for Translational Cancer Research (TranslaTUM) & Institute of Virology, Technical University of Munich, 81675 Munich, Germany
- Department of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
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12
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Schmidt G, Martens A, Koch C, Markmann M, Schneck E, Matt U, Hecker M, Tello K, Wolff M, Sander M, Vadász I. Nucleated red blood cells are a late biomarker in predicting intensive care unit mortality in patients with COVID-19 acute respiratory distress syndrome: an observational cohort study. Front Immunol 2024; 15:1313977. [PMID: 38304431 PMCID: PMC10830722 DOI: 10.3389/fimmu.2024.1313977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/04/2024] [Indexed: 02/03/2024] Open
Abstract
Background Nucleated red blood cells (nRBC) are precursor cells of the erythropoiesis that are absent from the peripheral blood under physiological conditions. Their presence is associated with adverse outcomes in critically ill patients. This study aimed to evaluate the predictive value of nRBC on mortality in intensive care unit (ICU) patients with COVID-19 acute respiratory distress syndrome (ARDS). Material and methods This retrospective, observational cohort study analyzed data on 206 ICU patients diagnosed with COVID-19 ARDS between March 2020 and March 2022. The primary endpoint was ICU mortality, and secondary endpoints included ICU and hospital stay lengths, ventilation hours, and the time courses of disease severity scores and clinical and laboratory parameters. Results Among the included patients, 68.9% tested positive for nRBC at least once during their ICU stay. A maximum nRBC of 105 µl-1 had the highest accuracy in predicting ICU mortality (area under the curve of the receiver operating characteristic [AUCROC] 0.780, p < 0.001, sensitivity 69.0%, specificity 75.5%). Mortality was significantly higher among patients with nRBC >105 µl-1 than ≤105 µl-1 (86.5% vs. 51.3%, p = 0.008). Compared to patients negative for nRBC in their peripheral blood, those positive for nRBC required longer mechanical ventilation (127 [44 - 289] h vs. 517 [255 - 950] h, p < 0.001), ICU stays (12 [8 - 19] vs. 27 [13 - 51] d, p < 0.001), and hospital stays (19 [12 - 29] d vs. 31 [16 - 58] d, p < 0.001). Peak Sepsis-related Organ Failure Assessment (SOFA), Simplified Acute Physiology Score, PaO2/FiO2, interleukin-6, and procalcitonin values were reached before the peak nRBC level. However, the predictive performance of the SOFA (AUCROC 0.842, p < 0.001) was considerably improved when a maximum SOFA score >8 and nRBC >105 µl-1 were combined. Discussion nRBC predict ICU mortality and indicate disease severity among patients with COVID-19 ARDS, and they should be considered a clinical alarm signal for a worse outcome. nRBC are a late predictor of ICU mortality compared to other established clinical scoring systems and laboratory parameters but improve the prediction accuracy when combined with the SOFA score.
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Affiliation(s)
- Götz Schmidt
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Justus Liebig University Giessen, Giessen, Germany
| | - Arnd Martens
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Koch
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Justus Liebig University Giessen, Giessen, Germany
| | - Melanie Markmann
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Justus Liebig University Giessen, Giessen, Germany
| | - Emmanuel Schneck
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Justus Liebig University Giessen, Giessen, Germany
| | - Ulrich Matt
- Department of Internal Medicine V, Universities of Giessen and Marburg Lung Center (UGMLC), Excellence Cluster Cardiopulmonary Institute (CPI), Member of the German Center for Lung Research (DZL), Justus-Liebig University, Giessen, Germany
| | - Matthias Hecker
- Department of Internal Medicine II, Universities of Giessen and Marburg Lung Center (UGMLC), Excellence Cluster Cardiopulmonary Institute (CPI), Member of the German Center for Lung Research (DZL), Justus-Liebig University, Giessen, Germany
| | - Khodr Tello
- Department of Internal Medicine II, Universities of Giessen and Marburg Lung Center (UGMLC), Excellence Cluster Cardiopulmonary Institute (CPI), Member of the German Center for Lung Research (DZL), Justus-Liebig University, Giessen, Germany
| | - Matthias Wolff
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Justus Liebig University Giessen, Giessen, Germany
| | - Michael Sander
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Justus Liebig University Giessen, Giessen, Germany
| | - István Vadász
- Department of Internal Medicine II, Universities of Giessen and Marburg Lung Center (UGMLC), Excellence Cluster Cardiopulmonary Institute (CPI), Member of the German Center for Lung Research (DZL), Justus-Liebig University, Giessen, Germany
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13
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Len JS, Koh CWT, Chan KR. The Functional Roles of MDSCs in Severe COVID-19 Pathogenesis. Viruses 2023; 16:27. [PMID: 38257728 PMCID: PMC10821470 DOI: 10.3390/v16010027] [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: 11/17/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Severe COVID-19 is a major cause of morbidity and mortality worldwide, especially among those with co-morbidities, the elderly, and the immunocompromised. However, the molecular determinants critical for severe COVID-19 progression remain to be fully elucidated. Meta-analyses of transcriptomic RNAseq and single-cell sequencing datasets comparing severe and mild COVID-19 patients have demonstrated that the early expansion of myeloid-derived suppressor cells (MDSCs) could be a key feature of severe COVID-19 progression. Besides serving as potential early prognostic biomarkers for severe COVID-19 progression, several studies have also indicated the functional roles of MDSCs in severe COVID-19 pathogenesis and possibly even long COVID. Given the potential links between MDSCs and severe COVID-19, we examine the existing literature summarizing the characteristics of MDSCs, provide evidence of MDSCs in facilitating severe COVID-19 pathogenesis, and discuss the potential therapeutic avenues that can be explored to reduce the risk and burden of severe COVID-19. We also provide a web app where users can visualize the temporal changes in specific genes or MDSC-related gene sets during severe COVID-19 progression and disease resolution, based on our previous study.
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Affiliation(s)
- Jia Soon Len
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
| | - Clara W. T. Koh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore;
| | - Kuan Rong Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore;
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14
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Huang T, He J, Zhou X, Pan H, He F, Du A, Yu B, Jiang N, Li X, Yuan K, Wang Z. Discovering common pathogenetic processes between COVID-19 and tuberculosis by bioinformatics and system biology approach. Front Cell Infect Microbiol 2023; 13:1280223. [PMID: 38162574 PMCID: PMC10757339 DOI: 10.3389/fcimb.2023.1280223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 11/07/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction The coronavirus disease 2019 (COVID-19) pandemic, stemming from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has persistently threatened the global health system. Meanwhile, tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tuberculosis) still continues to be endemic in various regions of the world. There is a certain degree of similarity between the clinical features of COVID-19 and TB, but the underlying common pathogenetic processes between COVID-19 and TB are not well understood. Methods To elucidate the common pathogenetic processes between COVID-19 and TB, we implemented bioinformatics and systematic research to obtain shared pathways and molecular biomarkers. Here, the RNA-seq datasets (GSE196822 and GSE126614) are used to extract shared differentially expressed genes (DEGs) of COVID-19 and TB. The common DEGs were used to identify common pathways, hub genes, transcriptional regulatory networks, and potential drugs. Results A total of 96 common DEGs were selected for subsequent analyses. Functional enrichment analyses showed that viral genome replication and immune-related pathways collectively contributed to the development and progression of TB and COVID-19. Based on the protein-protein interaction (PPI) network analysis, we identified 10 hub genes, including IFI44L, ISG15, MX1, IFI44, OASL, RSAD2, GBP1, OAS1, IFI6, and HERC5. Subsequently, the transcription factor (TF)-gene interaction and microRNA (miRNA)-gene coregulatory network identified 61 TFs and 29 miRNAs. Notably, we identified 10 potential drugs to treat TB and COVID-19, namely suloctidil, prenylamine, acetohexamide, terfenadine, prochlorperazine, 3'-azido-3'-deoxythymidine, chlorophyllin, etoposide, clioquinol, and propofol. Conclusion This research provides novel strategies and valuable references for the treatment of tuberculosis and COVID-19.
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Affiliation(s)
- Tengda Huang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jinyi He
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xinyi Zhou
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hongyuan Pan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Fang He
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ao Du
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Bingxuan Yu
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Nan Jiang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoquan Li
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Kefei Yuan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zhen Wang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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15
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Weeratunga P, Denney L, Bull JA, Repapi E, Sergeant M, Etherington R, Vuppussetty C, Turner GDH, Clelland C, Woo J, Cross A, Issa F, de Andrea CE, Melero Bermejo I, Sims D, McGowan S, Zurke YX, Ahern DJ, Gamez EC, Whalley J, Richards D, Klenerman P, Monaco C, Udalova IA, Dong T, Antanaviciute A, Ogg G, Knight JC, Byrne HM, Taylor S, Ho LP. Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs. Nat Commun 2023; 14:7216. [PMID: 37940670 PMCID: PMC10632491 DOI: 10.1038/s41467-023-42421-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
Single cell spatial interrogation of the immune-structural interactions in COVID -19 lungs is challenging, mainly because of the marked cellular infiltrate and architecturally distorted microstructure. To address this, we develop a suite of mathematical tools to search for statistically significant co-locations amongst immune and structural cells identified using 37-plex imaging mass cytometry. This unbiased method reveals a cellular map interleaved with an inflammatory network of immature neutrophils, cytotoxic CD8 T cells, megakaryocytes and monocytes co-located with regenerating alveolar progenitors and endothelium. Of note, a highly active cluster of immature neutrophils and CD8 T cells, is found spatially linked with alveolar progenitor cells, and temporally with the diffuse alveolar damage stage. These findings offer further insights into how immune cells interact in the lungs of severe COVID-19 disease. We provide our pipeline [Spatial Omics Oxford Pipeline (SpOOx)] and visual-analytical tool, Multi-Dimensional Viewer (MDV) software, as a resource for spatial analysis.
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Affiliation(s)
- Praveen Weeratunga
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Laura Denney
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Joshua A Bull
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Emmanouela Repapi
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Martin Sergeant
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rachel Etherington
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chaitanya Vuppussetty
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gareth D H Turner
- Department of Cellular Pathology and Radcliffe Department of Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Colin Clelland
- Anatomic Pathology, Weill Cornell Medical College, Doha, Qatar
| | - Jeongmin Woo
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Amy Cross
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Fadi Issa
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | | | - David Sims
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Simon McGowan
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - David J Ahern
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Eddie C Gamez
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Justin Whalley
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Duncan Richards
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Diseases, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Claudia Monaco
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Irina A Udalova
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Tao Dong
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Agne Antanaviciute
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Graham Ogg
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Stephen Taylor
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Ling-Pei Ho
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Respiratory Medicine Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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16
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Huang T, Jiang N, Song Y, Pan H, Du A, Yu B, Li X, He J, Yuan K, Wang Z. Bioinformatics and system biology approach to identify the influences of SARS-CoV-2 on metabolic unhealthy obese patients. Front Mol Biosci 2023; 10:1274463. [PMID: 37877121 PMCID: PMC10591333 DOI: 10.3389/fmolb.2023.1274463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Introduction: The severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) has posed a significant challenge to individuals' health. Increasing evidence shows that patients with metabolic unhealthy obesity (MUO) and COVID-19 have severer complications and higher mortality rate. However, the molecular mechanisms underlying the association between MUO and COVID-19 are poorly understood. Methods: We sought to reveal the relationship between MUO and COVID-19 using bioinformatics and systems biology analysis approaches. Here, two datasets (GSE196822 and GSE152991) were employed to extract differentially expressed genes (DEGs) to identify common hub genes, shared pathways, transcriptional regulatory networks, gene-disease relationship and candidate drugs. Results: Based on the identified 65 common DEGs, the complement-related pathways and neutrophil degranulation-related functions are found to be mainly affected. The hub genes, which included SPI1, CD163, C1QB, SIGLEC1, C1QA, ITGAM, CD14, FCGR1A, VSIG4 and C1QC, were identified. From the interaction network analysis, 65 transcription factors (TFs) were found to be the regulatory signals. Some infections, inflammation and liver diseases were found to be most coordinated with the hub genes. Importantly, Paricalcitol, 3,3',4,4',5-Pentachlorobiphenyl, PD 98059, Medroxyprogesterone acetate, Dexamethasone and Tretinoin HL60 UP have shown possibility as therapeutic agents against COVID-19 and MUO. Conclusion: This study provides new clues and references to treat both COVID-19 and MUO.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kefei Yuan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zhen Wang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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17
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Cheong JG, Ravishankar A, Sharma S, Parkhurst CN, Grassmann SA, Wingert CK, Laurent P, Ma S, Paddock L, Miranda IC, Karakaslar EO, Nehar-Belaid D, Thibodeau A, Bale MJ, Kartha VK, Yee JK, Mays MY, Jiang C, Daman AW, Martinez de Paz A, Ahimovic D, Ramos V, Lercher A, Nielsen E, Alvarez-Mulett S, Zheng L, Earl A, Yallowitz A, Robbins L, LaFond E, Weidman KL, Racine-Brzostek S, Yang HS, Price DR, Leyre L, Rendeiro AF, Ravichandran H, Kim J, Borczuk AC, Rice CM, Jones RB, Schenck EJ, Kaner RJ, Chadburn A, Zhao Z, Pascual V, Elemento O, Schwartz RE, Buenrostro JD, Niec RE, Barrat FJ, Lief L, Sun JC, Ucar D, Josefowicz SZ. Epigenetic memory of coronavirus infection in innate immune cells and their progenitors. Cell 2023; 186:3882-3902.e24. [PMID: 37597510 PMCID: PMC10638861 DOI: 10.1016/j.cell.2023.07.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 04/20/2023] [Accepted: 07/12/2023] [Indexed: 08/21/2023]
Abstract
Inflammation can trigger lasting phenotypes in immune and non-immune cells. Whether and how human infections and associated inflammation can form innate immune memory in hematopoietic stem and progenitor cells (HSPC) has remained unclear. We found that circulating HSPC, enriched from peripheral blood, captured the diversity of bone marrow HSPC, enabling investigation of their epigenomic reprogramming following coronavirus disease 2019 (COVID-19). Alterations in innate immune phenotypes and epigenetic programs of HSPC persisted for months to 1 year following severe COVID-19 and were associated with distinct transcription factor (TF) activities, altered regulation of inflammatory programs, and durable increases in myelopoiesis. HSPC epigenomic alterations were conveyed, through differentiation, to progeny innate immune cells. Early activity of IL-6 contributed to these persistent phenotypes in human COVID-19 and a mouse coronavirus infection model. Epigenetic reprogramming of HSPC may underlie altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors.
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Affiliation(s)
- Jin-Gyu Cheong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Arjun Ravishankar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Siddhartha Sharma
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Simon A Grassmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claire K Wingert
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paoline Laurent
- HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA
| | - Sai Ma
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Lucinda Paddock
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Emin Onur Karakaslar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Asa Thibodeau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael J Bale
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Vinay K Kartha
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Jim K Yee
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Minh Y Mays
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chenyang Jiang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew W Daman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alexia Martinez de Paz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dughan Ahimovic
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Victor Ramos
- The Rockefeller University, New York, NY 10065, USA
| | | | - Erik Nielsen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Ling Zheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew Earl
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Alisha Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lexi Robbins
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Karissa L Weidman
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sabrina Racine-Brzostek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - He S Yang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - David R Price
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Louise Leyre
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - André F Rendeiro
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Hiranmayi Ravichandran
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Junbum Kim
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alain C Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Northwell Health, Greenvale, NY 11548, USA
| | | | - R Brad Jones
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY 10065, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Edward J Schenck
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Robert J Kaner
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Zhen Zhao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Virginia Pascual
- Department of Pediatrics, Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Robert E Schwartz
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jason D Buenrostro
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Rachel E Niec
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; The Rockefeller University, New York, NY 10065, USA
| | - Franck J Barrat
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA; HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lindsay Lief
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
| | - Steven Z Josefowicz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA.
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18
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Hocini H, Wiedemann A, Blengio F, Lefebvre C, Cervantes-Gonzalez M, Foucat E, Tisserand P, Surenaud M, Coléon S, Prague M, Guillaumat L, Krief C, Fenwick C, Laouénan C, Bouadma L, Ghosn J, Pantaleo G, Thiébaut R, Lévy Y. Neutrophil Activation and Immune Thrombosis Profiles Persist in Convalescent COVID-19. J Clin Immunol 2023; 43:882-893. [PMID: 36943669 PMCID: PMC10029801 DOI: 10.1007/s10875-023-01459-x] [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: 12/23/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023]
Abstract
PURPOSE Following a severe COVID-19 infection, a proportion of individuals develop prolonged symptoms. We investigated the immunological dysfunction that underlies the persistence of symptoms months after the resolution of acute COVID-19. METHODS We analyzed cytokines, cell phenotypes, SARS-CoV-2 spike-specific and neutralizing antibodies, and whole blood gene expression profiles in convalescent severe COVID-19 patients 1, 3, and 6 months following hospital discharge. RESULTS We observed persistent abnormalities until month 6 marked by (i) high serum levels of monocyte/macrophage and endothelial activation markers, chemotaxis, and hematopoietic cytokines; (ii) a high frequency of central memory CD4+ and effector CD8+ T cells; (iii) a decrease in anti-SARS-CoV-2 spike and neutralizing antibodies; and (iv) an upregulation of genes related to platelet, neutrophil activation, erythrocytes, myeloid cell differentiation, and RUNX1 signaling. We identified a "core gene signature" associated with a history of thrombotic events, with upregulation of a set of genes involved in neutrophil activation, platelet, hematopoiesis, and blood coagulation. CONCLUSION The lack of restoration of gene expression to a normal profile after up to 6 months of follow-up, even in asymptomatic patients who experienced severe COVID-19, signals the need to carefully extend their clinical follow-up and propose preventive measures.
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Affiliation(s)
- Hakim Hocini
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Aurélie Wiedemann
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Fabiola Blengio
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Cécile Lefebvre
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Minerva Cervantes-Gonzalez
- Département Épidémiologie Biostatistiques Et Recherche Clinique, AP-HP, Hôpital Bichat, INSERM, Centre d'Investigation Clinique-Epidémiologie Clinique 1425, 75018, Paris, France
- UMR 1137, Université de Paris, INSERM, IAME, 75018, Paris, France
- APHP- Hôpital Bichat - Médecine Intensive et Réanimation des Maladies Infectieuses, Paris, France
| | - Emile Foucat
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Pascaline Tisserand
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Mathieu Surenaud
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Séverin Coléon
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Mélanie Prague
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
- Department of Public Health, Univ. Bordeaux, Inserm Bordeaux Population Health Research Centre, Inria SISTM, UMR 1219, Bordeaux, France
| | - Lydia Guillaumat
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Corinne Krief
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
| | - Craig Fenwick
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Cédric Laouénan
- Département Épidémiologie Biostatistiques Et Recherche Clinique, AP-HP, Hôpital Bichat, INSERM, Centre d'Investigation Clinique-Epidémiologie Clinique 1425, 75018, Paris, France
- UMR 1137, Université de Paris, INSERM, IAME, 75018, Paris, France
| | - Lila Bouadma
- UMR 1137, Université de Paris, INSERM, IAME, 75018, Paris, France
- APHP- Hôpital Bichat - Médecine Intensive et Réanimation des Maladies Infectieuses, Paris, France
| | - Jade Ghosn
- UMR 1137, Université de Paris, INSERM, IAME, 75018, Paris, France
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses Et Tropicales, 75018, Paris, France
| | - Giuseppe Pantaleo
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
- Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Rodolphe Thiébaut
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France
- Department of Public Health, Univ. Bordeaux, Inserm Bordeaux Population Health Research Centre, Inria SISTM, UMR 1219, Bordeaux, France
- CHU de Bordeaux, Pôle de Santé Publique, Service d'Information Médicale, Bordeaux, France
| | - Yves Lévy
- Vaccine Research Institute, Université Paris-Est Créteil, Faculté de Médecine, INSERM U955, Team 16, Créteil, France.
- Assistance Publique-Hôpitaux de Paris, Service Immunologie Clinique, Groupe Henri-Mondor Albert-Chenevier, Créteil, France.
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19
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Müller S, Schultze JL. Systems analysis of human innate immunity in COVID-19. Semin Immunol 2023; 68:101778. [PMID: 37267758 PMCID: PMC10201327 DOI: 10.1016/j.smim.2023.101778] [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: 02/02/2023] [Revised: 05/13/2023] [Accepted: 05/13/2023] [Indexed: 06/04/2023]
Abstract
Recent developments in sequencing technologies, the computer and data sciences, as well as increasingly high-throughput immunological measurements have made it possible to derive holistic views on pathophysiological processes of disease and treatment effects directly in humans. We and others have illustrated that incredibly predictive data for immune cell function can be generated by single cell multi-omics (SCMO) technologies and that these technologies are perfectly suited to dissect pathophysiological processes in a new disease such as COVID-19, triggered by SARS-CoV-2 infection. Systems level interrogation not only revealed the different disease endotypes, highlighted the differential dynamics in context of disease severity, and pointed towards global immune deviation across the different arms of the immune system, but was already instrumental to better define long COVID phenotypes, suggest promising biomarkers for disease and therapy outcome predictions and explains treatment responses for the widely used corticosteroids. As we identified SCMO to be the most informative technologies in the vest to better understand COVID-19, we propose to routinely include such single cell level analysis in all future clinical trials and cohorts addressing diseases with an immunological component.
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Affiliation(s)
- Sophie Müller
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Genomics & Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics & Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE and University of Bonn, Bonn, Germany.
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20
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Buccino F, Zagra L, Longo E, D'Amico L, Banfi G, Berto F, Tromba G, Vergani LM. Osteoporosis and Covid-19: Detected similarities in bone lacunar-level alterations via combined AI and advanced synchrotron testing. MATERIALS & DESIGN 2023; 231:112087. [PMID: 37323219 PMCID: PMC10257887 DOI: 10.1016/j.matdes.2023.112087] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/03/2023] [Accepted: 06/09/2023] [Indexed: 06/17/2023]
Abstract
While advanced imaging strategies have improved the diagnosis of bone-related pathologies, early signs of bone alterations remain difficult to detect. The Covid-19 pandemic has brought attention to the need for a better understanding of bone micro-scale toughening and weakening phenomena. This study used an artificial intelligence-based tool to automatically investigate and validate four clinical hypotheses by examining osteocyte lacunae on a large scale with synchrotron image-guided failure assessment. The findings indicate that trabecular bone features exhibit intrinsic variability related to external loading, micro-scale bone characteristics affect fracture initiation and propagation, osteoporosis signs can be detected at the micro-scale through changes in osteocyte lacunar features, and Covid-19 worsens micro-scale porosities in a statistically significant manner similar to the osteoporotic condition. Incorporating these findings with existing clinical and diagnostic tools could prevent micro-scale damages from progressing into critical fractures.
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Affiliation(s)
- Federica Buccino
- Department of Mechanical Engineering, Politecnico di Milano, 20156, Italy
| | - Luigi Zagra
- I.R.C.C.S Ospedale Galeazzi - Sant'Ambrogio, Milano 20157, Italy
| | - Elena Longo
- Elettra-Sincrotrone Trieste SCpA, Basovizza, Trieste 34149, Italy
| | - Lorenzo D'Amico
- Elettra-Sincrotrone Trieste SCpA, Basovizza, Trieste 34149, Italy
| | - Giuseppe Banfi
- I.R.C.C.S Ospedale Galeazzi - Sant'Ambrogio, Milano 20157, Italy
| | - Filippo Berto
- Università La Sapienza, Rome 00185, Italy
- NTNU, Norway
| | - Giuliana Tromba
- Elettra-Sincrotrone Trieste SCpA, Basovizza, Trieste 34149, Italy
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21
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Qin S, Yao X, Li W, Wang C, Xu W, Gan Z, Yang Y, Zhong A, Wang B, He Z, Wu J, Wu Q, Jiang W, Han Y, Wang F, Wang Z, Ke Y, Zhao J, Gao J, Qu L, Jin P, Guan M, Xia X, Bian X. Novel insight into the underlying dysregulation mechanisms of immune cell-to-cell communication by analyzing multitissue single-cell atlas of two COVID-19 patients. Cell Death Dis 2023; 14:286. [PMID: 37087411 PMCID: PMC10122452 DOI: 10.1038/s41419-023-05814-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/28/2023] [Accepted: 04/14/2023] [Indexed: 04/24/2023]
Abstract
How does SARS-CoV-2 cause lung microenvironment disturbance and inflammatory storm is still obscure. We here performed the single-cell transcriptome sequencing from lung, blood, and bone marrow of two dead COVID-19 patients and detected the cellular communication among them. Our results demonstrated that SARS-CoV-2 infection increase the frequency of cellular communication between alveolar type I cells (AT1) or alveolar type II cells (AT2) and myeloid cells triggering immune activation and inflammation microenvironment and then induce the disorder of fibroblasts, club, and ciliated cells, which may cause increased pulmonary fibrosis and mucus accumulation. Further study showed that the increase of T cells in the lungs may be mainly recruited by myeloid cells through ligands/receptors (e.g., ANXA1/FPR1, C5AR1/RPS19, and CCL5/CCR1). Interestingly, we also found that certain ligands/receptors (e.g., ANXA1/FPR1, CD74/COPA, CXCLs/CXCRs, ALOX5/ALOX5AP, CCL5/CCR1) are significantly activated and shared among lungs, blood and bone marrow of COVID-19 patients, implying that the dysregulation of ligands/receptors may lead to immune cell's activation, migration, and the inflammatory storm in different tissues of COVID-19 patients. Collectively, our study revealed a possible mechanism by which the disorder of cell communication caused by SARS-CoV-2 infection results in the lung inflammatory microenvironment and systemic immune responses across tissues in COVID-19 patients.
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Affiliation(s)
- Shijie Qin
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
- Laboratory for Comparative Genomics and Bioinformatics, College of Life Science, Nanjing Normal University, 210046, Nanjing, Jiangsu, China
| | - Xiaohong Yao
- Institute of Pathology, Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
| | - Weiwei Li
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Canbiao Wang
- Laboratory for Comparative Genomics and Bioinformatics, College of Life Science, Nanjing Normal University, 210046, Nanjing, Jiangsu, China
| | - Weijun Xu
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
- Department of Gastroenterology, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Zhenhua Gan
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
| | - Yang Yang
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Aifang Zhong
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
- Medical Technical Support Division, the 904th Hospital, 213003, Changzhou, Jiangsu, China
| | - Bin Wang
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
- Department of Gastroenterology, Daping Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Zhicheng He
- Institute of Pathology, Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
| | - Jian Wu
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Qiuyue Wu
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Weijun Jiang
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Ying Han
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Fan Wang
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Zhihua Wang
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
- Department of Laboratory Medicine and Blood Transfusion, the 907th Hospital, 350702, Nanping, Fujian, China
| | - Yuehua Ke
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
- Chinese PLA Center for Disease Control and Prevention, 100070, Beijing, China
| | - Jun Zhao
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China
| | - Junyin Gao
- Pulmonary and Critical Care Medicine, Yancheng No.1 People's Hospital, 224000, Yancheng, Jiangsu, China
| | - Liang Qu
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China
- Department of Laboratory Medicine, 920 Hospital of the Joint Service Support Force of the Chinese People's Liberation Army, 650032, Kunming, Yunnan, China
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics, College of Life Science, Nanjing Normal University, 210046, Nanjing, Jiangsu, China
| | - Miao Guan
- Laboratory for Comparative Genomics and Bioinformatics, College of Life Science, Nanjing Normal University, 210046, Nanjing, Jiangsu, China.
| | - Xinyi Xia
- Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangsu, China.
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China.
| | - Xiuwu Bian
- Institute of Pathology, Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China.
- Joint Expert Group for COVID-19, Department of Laboratory Medicine & Blood Transfusion, Wuhan Huoshenshan Hospital, 430100, Wuhan, Hubei, China.
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22
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Rodriguez-Rodriguez L, Gillet L, Machiels B. Shaping of the alveolar landscape by respiratory infections and long-term consequences for lung immunity. Front Immunol 2023; 14:1149015. [PMID: 37081878 PMCID: PMC10112541 DOI: 10.3389/fimmu.2023.1149015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/15/2023] [Indexed: 04/07/2023] Open
Abstract
Respiratory infections and especially viral infections, along with other extrinsic environmental factors, have been shown to profoundly affect macrophage populations in the lung. In particular, alveolar macrophages (AMs) are important sentinels during respiratory infections and their disappearance opens a niche for recruited monocytes (MOs) to differentiate into resident macrophages. Although this topic is still the focus of intense debate, the phenotype and function of AMs that recolonize the niche after an inflammatory insult, such as an infection, appear to be dictated in part by their origin, but also by local and/or systemic changes that may be imprinted at the epigenetic level. Phenotypic alterations following respiratory infections have the potential to shape lung immunity for the long-term, leading to beneficial responses such as protection against allergic airway inflammation or against other infections, but also to detrimental responses when associated with the development of immunopathologies. This review reports the persistence of virus-induced functional alterations in lung macrophages, and discusses the importance of this imprinting in explaining inter-individual and lifetime immune variation.
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23
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Fisher L, Asnani M. Acute kidney injury in Jamaicans with sickle cell disease hospitalized with COVID-19 infection. EJHAEM 2023; 4:37-44. [PMID: 36819174 PMCID: PMC9928646 DOI: 10.1002/jha2.636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 06/18/2023]
Abstract
Despite a high occurrence of acute kidney injury (AKI) with COVID-19 infection, there are no data on its incidence in sickle cell disease (SCD). We performed a single-center retrospective chart review of persons aged >1 year with SCD, COVID-19 infection and no prior dialysis requirement hospitalized from June 1, 2020 to May 31, 2022. Demographics, clinical, laboratory characteristics and outcomes were abstracted. AKI was defined using Kidney Disease Improving Global Outcomes (KDIGO) criteria. Of 38 patients meeting study criteria (60.6% female, mean age ± SD 38.6 ± 15.9 years), 3 (7.9%) were COVID vaccinated. Fifty-five percent (55%) developed AKI with 7.9% (n = 3) requiring dialysis. Participants with AKI were older (44.9 versus 30.8 years, p = 0.005), with a higher proportion having baseline chronic kidney disease (52% versus 0%, p = 0.001). Severe COVID infection [age-adjusted odds ratio (aOR): 8.93, 95%CI: 1.73-45.99, p = 0.033], red cell transfusion (aOR 7.92, 1.47-42.69) and decrease in hemoglobin per unit from baseline (aOR 2.85, 1.24-2.28) were associated with AKI. Five persons died in hospital, with AKI resulting in higher median length of stay (12 versus 5 days, p = 0.007). Targeted COVID-19 preventative measures and multinational longitudinal studies to ascertain the impact of AKI and COVID-19 infection in SCD are needed.
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Affiliation(s)
- Lori‐Ann Fisher
- Department of MedicineThe University of the West IndiesMonaKingstonJamaica
- Caribbean Institute for Health ResearchThe University of the West IndiesMonaKingstonJamaica
| | - Monika Asnani
- Caribbean Institute for Health ResearchThe University of the West IndiesMonaKingstonJamaica
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24
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Prado CADS, Fonseca DLM, Singh Y, Filgueiras IS, Baiocchi GC, Plaça DR, Marques AHC, Dantas-Komatsu RCS, Usuda JN, Freire PP, Salgado RC, Napoleao SMDS, Ramos RN, Rocha V, Zhou G, Catar R, Moll G, Camara NOS, de Miranda GC, Calich VLG, Giil LM, Mishra N, Tran F, Luchessi AD, Nakaya HI, Ochs HD, Jurisica I, Schimke LF, Cabral-Marques O. Integrative systems immunology uncovers molecular networks of the cell cycle that stratify COVID-19 severity. J Med Virol 2023; 95:e28450. [PMID: 36597912 PMCID: PMC10107240 DOI: 10.1002/jmv.28450] [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: 10/13/2022] [Revised: 11/24/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023]
Abstract
Several perturbations in the number of peripheral blood leukocytes, such as neutrophilia and lymphopenia associated with Coronavirus disease 2019 (COVID-19) severity, point to systemic molecular cell cycle alterations during severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. However, the landscape of cell cycle alterations in COVID-19 remains primarily unexplored. Here, we performed an integrative systems immunology analysis of publicly available proteome and transcriptome data to characterize global changes in the cell cycle signature of COVID-19 patients. We found significantly enriched cell cycle-associated gene co-expression modules and an interconnected network of cell cycle-associated differentially expressed proteins (DEPs) and genes (DEGs) by integrating the molecular data of 1469 individuals (981 SARS-CoV-2 infected patients and 488 controls [either healthy controls or individuals with other respiratory illnesses]). Among these DEPs and DEGs are several cyclins, cell division cycles, cyclin-dependent kinases, and mini-chromosome maintenance proteins. COVID-19 patients partially shared the expression pattern of some cell cycle-associated genes with other respiratory illnesses but exhibited some specific differential features. Notably, the cell cycle signature predominated in the patients' blood leukocytes (B, T, and natural killer cells) and was associated with COVID-19 severity and disease trajectories. These results provide a unique global understanding of distinct alterations in cell cycle-associated molecules in COVID-19 patients, suggesting new putative pathways for therapeutic intervention.
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Affiliation(s)
- Caroline Aliane de Souza Prado
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Dennyson Leandro M Fonseca
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, Brazil
| | - Youvika Singh
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Gabriela Crispim Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandre H C Marques
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Júlia N Usuda
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula Paccielli Freire
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ranieri Coelho Salgado
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Rodrigo Nalio Ramos
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil.,Instituto D'Or de Ensino e Pesquisa, Hospital São Luiz, São Paulo, Brazil
| | - Vanderson Rocha
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil.,Instituto D'Or de Ensino e Pesquisa, Hospital São Luiz, São Paulo, Brazil.,Fundação Pró-Sangue-Hemocentro de São Paulo, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil.,Department of Hematology, Churchill Hospital, University of Oxford, Oxford, UK
| | - Guangyan Zhou
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Rusan Catar
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
| | - Guido Moll
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany.,Berlin Institute of Health (BIH) and Berlin Center for Regenerative Therapies (BCRT), Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin-Brandenburg School for Regenerative Therapies (BSRT), all Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | - Gustavo Cabral de Miranda
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vera Lúcia Garcia Calich
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lasse M Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany.,Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andre Ducati Luchessi
- Department of Clinical and Toxicology Analysis, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Instituto Israelita de Ensino e Pesquisa Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Research Institute, Seattle, Washington, USA
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.,Departments of Medical Biophysics and Computer Science, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.,Krembil Research Institute, UHN, Data Science Discovery Centre, Toronto, Ontario, Canada
| | - Lena F Schimke
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Otavio Cabral-Marques
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Pharmacy and Postgraduate Program of Health and Science, Federal University of Rio Grande do Norte, Natal, Brazil.,Department of Medicine, Division of Molecular Medicine, University of São Paulo School of Medicine, São Paulo, Brazil.,Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, São Paulo, Brazil
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25
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Siegenthaler AG, Ghelani G, Brady A, Loon T, Madhira BR. Hematologic Abnormalities After COVID-19 Infection: A Case of Coombs-Negative Hemolytic Anemia and Thrombocytopenia. J Investig Med High Impact Case Rep 2023; 11:23247096231207687. [PMID: 37882166 PMCID: PMC10604495 DOI: 10.1177/23247096231207687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023] Open
Abstract
The occurrence of hemolytic anemia in patients with active SARS-CoV-2 infection has been documented in medical literature. While relatively uncommon, there have been instances where this condition presents as a Coombs-negative hemolytic anemia. In this research study, we report a distinctive case of Coombs-negative hemolytic anemia and thrombocytopenia in a patient with a known history of COVID-19 infection. The patient demonstrated a favorable response to treatment involving the administration of steroids and intravenous immunoglobulin (IVIG) therapy. This case adds to the existing body of evidence regarding the hematological manifestations of SARS-CoV-2 infection, highlighting the importance of considering and managing hematological complications in patients with COVID-19.
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Affiliation(s)
| | - Ghanshyam Ghelani
- State University of New York Upstate Medical University, Syracuse, USA
| | - Amy Brady
- State University of New York Upstate Medical University, Syracuse, USA
| | - Taylor Loon
- State University of New York Upstate Medical University, Syracuse, USA
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26
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Ratnasiri K, Wilk AJ, Lee MJ, Khatri P, Blish CA. Single-cell RNA-seq methods to interrogate virus-host interactions. Semin Immunopathol 2023; 45:71-89. [PMID: 36414692 PMCID: PMC9684776 DOI: 10.1007/s00281-022-00972-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The twenty-first century has seen the emergence of many epidemic and pandemic viruses, with the most recent being the SARS-CoV-2-driven COVID-19 pandemic. As obligate intracellular parasites, viruses rely on host cells to replicate and produce progeny, resulting in complex virus and host dynamics during an infection. Single-cell RNA sequencing (scRNA-seq), by enabling broad and simultaneous profiling of both host and virus transcripts, represents a powerful technology to unravel the delicate balance between host and virus. In this review, we summarize technological and methodological advances in scRNA-seq and their applications to antiviral immunity. We highlight key scRNA-seq applications that have enabled the understanding of viral genomic and host response heterogeneity, differential responses of infected versus bystander cells, and intercellular communication networks. We expect further development of scRNA-seq technologies and analytical methods, combined with measurements of additional multi-omic modalities and increased availability of publicly accessible scRNA-seq datasets, to enable a better understanding of viral pathogenesis and enhance the development of antiviral therapeutics strategies.
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Affiliation(s)
- Kalani Ratnasiri
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Aaron J. Wilk
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Madeline J. Lee
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Purvesh Khatri
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Medicine, Center for Biomedical Informatics Research, Stanford, CA, USA. .,Inflammatix, Inc., Sunnyvale, CA, 94085, USA.
| | - Catherine A. Blish
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.499295.a0000 0004 9234 0175Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
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27
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Wang X, Yin X, Zhang B, Liu C, Lin Y, Huang X, Li Y, Shen C, Zheng W, Fu G, Chen J, Wen Y, Zhang W, Pan BS, Fang M, Zheng Z, Zhang Z, Yuan Q, Fu G, Li S, Zhang J, Chen Y, Xia N, Zhao Q. A prophylactic effect of aluminium-based adjuvants against respiratory viruses via priming local innate immunity. Emerg Microbes Infect 2022; 11:914-925. [PMID: 35254215 PMCID: PMC8967214 DOI: 10.1080/22221751.2022.2050951] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Infection caused by respiratory viruses can lead to a severe respiratory disease and even death. Vaccination is the most effective way to prevent the disease, but it cannot be quickly applied when facing an emerging infectious disease. Here, we demonstrated that immunization with an aluminium-zinc hybrid particulate adjuvant (FH-001) alone, bearing great resemblance in morphology with commonly used aluminium-based adjuvants in vaccines, could quickly induce mice to generate a broadly protective immune response to resist the lethal challenge of influenza B viruses. Furthermore, a multi-omics-based analysis revealed that the alveolar macrophage and type I interferon pathway, rather than adaptive immunity and type II interferon pathway, were essential for the observed prophylactic effect of FH-001. More importantly, a similar protective effect was observed against influenza A virus strain A/Shanghai/02/2013(H7N9), A/California/04/2009(H1N1) and respiratory syncytial virus. Therefore, we introduced here a new and promising strategy that can be quickly applied during the outbreak of emerging respiratory viruses.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China.,Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Xiaochen Yin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Boya Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Chenfeng Liu
- Department of Cell Biology, School of Life Science, Anhui Medical University, Hefei, People's Republic of China
| | - Yahua Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Xiaofen Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Yufang Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Chenguang Shen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Weibin Zheng
- School of Life Science, Xiamen University, Xiamen, People's Republic of China
| | - Guofeng Fu
- School of Life Science, Xiamen University, Xiamen, People's Republic of China
| | - Junyu Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Yanling Wen
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Wei Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | | | - Mujin Fang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Zizheng Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Quan Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Guo Fu
- School of Life Science, Xiamen University, Xiamen, People's Republic of China
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Yixin Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China
| | - Qinjian Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, People's Republic of China.,College of Pharmacy, Chongqing Medical University, Chongqing, People's Republic of China
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28
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Gelon L, Fromont L, Lefrançais E. Occurrence and role of lung megakaryocytes in infection and inflammation. Front Immunol 2022; 13:1029223. [PMID: 36524131 PMCID: PMC9745136 DOI: 10.3389/fimmu.2022.1029223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
Megakaryocytes (MKs) are large cells giving rise to platelets. It is well established that in adults, MKs develop from hematopoietic stem cells and reside in the bone marrow. MKs are also rare but normal constituents of the venous blood returning to the lungs, and MKs are found in the lung vasculature (MKcirc), suggesting that these cells are migrants from the bone marrow and get trapped in lung capillaries where the final steps of platelet production can occur. An unprecedented increase in the number of lung and circulating MKs was described in coronavirus disease 2019 (COVID-19) patients, suggesting that lung thrombopoiesis may be increased during lung infection and/or thromboinflammation. In addition to the population of platelet-producing intravascular MKs in the lung, a population of lung-resident megakaryocytes (MKL) has been identified and presents a specific immune signature compared to its bone marrow counterparts. Recent single-cell analysis and intravital imaging have helped us gain a better understanding of these populations in mouse and human. This review aims at summarizing the recent data on increased occurrence of lung MKs and discusses their origin, specificities, and potential role in homeostasis and inflammatory and infectious lung diseases. Here, we address remaining questions, controversies, and methodologic challenges for further studies of both MKcirc and MKL.
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29
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Qin R, Kurz E, Chen S, Zeck B, Chiribogas L, Jackson D, Herchen A, Attia T, Carlock M, Rapkiewicz A, Bar-Sagi D, Ritchie B, Ross TM, Mahal LK. α2,6-Sialylation Is Upregulated in Severe COVID-19, Implicating the Complement Cascade. ACS Infect Dis 2022; 8:2348-2361. [PMID: 36219583 PMCID: PMC9578644 DOI: 10.1021/acsinfecdis.2c00421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Indexed: 01/29/2023]
Abstract
Better understanding of the molecular mechanisms underlying COVID-19 severity is desperately needed in current times. Although hyper-inflammation drives severe COVID-19, precise mechanisms triggering this cascade and what role glycosylation might play therein are unknown. Here we report the first high-throughput glycomic analysis of COVID-19 plasma samples and autopsy tissues. We find that α2,6-sialylation is upregulated in the plasma of patients with severe COVID-19 and in autopsied lung tissue. This glycan motif is enriched on members of the complement cascade (e.g., C5, C9), which show higher levels of sialylation in severe COVID-19. In the lung tissue, we observe increased complement deposition, associated with elevated α2,6-sialylation levels, corresponding to elevated markers of poor prognosis (IL-6) and fibrotic response. We also observe upregulation of the α2,6-sialylation enzyme ST6GAL1 in patients who succumbed to COVID-19. Our work identifies a heretofore undescribed relationship between sialylation and complement in severe COVID-19, potentially informing future therapeutic development.
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Affiliation(s)
- Rui Qin
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Emma Kurz
- Department
of Cell Biology, NYU Grossman School of
Medicine, 550 First Avenue, New York, New York 10016, United
States
| | - Shuhui Chen
- Department
of Chemistry, Biomedical Research Institute, New York University, New York, New York10003, United States
| | - Briana Zeck
- Center
for Biospecimen Research and Development, NYU Langone, New York, New York 10016, United
States
| | - Luis Chiribogas
- Center
for Biospecimen Research and Development, NYU Langone, New York, New York 10016, United
States
| | - Dana Jackson
- University
of Alberta Hospital, Edmonton, Alberta T6G 2B7, Canada
| | - Alex Herchen
- University
of Alberta Hospital, Edmonton, Alberta T6G 2B7, Canada
| | - Tyson Attia
- University
of Alberta Hospital, Edmonton, Alberta T6G 2B7, Canada
| | - Michael Carlock
- Center for
Vaccines and Immunology, University of Georgia, Athens, Georgia 30605, United States
| | - Amy Rapkiewicz
- Department
of Pathology, NYU Long Island School of
Medicine, Mineola, New York 11501, United
States
| | - Dafna Bar-Sagi
- Department
of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York 10016, United States
| | - Bruce Ritchie
- University
of Alberta Hospital, Edmonton, Alberta T6G 2B7, Canada
| | - Ted M. Ross
- Center for
Vaccines and Immunology, University of Georgia, Athens, Georgia 30605, United States
| | - Lara K. Mahal
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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30
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Skewed fate and hematopoiesis of CD34 + HSPCs in umbilical cord blood amid the COVID-19 pandemic. iScience 2022; 25:105544. [PMID: 36406860 PMCID: PMC9650991 DOI: 10.1016/j.isci.2022.105544] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/11/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022] Open
Abstract
Umbilical cord blood (UCB) is an irreplaceable source for hematopoietic stem progenitor cells (HSPCs). However, the effects of SARS-CoV-2 infection and COVID-19 vaccination on UCB phenotype, specifically the HSPCs therein, are currently unknown. We thus evaluated any effects of SARS-CoV-2 infection and/or COVID-19 vaccination from the mother on the fate and functionalities of HSPCs in the UCB. The numbers and frequencies of HSPCs in the UCB decreased significantly in donors with previous SARS-CoV-2 infection and more so with COVID-19 vaccination via the induction of apoptosis, likely mediated by IFN-γ-dependent pathways. Two independent hematopoiesis assays, a colony forming unit assay and a mouse humanization assay, revealed skewed hematopoiesis of HSPCs obtained from donors delivered from mothers with SARS-CoV-2 infection history. These results indicate that SARS-CoV-2 infection and COVID-19 vaccination impair the functionalities and survivability of HSPCs in the UCB, which would make unprecedented concerns on the future of HSPC-based therapies.
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31
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Kiselevskiy MV, Anisimova NY, Bilan MI, Usov AI, Ustyuzhanina NE, Petkevich AA, Shubina IZ, Morozevich GE, Nifantiev NE. Prospects for the Use of Marine Sulfated Fucose-Rich Polysaccharides in Treatment and Prevention of COVID-19 and Post-COVID-19 Syndrome. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022; 48:1109-1122. [PMID: 36325402 PMCID: PMC9584273 DOI: 10.1134/s1068162022060152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/18/2022] [Accepted: 07/29/2022] [Indexed: 01/03/2023]
Abstract
Symptoms of the new coronavirus infection that appeared in 2019 (COVID-19) range from low fever and fatigue to acute pneumonia and multiple organ failure. The clinical picture of COVID-19 is heterogeneous and involves most physiological systems; therefore, drugs with a wide spectrum of mechanism of action are required. The choice of the treatment strategy for post-COVID-19 syndrome is still a challenge to be resolved. Polysaccharides with a high fucose content derived from seaweed and marine animals can form the basis for the subsequent development of promising agents for the treatment of COVID-19 and post-COVID-19 syndrome. This class of biopolymers is characterized by a variety of biological activities, including antiviral, antithrombotic, anticoagulant, hemo-stimulating, anti-inflammatory and immune-regulatory. Low molecular weight derivatives of these polysaccharides, as well as synthetic oligosaccharides with a sufficient amount and sulfation type may be considered as the most promising compounds due to their better bioavailability, which undoubtedly increases their therapeutic potential.
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Affiliation(s)
- M. V. Kiselevskiy
- Blokhin National Medical Research Center of Oncology, 115552 Moscow, Russia
| | - N. Yu. Anisimova
- Blokhin National Medical Research Center of Oncology, 115552 Moscow, Russia
| | - M. I. Bilan
- Laboratory of Glycoconjugate Chemistry, Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A. I. Usov
- Laboratory of Glycoconjugate Chemistry, Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - N. E. Ustyuzhanina
- Laboratory of Glycoconjugate Chemistry, Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A. A. Petkevich
- Blokhin National Medical Research Center of Oncology, 115552 Moscow, Russia
| | - I. Zh. Shubina
- Blokhin National Medical Research Center of Oncology, 115552 Moscow, Russia
| | - G. E. Morozevich
- Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - N. E. Nifantiev
- Laboratory of Glycoconjugate Chemistry, Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
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32
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Tyrkalska SD, Martínez-López A, Arroyo AB, Martínez-Morcillo FJ, Candel S, García-Moreno D, Mesa-del-Castillo P, Cayuela ML, Mulero V. Differential proinflammatory activities of Spike proteins of SARS-CoV-2 variants of concern. SCIENCE ADVANCES 2022; 8:eabo0732. [PMID: 36112681 PMCID: PMC9481140 DOI: 10.1126/sciadv.abo0732] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic turned the whole world upside down in a short time. One of the main challenges faced has been to understand COVID-19-associated life-threatening hyperinflammation, the so-called cytokine storm syndrome (CSS). We report here the proinflammatory role of Spike (S) proteins from different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern in zebrafish. We found that wild-type/Wuhan variant S1 (S1WT) promoted neutrophil and macrophage recruitment, local and systemic hyperinflammation, emergency myelopoiesis, and hemorrhages. In addition, S1γ was more proinflammatory S1δ was less proinflammatory than S1WT, and, notably, S1β promoted delayed and long-lasting inflammation. Pharmacological inhibition of the canonical inflammasome alleviated S1-induced inflammation and emergency myelopoiesis. In contrast, genetic inhibition of angiotensin-converting enzyme 2 strengthened the proinflammatory activity of S1, and angiotensin (1-7) fully rescued S1-induced hyperinflammation and hemorrhages. These results shed light into the mechanisms orchestrating the COVID-19-associated CSS and the host immune response to different SARS-CoV-2 S protein variants.
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Affiliation(s)
- Sylwia D. Tyrkalska
- Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Corresponding author. (S.D.T.); (M.L.C); (V.M.)
| | - Alicia Martínez-López
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana B. Arroyo
- Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Francisco J. Martínez-Morcillo
- Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Sergio Candel
- Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Diana García-Moreno
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Pablo Mesa-del-Castillo
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain
| | - María L. Cayuela
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain
- Corresponding author. (S.D.T.); (M.L.C); (V.M.)
| | - Victoriano Mulero
- Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Corresponding author. (S.D.T.); (M.L.C); (V.M.)
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33
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Liu W, Jia J, Dai Y, Chen W, Pei G, Yan Q, Zhao Z. Delineating COVID-19 immunological features using single-cell RNA sequencing. Innovation (N Y) 2022; 3:100289. [PMID: 35879967 PMCID: PMC9299978 DOI: 10.1016/j.xinn.2022.100289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/16/2022] [Indexed: 11/24/2022] Open
Abstract
Understanding the molecular mechanisms of coronavirus disease 2019 (COVID-19) pathogenesis and immune response is vital for developing therapies. Single-cell RNA sequencing has been applied to delineate the cellular heterogeneity of the host response toward COVID-19 in multiple tissues and organs. Here, we review the applications and findings from over 80 original COVID-19 single-cell RNA sequencing studies as well as many secondary analysis studies. We describe that single-cell RNA sequencing reveals multiple features of COVID-19 patients with different severity, including cell populations with proportional alteration, COVID-19-induced genes and pathways, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in single cells, and adaptation of immune repertoire. We also collect published single-cell RNA sequencing datasets from original studies. Finally, we discuss the limitations in current studies and perspectives for future advance.
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Affiliation(s)
- Wendao Liu
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Johnathan Jia
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Wenhao Chen
- Immunobiology and Transplant Science Center, Department of Surgery, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Surgery, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Qiheng Yan
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
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Abstract
PURPOSE OF REVIEW Although COVID-19 was originally characterized as a respiratory disease, recent findings have shown lingering side effects in those who have recovered, and much is still unknown about the long-term consequences of the illness. Thus, the potential of unearthing multi-system dysfunction is high, with current data revealing significant impacts on musculoskeletal health. RECENT FINDINGS Multiple animal models of COVID-19 infection have revealed significant post-infection bone loss at several different skeletal sites. While how this loss occurred is unknown, this current review discusses the primary bone loss studies, and examines the possible mechanisms of action including: direct infection of bone marrow macrophages or hematopoietic progenitors, a proinflammatory response as a result of the COVID-19 induced cytokine storm, and/or a result of hypoxia and oxidative stress. This review will further examine how therapeutics used to treat COVID-19 affect the skeletal system. Finally, this review will examine the possible consequence that delayed care and limited healthcare accessibility has on musculoskeletal-related patient outcomes. It is important to investigate the potential impact COVID-19 infection has on musculoskeletal health.
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Affiliation(s)
- Olatundun D Awosanya
- Department of Orthopaedic Surgery, Indiana University School of Medicine, 635 Barnhill Drive, MS 549, Indianapolis, IN, 46202, USA
| | - Ushashi C Dadwal
- Department of Orthopaedic Surgery, Indiana University School of Medicine, 635 Barnhill Drive, MS 549, Indianapolis, IN, 46202, USA
| | - Erik A Imel
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Qigui Yu
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Melissa A Kacena
- Department of Orthopaedic Surgery, Indiana University School of Medicine, 635 Barnhill Drive, MS 549, Indianapolis, IN, 46202, USA.
- Roudebush VA Medical Center, Indianapolis, IN, USA.
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35
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Drug-Target Network Study Reveals the Core Target-Protein Interactions of Various COVID-19 Treatments. Genes (Basel) 2022; 13:genes13071210. [PMID: 35885993 PMCID: PMC9316565 DOI: 10.3390/genes13071210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 02/04/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has caused a dramatic loss of human life and devastated the worldwide economy. Numerous efforts have been made to mitigate COVID-19 symptoms and reduce the death rate. We conducted literature mining of more than 250 thousand published works and curated the 174 most widely used COVID-19 medications. Overlaid with the human protein-protein interaction (PPI) network, we used Steiner tree analysis to extract a core subnetwork that grew from the pharmacological targets of ten credible drugs ascertained by the CTD database. The resultant core subnetwork consisted of 34 interconnected genes, which were associated with 36 drugs. Immune cell membrane receptors, the downstream cellular signaling cascade, and severe COVID-19 symptom risk were significantly enriched for the core subnetwork genes. The lung mast cell was most enriched for the target genes among 1355 human tissue-cell types. Human bronchoalveolar lavage fluid COVID-19 single-cell RNA-Seq data highlighted the fact that T cells and macrophages have the most overlapping genes from the core subnetwork. Overall, we constructed an actionable human target-protein module that mainly involved anti-inflammatory/antiviral entry functions and highly overlapped with COVID-19-severity-related genes. Our findings could serve as a knowledge base for guiding drug discovery or drug repurposing to confront the fast-evolving SARS-CoV-2 virus and other severe infectious diseases.
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36
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Shi K, Li H, Chang T, He W, Kong Y, Qi C, Li R, Huang H, Zhu Z, Zheng P, Ruan Z, Zhou J, Shi FD, Liu Q. Bone marrow hematopoiesis drives multiple sclerosis progression. Cell 2022; 185:2234-2247.e17. [PMID: 35709748 DOI: 10.1016/j.cell.2022.05.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/01/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022]
Abstract
Multiple sclerosis (MS) is a T cell-mediated autoimmune disease of the central nervous system (CNS). Bone marrow hematopoietic stem and progenitor cells (HSPCs) rapidly sense immune activation, yet their potential interplay with autoreactive T cells in MS is unknown. Here, we report that bone marrow HSPCs are skewed toward myeloid lineage concomitant with the clonal expansion of T cells in MS patients. Lineage tracing in experimental autoimmune encephalomyelitis, a mouse model of MS, reveals remarkable bone marrow myelopoiesis with an augmented output of neutrophils and Ly6Chigh monocytes that invade the CNS. We found that myelin-reactive T cells preferentially migrate into the bone marrow compartment in a CXCR4-dependent manner. This aberrant bone marrow myelopoiesis involves the CCL5-CCR5 axis and augments CNS inflammation and demyelination. Our study suggests that targeting the bone marrow niche presents an avenue to treat MS and other autoimmune disorders.
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Affiliation(s)
- Kaibin Shi
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin 300052, China; Center for Neurological Diseases, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Handong Li
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ting Chang
- Department of Neurology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, China
| | - Wenyan He
- Center for Neurological Diseases, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Ying Kong
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Caiyun Qi
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ran Li
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Huachen Huang
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zhibao Zhu
- Department of Neurology, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Pei Zheng
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zhe Ruan
- Department of Neurology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi 710038, China
| | - Jie Zhou
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Fu-Dong Shi
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin 300052, China; Center for Neurological Diseases, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Qiang Liu
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin 300052, China.
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37
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Balandrán JC, Zamora-Herrera G, Romo-Rodríguez R, Pelayo R. Emergency Hematopoiesis in the Pathobiology of COVID-19: The Dark Side of an Early Innate Protective Mechanism. J Interferon Cytokine Res 2022; 42:393-405. [PMID: 35675647 DOI: 10.1089/jir.2022.0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The recognition of pathogens to which we are constantly exposed induces the immediate replenishment of innate immune cells from the most primitive stages of their development through emergency hematopoiesis, a central mechanism contributing to early infection control. However, as with other protective mechanisms, its functional success is at risk when the excess of inducing signals accelerates immunological catastrophes. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection exhibits a clinical spectrum that ranges from completely asymptomatic states to fatal outcomes, with the amplification of inflammatory components being the critical point that determine the progress, complication, and severity of the disease. This review focuses on the most relevant findings that entail emergency hematopoiesis to SARS-CoV-2 infection response and revolutionize our understanding of the mechanisms governing the clinical prognosis of COVID-19. Of special interest are the metabolic or hyperinflammatory conditions in aging that exacerbate the phenomenon and favor the uncontrolled emergency myelopoiesis leading to the evolution of severe disease.
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Affiliation(s)
- Juan Carlos Balandrán
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA.,Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, New York, USA
| | - Gabriela Zamora-Herrera
- Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Rubí Romo-Rodríguez
- Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Rosana Pelayo
- Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
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38
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Chen T, Polak P, Uryasev S. Classification and severity progression measure of COVID-19 patients using pairs of multi-omic factors. J Appl Stat 2022; 50:2473-2503. [PMID: 37529561 PMCID: PMC10388828 DOI: 10.1080/02664763.2022.2064975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/06/2022] [Indexed: 10/18/2022]
Abstract
Early detection and effective treatment of severe COVID-19 patients remain two major challenges during the current pandemic. Analysis of molecular changes in blood samples of severe patients is one of the promising approaches to this problem. From thousands of proteomic, metabolomic, lipidomic, and transcriptomic biomarkers selected in other research, we identify several pairs of biomarkers that after additional nonlinear spline transformation are highly effective in classifying and predicting severe COVID-19 cases. The performance of these pairs is evaluated in-sample, in a cross-validation exercise, and in an out-of-sample analysis on two independent datasets. We further improve our classifier by identifying complementary pairs using hierarchical clustering. In a result, we achieve 96-98% AUC on the validation data. Our findings can help medical experts to identify small groups of biomarkers that after nonlinear transformation can be used to construct a cost-effective test for patient screening and prediction of severity progression.
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Affiliation(s)
- Teng Chen
- Department of Applied Math & Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Paweł Polak
- Department of Applied Math & Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Stanislav Uryasev
- Department of Applied Math & Statistics, Stony Brook University, Stony Brook, NY, USA
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39
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Bonora BM, Fogar P, Zuin J, Falaguasta D, Cappellari R, Cattelan A, Marinello S, Ferrari A, Avogaro A, Plebani M, Basso D, Fadini GP. Hyperglycemia, Reduced Hematopoietic Stem Cells, and Outcome of COVID-19. Diabetes 2022; 71:788-794. [PMID: 35061020 DOI: 10.2337/db21-0965] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/15/2022] [Indexed: 12/15/2022]
Abstract
Admission hyperglycemia has emerged worldwide as a predictor of poor coronavirus disease 2019 (COVID-19) outcome. Hyperglycemia leads to a defect in circulating hematopoietic stem/progenitor cells (HSPCs), which, in turn, predicts diabetic complications. Here, we explored whether reduced HSPCs mediated at least part of the prognostic effect of hyperglycemia on COVID-19 outcome. We found that patients with COVID-19 (n = 100) hospitalized in a nonintensive setting displayed dramatically (50-60%) reduced levels of HSPCs measured by flow cytometry as CD34+, CD34+CD45dim, or CD34+CD133+ cells, compared with control subjects (n = 595). This finding was highly significant (all P < 10-10) after multivariable adjustment, or manual 1:1 patient match, or propensity score matching. Admission hyperglycemia (≥7.0 mmol/L) was present in 45% of patients, was associated with a significant further ∼30% HSPCs reduction, and predicted a 2.6-fold increased risk of the primary outcome of adverse COVID-19 course (admittance to the intensive care unit or death). Low HSPCs were also associated with advanced age, higher peak C-reactive protein, and neutrophil-to-lymphocyte ratio. Independently from confounders, 1 SD lower CD34+ HSPCs was associated with a more than threefold higher risk of adverse outcome. Upon formal analysis, reduction of HSPCs was a significant mediator of the admission hyperglycemia on COVID-19 outcome, being responsible for 28% of its prognostic effect.
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Affiliation(s)
- Benedetta Maria Bonora
- Department of Medicine, University of Padova, Padua, Italy
- Veneto Institute of Molecular Medicine, Padua, Italy
| | - Paola Fogar
- Department of Medicine, University of Padova, Padua, Italy
| | - Jenny Zuin
- Department of Medicine, University of Padova, Padua, Italy
| | | | | | | | | | - Anna Ferrari
- Department of Medicine, University of Padova, Padua, Italy
| | - Angelo Avogaro
- Department of Medicine, University of Padova, Padua, Italy
| | - Mario Plebani
- Department of Medicine, University of Padova, Padua, Italy
| | - Daniela Basso
- Department of Medicine, University of Padova, Padua, Italy
| | - Gian Paolo Fadini
- Department of Medicine, University of Padova, Padua, Italy
- Veneto Institute of Molecular Medicine, Padua, Italy
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40
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New insights into Human Hematopoietic Stem and Progenitor Cells via Single-Cell Omics. Stem Cell Rev Rep 2022; 18:1322-1336. [PMID: 35318612 PMCID: PMC8939482 DOI: 10.1007/s12015-022-10330-2] [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] [Accepted: 01/09/2022] [Indexed: 10/25/2022]
Abstract
Residing at the apex of the hematopoietic hierarchy, hematopoietic stem and progenitor cells (HSPCs) give rise to all mature blood cells. In the last decade, significant progress has been made in single-cell RNA sequencing as well as multi-omics technologies that have facilitated elucidation of the heterogeneity of previously defined human HSPCs. From the embryonic stage through the adult stage to aging, single-cell studies have enabled us to trace the origins of hematopoietic stem cells (HSCs), demonstrating different hematopoietic differentiation during development, as well as identifying novel cell populations. In both hematological benign diseases and malignancies, single-cell omics technologies have begun to reveal tissue heterogeneity and have permitted mapping of microenvironmental ecosystems and tracking of cell subclones, thereby greatly broadening our understanding of disease development. Furthermore, advances have also been made in elucidating the molecular mechanisms for relapse and identifying therapeutic targets of hematological disorders and other non-hematological diseases. Extensive exploration of hematopoiesis at the single-cell level may thus have great potential for broad clinical applications of HSPCs, as well as disease prognosis.
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41
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Elahi S. Hematopoietic responses to SARS-CoV-2 infection. Cell Mol Life Sci 2022; 79:187. [PMID: 35284964 PMCID: PMC8918078 DOI: 10.1007/s00018-022-04220-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/03/2022] [Accepted: 02/22/2022] [Indexed: 01/09/2023]
Abstract
Under physiological conditions, hematopoietic stem and progenitor cells (HSPCs) in the bone marrow niches are responsible for the highly regulated and interconnected hematopoiesis process. At the same time, they must recognize potential threats and respond promptly to protect the host. A wide spectrum of microbial agents/products and the consequences of infection-induced mediators (e.g. cytokines, chemokines, and growth factors) can have prominent impact on HSPCs. While COVID-19 starts as a respiratory tract infection, it is considered a systemic disease which profoundly alters the hematopoietic system. Lymphopenia, neutrophilia, thrombocytopenia, and stress erythropoiesis are the hallmark of SARS-CoV-2 infection. Moreover, thrombocytopenia and blood hypercoagulability are common among COVID-19 patients with severe disease. Notably, the invasion of erythroid precursors and progenitors by SARS-CoV-2 is a cardinal feature of COVID-19 disease which may in part explain the mechanism underlying hypoxia. These pieces of evidence support the notion of skewed steady-state hematopoiesis to stress hematopoiesis following SARS-CoV-2 infection. The functional consequences of these alterations depend on the magnitude of the effect, which launches a unique hematopoietic response that is associated with increased myeloid at the expense of decreased lymphoid cells. This article reviews some of the key pathways including the infectious and inflammatory processes that control hematopoiesis, followed by a comprehensive review that summarizes the latest evidence and discusses how SARS-CoV-2 infection impacts hematopoiesis.
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Affiliation(s)
- Shokrollah Elahi
- Faculty of Medicine and Dentistry, School of Dentistry, Division of Foundational Sciences, Department of Oncology, and Li Ka Shing Institute of Virology, University of Alberta, 7020 Katz Group Centre, 11361-87th Ave NW, Edmonton, AB T6G 2E1 Canada
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