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Ren J, Gao Q, Zhou X, Chen L, Guo W, Feng K, Hu J, Huang T, Cai YD. Identification of gene and protein signatures associated with long-term effects of COVID-19 on the immune system after patient recovery by analyzing single-cell multi-omics data using a machine learning approach. Vaccine 2024; 42:126253. [PMID: 39182316 DOI: 10.1016/j.vaccine.2024.126253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 08/17/2024] [Accepted: 08/17/2024] [Indexed: 08/27/2024]
Abstract
Viral infections significantly impact the immune system, and impact will persist until recovery. However, the influence of severe acute respiratory syndrome coronavirus 2 infection on the homeostatic immune status and secondary immune response in recovered patients remains unclear. To investigate these persistent alterations, we employed five feature-ranking algorithms (LASSO, MCFS, RF, CATBoost, and XGBoost), incremental feature selection, synthetic minority oversampling technique and two classification algorithms (decision tree and k-nearest neighbors) to analyze multi-omics data (surface proteins and transcriptome) from coronavirus disease 2019 (COVID-19) recovered patients and healthy controls post-influenza vaccination. The single-cell multi-omics dataset was divided into five subsets corresponding to five immune cell subtypes: B cells, CD4+ T cells, CD8+ T cells, Monocytes, and Natural Killer cells. Each cell was represented by 28,402 scRNA-seq (RNA) features, 3 Hash Tag Oligo (HTO) features, 138 Cellular indexing of transcriptomes and epitopes by sequencing (CITE) features and 23,569 Single Cell Transform (SCT) features. Some multi-omics markers were identified and effective classifiers were constructed. Our findings indicate a distinct immune status in COVID-19 recovered patients, characterized by low expression of ribosomal protein (RPS26) and high expression of immune cell surface proteins (CD33, CD48). Notably, TMEM176B, a membrane protein, was highly expressed in monocytes of COVID-19 convalescent patients. These observations aid in discerning molecular differences among immune cell subtypes and contribute to understanding the prolonged effects of COVID-19 on the immune system, which is valuable for treating infectious diseases like COVID-19.
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Affiliation(s)
- JingXin Ren
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Qian Gao
- Department of Pharmacy, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - XianChao Zhou
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Jerry Hu
- Department of Natural Sciences and Mathematics, College of Natural and Applied Science, University of Houston - Victoria, Victoria, TX 77901, USA.
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
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Wang B, Golubov J, Oswald EM, Poon P, Wei Q, Lett C, Shehadeh F, Kaczynski M, Felix LO, Mishra B, Mylona EK, Wipperman MF, Chio E, Hamon SC, Hooper AT, Somersan-Karakaya S, Musser BJ, Petro CD, Hamilton JD, Sleeman MA, Kalliolias GD, Mylonakis E, Skokos D. Potential immunomodulatory effects of CAS+IMD monoclonal antibody cocktail in hospitalized patients with COVID-19. EBioMedicine 2024; 108:105334. [PMID: 39270622 DOI: 10.1016/j.ebiom.2024.105334] [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: 01/19/2024] [Revised: 08/19/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Passive administration of SARS-CoV-2 neutralizing monoclonal antibodies (mAbs), such as CAS + IMD (Casirivimab + Imdevimab) antibody cocktail demonstrated beneficial effects on clinical outcomes in hospitalized patients with COVID-19 who were seronegative at baseline and outpatients. However, little is known about their impact on the host immunophenotypes. METHODS We conducted an immunoprofiling study in 46 patients from a single site of a multi-site trial of CAS + IMD in hospitalized patients. We collected longitudinal samples during October 2020 ∼ April 2021, prior to the emergence of the Delta and Omicron variants and the use of COVID-19 vaccines. All collected samples were analyzed without exclusion and post-hoc statistical analysis was performed. We examined the dynamic interplay of CAS + IMD with host immunity applying dimensional reduction approach on plasma proteomics and high dimensional flow cytometry data. FINDINGS Using an unbiased clustering method, we identified unique immunophenotypes associated with acute inflammation and disease resolution. Compared to placebo group, administration of CAS + IMD accelerated the transition from an acute inflammatory immunophenotype, to a less inflammatory or "resolving" immunophenotype, as characterized by reduced tissue injury, proinflammatory markers and restored lymphocyte/monocyte imbalance independent of baseline serostatus. Moreover, CAS + IMD did not impair the magnitude or the quality of host T cell immunity against SARS-CoV-2 spike protein. INTERPRETATION Our results identified immunophenotypic changes indicative of a possible SARS-CoV-2 neutralizing antibodies-induced anti-inflammatory effect, without an evident impairment of cellular antiviral immunity, suggesting that further studies of Mabs effects on SAS-CoV-2 or other viral mediated inflammation are warranted. FUNDING Regeneron Pharmaceuticals Inc and federal funds from the Department of Health and Human Services; Administration for Strategic Preparedness and Response; Biomedical Advanced Research and Development Authority, under OT number: HHSO100201700020C.
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Affiliation(s)
- Bei Wang
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | | | - Erin M Oswald
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | - Patrick Poon
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | - Qiaozhi Wei
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | - Clarissa Lett
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | - Fadi Shehadeh
- Division of Infectious Diseases, Department of Medicine, The Brown Alpert Medical School and the Miriam Hospital, Providence, RI, USA; Department of Medicine, Houston Methodist Academic Institute, Houston, TX, 77030, USA
| | - Matthew Kaczynski
- Division of Infectious Diseases, Department of Medicine, The Brown Alpert Medical School and the Miriam Hospital, Providence, RI, USA
| | - Lewis Oscar Felix
- Division of Infectious Diseases, Department of Medicine, The Brown Alpert Medical School and the Miriam Hospital, Providence, RI, USA; Department of Medicine, Houston Methodist Academic Institute, Houston, TX, 77030, USA
| | - Biswajit Mishra
- Division of Infectious Diseases, Department of Medicine, The Brown Alpert Medical School and the Miriam Hospital, Providence, RI, USA; Department of Medicine, Houston Methodist Academic Institute, Houston, TX, 77030, USA
| | - Evangelia K Mylona
- Division of Infectious Diseases, Department of Medicine, The Brown Alpert Medical School and the Miriam Hospital, Providence, RI, USA; Department of Medicine, Houston Methodist Academic Institute, Houston, TX, 77030, USA
| | | | - Erica Chio
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | - Sara C Hamon
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | - Andrea T Hooper
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | | | - Bret J Musser
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | | | | | - Matthew A Sleeman
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | | | - Eleftherios Mylonakis
- Division of Infectious Diseases, Department of Medicine, The Brown Alpert Medical School and the Miriam Hospital, Providence, RI, USA; Department of Medicine, Houston Methodist Academic Institute, Houston, TX, 77030, USA
| | - Dimitris Skokos
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA.
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Dwivedi A, Ui Mhaonaigh A, Carroll M, Khosravi B, Batten I, Ballantine RS, Hendricken Phelan S, O'Doherty L, George AM, Sui J, Hawerkamp HC, Fallon PG, Noppe E, Mason S, Conlon N, Ni Cheallaigh C, Finlay CM, Little MA, Bioresource OBOTSJATTARS. Emergence of dysfunctional neutrophils with a defect in arginase-1 release in severe COVID-19. JCI Insight 2024; 9:e171659. [PMID: 39253969 PMCID: PMC11385094 DOI: 10.1172/jci.insight.171659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/18/2024] [Indexed: 09/11/2024] Open
Abstract
Neutrophilia occurs in patients infected with SARS-CoV-2 (COVID-19) and is predictive of poor outcomes. Here, we link heterogenous neutrophil populations to disease severity in COVID-19. We identified neutrophils with features of cellular aging and immunosuppressive capacity in mild COVID-19 and features of neutrophil immaturity and activation in severe disease. The low-density neutrophil (LDN) number in circulating blood correlated with COVID-19 severity. Many of the divergent neutrophil phenotypes in COVID-19 were overrepresented in the LDN fraction and were less detectable in normal-density neutrophils. Functionally, neutrophils from patients with severe COVID-19 displayed defects in neutrophil extracellular trap formation and reactive oxygen species production. Soluble factors secreted by neutrophils from these patients inhibited T cell proliferation. Neutrophils from patients with severe COVID-19 had increased expression of arginase-1 protein, a feature that was retained in convalescent patients. Despite this increase in intracellular expression, there was a reduction in arginase-1 release by neutrophils into serum and culture supernatants. Furthermore, neutrophil-mediated T cell suppression was independent of arginase-1. Our results indicate the presence of dysfunctional, activated, and immature neutrophils in severe COVID-19.
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Affiliation(s)
| | | | | | | | - Isabella Batten
- Department of Medical Gerontology, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | | | | | - Laura O'Doherty
- Wellcome Trust, Clinical Research Facility
- Department of Infectious Diseases; and
| | | | - Jacklyn Sui
- Department of Medical Gerontology, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
- Department of Immunology, St James's Hospital, Dublin, Ireland
| | | | - Padraic G Fallon
- School of Medicine, Trinity Biomedical Sciences Institute
- Department of Immunology, Trinity Translational Medicine Institute; and
| | - Elnè Noppe
- Department of Critical Care, Tallaght University Hospital, Trinity College Dublin, Dublin, Ireland
| | - Sabina Mason
- Department of Critical Care, Tallaght University Hospital, Trinity College Dublin, Dublin, Ireland
| | - Niall Conlon
- Department of Infectious Diseases; and
- Department of Immunology, St James's Hospital, Dublin, Ireland
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Abiri E, Mirzaii M, Moghbeli M, Atashi A, Harati AA. Investigating the relationship between lymphocyte cells apoptosis and DNA damage and oxidative stress and therapeutic and clinical outcomes of COVID-19 elderly patients. BMC Infect Dis 2024; 24:940. [PMID: 39251946 PMCID: PMC11385507 DOI: 10.1186/s12879-024-09734-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/07/2024] [Indexed: 09/11/2024] Open
Abstract
BACKGROUND While COVID-19 has been controlled and deaths have decreased, the long-term consequences of COVID-19 remain a challenge we face today. This study was conducted to determine the relationship between the apoptosis of lymphocyte cells with DNA damage and oxidative stress and the therapeutic and clinical outcomes of elderly patients with COVID-19. METHODS This study was conducted from April 2020 to May 2021 (the period of severe attacks of the epidemic peak of COVID-19) and September 2022 (the post-COVID-19 period). The study groups included elderly patients with COVID-19 hospitalized in the ICU and normal wards of the hospital as well as elderly patients with influenza. A polymerase chain reaction was used to check the validity of the studied diseases. The Annexin V/Propidium Iodide method was used to evaluate the level of apoptosis. Genotoxic effects and DNA damage were assessed by the comet assay method. Total antioxidant status (TAS), total oxidant status (TOS), and myeloperoxidase activity (MPO) were measured by photometric methods. RESULTS The highest level of apoptosis in peripheral blood lymphocytes and the highest level of DNA damage were observed at both times in the intubated-ICU and non-intubated-ICU groups. In all groups, there was a significant increase in peripheral blood lymphocyte apoptosis levels and DNA damage levels compared to the healthy control group (p < 0.01). The level of apoptosis and DNA damage decreased significantly in the post-COVID-19 period (p < 0.01). In the investigation of oxidative stress biomarkers, the oxidative stress index, including TOS and MPO levels, increased in patients (p < 0.01), and the TAS level decreased (p < 0.01). CONCLUSION It shows that the apoptosis of lymphocyte cells, DNA damage, and oxidative stress can be effective in prognostic decisions and is a suitable predictor for diagnosing the condition of patients with viral infections such as COVID-19 and influenza.
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Affiliation(s)
- Elaheh Abiri
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
| | - Mehdi Mirzaii
- Department of Biology, Haftham Tir Square - Shahroud University of Medical Sciences and Health Services, Shahroud, Iran.
| | - Majid Moghbeli
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
| | - Amir Atashi
- Department of Biology, Haftham Tir Square - Shahroud University of Medical Sciences and Health Services, Shahroud, Iran
| | - Ahad Ali Harati
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
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5
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Wang M, Zhang D, Lei T, Zhou Y, Qin H, Wu Y, Liu S, Zhang L, Jia K, Dong Y, Wang S, Li Y, Fan Y, Gui L, Dong Y, Zhang W, Li Z, Hou J. Interferon-responsive neutrophils and macrophages extricate SARS-CoV-2 Omicron critical patients from the nasty fate of sepsis. J Med Virol 2024; 96:e29889. [PMID: 39206862 DOI: 10.1002/jmv.29889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/24/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
The SARS-CoV-2 Omicron variant is characterized by its high transmissibility, which has caused a worldwide epidemiological event. Yet, it turns ominous once the disease progression degenerates into severe pneumonia and sepsis, presenting a horrendous lethality. To elucidate the alveolar immune or inflammatory landscapes of Omicron critical-ill patients, we performed single-cell RNA-sequencing (scRNA-seq) of bronchoalveolar lavage fluid (BALF) from the patients with critical pneumonia caused by Omicron infection, and analyzed the correlation between the clinical severity scores and different immune cell subpopulations. In the BALF of Omicron critical patients, the alveolar violent myeloid inflammatory environment was determined. ISG15+ neutrophils and CXCL10+ macrophages, both expressed the interferon-stimulated genes (ISGs), were negatively correlated with clinical pulmonary infection score, while septic CST7+ neutrophils and inflammatory VCAN+ macrophages were positively correlated with sequential organ failure assessment. The percentages of ISG15+ neutrophils were associated with more protective alveolar epithelial cells, and may reshape CD4+ T cells to the exhaustive phenotype, thus preventing immune injuries. The CXCL10+ macrophages may promote plasmablast/plasma cell survival and activation as well as the production of specific antibodies. As compared to the previous BALF scRNA-seq data from SARS-CoV-2 wild-type/Alpha critical patients, the subsets of neutrophils and macrophages with pro-inflammatory and immunoregulatory features presented obvious distinctions, suggesting an immune disparity in Omicron variants. Overall, this study provides a BALF single-cell atlas of Omicron critical patients, and suggests that alveolar interferon-responsive neutrophils and macrophages may extricate SARS-CoV-2 Omicron critical patients from the nasty fate of sepsis.
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Affiliation(s)
- Mu Wang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Dingji Zhang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Ting Lei
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Ye Zhou
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Hao Qin
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Second Military Medical University, Shanghai, China
| | - Yanfeng Wu
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Shuxun Liu
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Liyuan Zhang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Kaiwei Jia
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Yue Dong
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Suyuan Wang
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Yunhui Li
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Yiwen Fan
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Liangchen Gui
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Yuchao Dong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Second Military Medical University, Shanghai, China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Second Military Medical University, Shanghai, China
| | - Zhixuan Li
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
| | - Jin Hou
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Military Medical University, Shanghai, China
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6
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Francavilla B, Velletrani G, Fiorelli D, Maurantonio S, Passali FM, Schirinzi T, Bernardini S, Di Girolamo S, Nuccetelli M. Circulating calprotectin as a potential biomarker of persistent olfactory dysfunctions in Post-COVID-19 patients. Cytokine 2024; 181:156688. [PMID: 38963942 DOI: 10.1016/j.cyto.2024.156688] [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: 04/05/2024] [Revised: 06/20/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
BACKGROUND This longitudinal prospective study aims to investigate the potential of circulating calprotectin (cCLP) as a biomarker in persistent olfactory dysfunctions following COVID-19 infection. METHODS Thirty-six patients with persistent hyposmia or anosmia post COVID-19 were enrolled (HT0) and re-evaluated after three months of olfactory training (HT1). Two control groups included 18 subjects without olfactory defects post COVID-19 (CG1) and 18 healthy individuals (CG2). Nasal brushing of the olfactory cleft and blood collection were performed to assess circulating calprotectin levels. RESULTS Higher calprotectin levels were observed in serum and nasal supernatant of hyposmic patients (HT0) compared to control groups (CG1 and CG2). Post-olfactory training (HT1), olfactory function improved significantly, paralleled by decreased calprotectin levels in serum and nasal samples. Circulating calprotectin holds potential as a biomarker in persistent olfactory dysfunctions after COVID-19. The decrease in calprotectin levels post-olfactory training implies a role in monitoring and evaluating treatment responses. DISCUSSION AND CONCLUSIONS These findings contribute to the growing literature on potential biomarkers in post-COVID-19 olfactory dysfunctions and underscore the importance of investigating novel biomarkers for personalized patient management. Nevertheless, further studies are needed to validate the application of calprotectin assay in nasal diseases and its correlation with nasal cytology.
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Affiliation(s)
- Beatrice Francavilla
- Department of Otorhinolaryngology, University of Rome "Tor Vergata", Rome 00133 Italy
| | - Gianluca Velletrani
- Department of Otorhinolaryngology, University of Rome "Tor Vergata", Rome 00133 Italy.
| | - Denise Fiorelli
- Department of Experimental Medicine, University of "Tor Vergata", Rome 00133 Italy
| | - Sara Maurantonio
- Department of Otorhinolaryngology, University of Rome "Tor Vergata", Rome 00133 Italy
| | | | - Tommaso Schirinzi
- Department of Neurology, University of Rome "Tor Vergata", Rome 00133 Italy
| | - Sergio Bernardini
- Department of Experimental Medicine, University of "Tor Vergata", Rome 00133 Italy
| | - Stefano Di Girolamo
- Department of Otorhinolaryngology, University of Rome "Tor Vergata", Rome 00133 Italy
| | - Marzia Nuccetelli
- Department of Experimental Medicine, University of "Tor Vergata", Rome 00133 Italy
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7
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Friedrich VD, Pennitz P, Wyler E, Adler JM, Postmus D, Müller K, Teixeira Alves LG, Prigann J, Pott F, Vladimirova D, Hoefler T, Goekeri C, Landthaler M, Goffinet C, Saliba AE, Scholz M, Witzenrath M, Trimpert J, Kirsten H, Nouailles G. Neural network-assisted humanisation of COVID-19 hamster transcriptomic data reveals matching severity states in human disease. EBioMedicine 2024:105312. [PMID: 39317638 DOI: 10.1016/j.ebiom.2024.105312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 09/26/2024] Open
Abstract
BACKGROUND Translating findings from animal models to human disease is essential for dissecting disease mechanisms, developing and testing precise therapeutic strategies. The coronavirus disease 2019 (COVID-19) pandemic has highlighted this need, particularly for models showing disease severity-dependent immune responses. METHODS Single-cell transcriptomics (scRNAseq) is well poised to reveal similarities and differences between species at the molecular and cellular level with unprecedented resolution. However, computational methods enabling detailed matching are still scarce. Here, we provide a structured scRNAseq-based approach that we applied to scRNAseq from blood leukocytes originating from humans and hamsters affected with moderate or severe COVID-19. FINDINGS Integration of data from patients with COVID-19 with two hamster models that develop moderate (Syrian hamster, Mesocricetus auratus) or severe (Roborovski hamster, Phodopus roborovskii) disease revealed that most cellular states are shared across species. A neural network-based analysis using variational autoencoders quantified the overall transcriptomic similarity across species and severity levels, showing highest similarity between neutrophils of Roborovski hamsters and patients with severe COVID-19, while Syrian hamsters better matched patients with moderate disease, particularly in classical monocytes. We further used transcriptome-wide differential expression analysis to identify which disease stages and cell types display strongest transcriptional changes. INTERPRETATION Consistently, hamsters' response to COVID-19 was most similar to humans in monocytes and neutrophils. Disease-linked pathways found in all species specifically related to interferon response or inhibition of viral replication. Analysis of candidate genes and signatures supported the results. Our structured neural network-supported workflow could be applied to other diseases, allowing better identification of suitable animal models with similar pathomechanisms across species. FUNDING This work was supported by German Federal Ministry of Education and Research, (BMBF) grant IDs: 01ZX1304B, 01ZX1604B, 01ZX1906A, 01ZX1906B, 01KI2124, 01IS18026B and German Research Foundation (DFG) grant IDs: 14933180, 431232613.
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Affiliation(s)
- Vincent D Friedrich
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany; Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Leipzig, Germany
| | - Peter Pennitz
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany
| | - Emanuel Wyler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Julia M Adler
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
| | - Dylan Postmus
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Liverpool School of Tropical Medicine, Department of Tropical Disease Biology, Liverpool, United Kingdom
| | - Kristina Müller
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany
| | - Luiz Gustavo Teixeira Alves
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Julia Prigann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Gladstone Institutes, San Francisco, USA
| | - Fabian Pott
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Thomas Hoefler
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
| | - Cengiz Goekeri
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany; Cyprus International University, Faculty of Medicine, Nicosia, Cyprus
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany; Humboldt-Universität zu Berlin, Institut fuer Biologie, Berlin, Germany
| | - Christine Goffinet
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Liverpool School of Tropical Medicine, Department of Tropical Disease Biology, Liverpool, United Kingdom
| | - Antoine-Emmanuel Saliba
- Faculty of Medicine, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Markus Scholz
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany; University of Leipzig, Faculty of Mathematics and Computer Science, Leipzig, Germany
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany; German Center for Lung Research (DZL), Berlin, Germany
| | - Jakob Trimpert
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
| | - Holger Kirsten
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany.
| | - Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany.
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8
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Keller D, Mester P, Räth U, Krautbauer S, Schmid S, Greifenberg V, Müller M, Kunst C, Buechler C, Pavel V. Calprotectin, a Promising Serological Biomarker for the Early Diagnosis of Superinfections with Multidrug-Resistant Bacteria in Patients with COVID-19. Int J Mol Sci 2024; 25:9294. [PMID: 39273246 PMCID: PMC11394900 DOI: 10.3390/ijms25179294] [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: 08/05/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
Bacterial and fungal superinfections are common in COVID-19, and early diagnosis can enable timely intervention. Serum calprotectin levels increase with bacterial, fungal, and viral infections. This study evaluated serum calprotectin as a diagnostic and prognostic tool for microbial superinfections in COVID-19. Serum samples from adult patients with moderate and severe COVID-19 were collected during hospitalization from 2020 to 2024. Calprotectin levels were measured using an enzyme-linked immunosorbent assay in 63 patients with moderate COVID-19, 60 patients with severe COVID-19, and 34 healthy individuals. Calprotectin serum levels were elevated in patients with moderate COVID-19 compared with controls, and these levels were further increased in the severe cases. Patients with severe COVID-19 and vancomycin-resistant enterococci (VRE) bacteremia had elevated calprotectin levels, but their C-reactive protein and procalcitonin levels were not increased. Fungal superinfections and herpes simplex virus reactivation did not change the calprotectin levels. A calprotectin concentration of 31.29 µg/mL can be used to diagnose VRE bloodstream infection with 60% sensitivity and 96% specificity. These data suggest that serum calprotectin may be a promising biomarker for the early detection of VRE bloodstream infections in patients with COVID-19.
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Affiliation(s)
- Dennis Keller
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Patricia Mester
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Ulrich Räth
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Sabrina Krautbauer
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Stephan Schmid
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Verena Greifenberg
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Martina Müller
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Claudia Kunst
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Christa Buechler
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Vlad Pavel
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
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9
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Rajput Y, Neral A, Sherwani N, Jain V, Sahu M, Paikra F, Kushwaha A, Sahu A, Lodhi H, Sundrani O, Panda RK, Jain V, Shammas MA, Pal J. A novel metric-based approach of scoring early host immune response from oro-nasopharyngeal swabs predicts COVID-19 outcome. Sci Rep 2024; 14:19510. [PMID: 39174586 PMCID: PMC11341902 DOI: 10.1038/s41598-024-70161-8] [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: 02/05/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024] Open
Abstract
Unpredictable fatal outcome of COVID-19 is attributed to dysregulated inflammation. Impaired early adaptive immune response leads to late-stage inflammatory outcome. The purpose of this study was to develop biomarkers for early detection of host immune impairment at first diagnosis from leftover RNA samples, which may in turn identify high risk patients. Leftover RNA samples of COVID-19 patients at first diagnosis were stored. Following prospective follow-up, the samples were shorted and categorized into outcome groups. Impaired adaptive T cell response (severity score) and Impaired IL-10 response (undetectable IL-10 in the presence of high expression of a representative interferon response gene) were determined by RT-PCR based assay. We demonstrate that a T cell response based 'severity score' comprising rational combination of Ct values of a target genes' signature can predict high risk noncomorbid potentially critical COVID-19 patients with a sensitivity of 91% (95% CI 58.7-99.8) and specificity of 92.6% (95% CI 75.7-99) (AUC:0.88). Although inclusion of comorbid patients reduced sensitivity to 77% (95% CI 54.6-92.2), the specificity was still 94% (95% CI 79.8-99.3) (AUC:0.82). The same for 'impaired IL-10 response' were little lower to predict high risk noncomorbid patients 64.2% (95% CI 35.1-87.2) and 82% (95% CI 65.5-93.2) respectively. Inclusion of comorbid patients drastically reduce sensitivity and specificity51.6% (95% CI 33.1-69.8) and 80.5% (95% CI 64.0-91.8) respectively. As best of our knowledge this is the first demonstration of a metric-based approach showing the 'severity score' as an indicator of early adoptive immune response, could be used as predictor of severe COVID-19 outcome at the time of first diagnosis using the same leftover swab RNA. The work flow could reduce expenditure and reporting time of the prognostic test for an earliest clinical decision ensuring possibility of early rational management.
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Affiliation(s)
- Yogita Rajput
- Multidisciplinary Research Units (MRU), Pt. J.N.M. Medical College, Raipur, Chhattisgarh, 492001, India
| | - Arvind Neral
- Department of Microbiology, Pt. J.N.M. Medical College, Raipur, C.G., India
- Department of Pathology, Pt. J.N.M. Medical College, Raipur, C.G, India
| | - Nikita Sherwani
- Department of Microbiology, Pt. J.N.M. Medical College, Raipur, C.G., India
| | - Vijaylakshmi Jain
- Department of Microbiology, Pt. J.N.M. Medical College, Raipur, C.G., India
| | - Malti Sahu
- Multidisciplinary Research Units (MRU), Pt. J.N.M. Medical College, Raipur, Chhattisgarh, 492001, India
| | - Fulsay Paikra
- Multidisciplinary Research Units (MRU), Pt. J.N.M. Medical College, Raipur, Chhattisgarh, 492001, India
| | - Aarti Kushwaha
- Multidisciplinary Research Units (MRU), Pt. J.N.M. Medical College, Raipur, Chhattisgarh, 492001, India
| | - Aparna Sahu
- Department of Microbiology, Pt. J.N.M. Medical College, Raipur, C.G., India
| | - Heeramani Lodhi
- Department of Anaesthesia and Pain Management, Pt. J.N.M. Medical College, Raipur, C.G, India
| | - Omprakash Sundrani
- Department of Critical Care Medicine, Pt. J.N.M. Medical College, Raipur, C.G., India
| | - Ravindra Kumar Panda
- Department of Respiratory Medicine, Pt. J.N.M. Medical College, Raipur, C.G., India
| | - Vinit Jain
- Superintendent (past), Dr. BRAM Hospital Raipur CG and Department of Orthopaedics, Pt. J.N.M. Medical College, Raipur, C.G., India
| | - Masood A Shammas
- Department of Adult Oncology, Harvard (Dana Farber) Cancer Institute and VA Health Care System, Boston, MA, USA
| | - Jagannath Pal
- Multidisciplinary Research Units (MRU), Pt. J.N.M. Medical College, Raipur, Chhattisgarh, 492001, India.
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10
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Noh JY, Han HW, Kim DM, Giles ED, Farnell YZ, Wright GA, Sun Y. Innate immunity in peripheral tissues is differentially impaired under normal and endotoxic conditions in aging. Front Immunol 2024; 15:1357444. [PMID: 39221237 PMCID: PMC11361940 DOI: 10.3389/fimmu.2024.1357444] [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: 12/18/2023] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
Chronic low-grade inflammation is a hallmark of aging, aka "inflammaging", which is linked to a wide range of age-associated diseases. Immune dysfunction increases disease susceptibility, and increases morbidity and mortality of aging. Innate immune cells, including monocytes, macrophages and neutrophils, are the first responders of host defense and the key mediators of various metabolic and inflammatory insults. Currently, the understanding of innate immune programming in aging is largely fragmented. Here we investigated the phenotypic and functional properties of innate immune cells in various peripheral tissues of young and aged mice under normal and endotoxic conditions. Under the steady state, aged mice showed elevated pro-inflammatory monocytes/macrophages in peripheral blood, adipose tissue, liver, and colon. Under lipopolysaccharide (LPS)-induced inflammatory state, the innate immune cells of aged mice showed a different response to LPS stimulus than that of young mice. LPS-induced immune responses displayed differential profiles in different tissues and cell types. In the peripheral blood, when responding to LPS, the aged mice showed higher neutrophils, but lower pro-inflammatory monocytes than that in young mice. In the peritoneal fluid, while young mice exhibited significantly elevated pro-inflammatory neutrophils and macrophages in response to LPS, aged mice exhibited decreased pro-inflammatory neutrophils and variable cytokine responses in macrophages. In the adipose tissue, LPS induced less infiltrated neutrophils but more infiltrated macrophages in old mice than young mice. In the liver, aged mice showed a more robust increase of pro-inflammatory macrophages compared to that in young mice under LPS stimulation. In colon, macrophages showed relatively mild response to LPS in both young and old mice. We have further tested bone-marrow derived macrophages (BMDM) from young and aged mice, we found that BMDM from aged mice have impaired polarization, displaying higher expression of pro-inflammatory markers than those from young mice. These data collectively suggest that innate immunity in peripheral tissues is impaired in aging, and the dysregulation of immunity is tissue- and cell-dependent. Our findings in the rodent model underscore the complexity of aging immunity. Further investigation is needed to determine whether the immune profile observed in aged mice is applicable in age-associated diseases in humans.
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Affiliation(s)
- Ji Yeon Noh
- Department of Nutrition, Texas A&M University, College Station, TX, United States
| | - Hye Won Han
- Department of Nutrition, Texas A&M University, College Station, TX, United States
| | - Da Mi Kim
- Department of Nutrition, Texas A&M University, College Station, TX, United States
| | - Erin D. Giles
- School of Kinesiology, University of Michigan, Ann Arbor, MI, United States
| | - Yuhua Z. Farnell
- Department of Poultry Science, Texas A&M University, College Station, TX, United States
| | - Gus A. Wright
- Department of Veterinary Pathobiology, Texas A&M University,
College Station, TX, United States
| | - Yuxiang Sun
- Department of Nutrition, Texas A&M University, College Station, TX, United States
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, United States
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11
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Zhao K, So HC, Lin Z. scParser: sparse representation learning for scalable single-cell RNA sequencing data analysis. Genome Biol 2024; 25:223. [PMID: 39152499 PMCID: PMC11328435 DOI: 10.1186/s13059-024-03345-0] [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: 07/31/2023] [Accepted: 07/23/2024] [Indexed: 08/19/2024] Open
Abstract
The rapid rise in the availability and scale of scRNA-seq data needs scalable methods for integrative analysis. Though many methods for data integration have been developed, few focus on understanding the heterogeneous effects of biological conditions across different cell populations in integrative analysis. Our proposed scalable approach, scParser, models the heterogeneous effects from biological conditions, which unveils the key mechanisms by which gene expression contributes to phenotypes. Notably, the extended scParser pinpoints biological processes in cell subpopulations that contribute to disease pathogenesis. scParser achieves favorable performance in cell clustering compared to state-of-the-art methods and has a broad and diverse applicability.
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Affiliation(s)
- Kai Zhao
- Department of Statistics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Cheong So
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Kunming Institute of Zoology and The Chinese University of Hong Kong, Hong Kong SAR, China.
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
- Margaret K.L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
- Brain and Mind Institute, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
- Hong Kong Branch of the Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Zhixiang Lin
- Department of Statistics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
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12
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Chen M, Wu Q, Shao N, Lai X, Lin H, Chen M, Wu Y, Chen J, Lin Q, Huang J, Chen X, Yan W, Chen S, Li H, Wu D, Yang M, Deng C. The significance of CD16+ monocytes in the occurrence and development of chronic thromboembolic pulmonary hypertension: insights from single-cell RNA sequencing. Front Immunol 2024; 15:1446710. [PMID: 39192976 PMCID: PMC11347785 DOI: 10.3389/fimmu.2024.1446710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 07/17/2024] [Indexed: 08/29/2024] Open
Abstract
Background Chronic thromboembolic pulmonary hypertension (CTEPH) is a serious pulmonary vascular disease characterized by residual thrombi in the pulmonary arteries and distal pulmonary microvascular remodeling. The pathogenesis of CTEPH remains unclear, but many factors such as inflammation, immunity, coagulation and angiogenesis may be involved. Monocytes are important immune cells that can differentiate into macrophages and dendritic cells and play an important role in thrombus formation. However, the distribution, gene expression profile and differentiation trajectory of monocyte subsets in CTEPH patients have not been systematically studied. This study aims to reveal the characteristics and functions of monocytes in CTEPH patients using single-cell sequencing technology, and to provide new insights for the diagnosis and treatment of CTEPH. Methods Single-cell RNA sequencing (scRNA-seq) were performed to analyze the transcriptomic features of peripheral blood mononuclear cells (PBMCs) from healthy controls, CTEPH patients and the tissues from CTEPH patients after the pulmonary endarterectomy (PEA). We established a CTEPH rat model with chronic pulmonary embolism caused by repeated injection of autologous thrombi through a central venous catheter, and used flow cytometry to detect the proportion changes of monocyte subsets in CTEPH patients and CTEPH rat model. We also observed the infiltration degree of macrophage subsets in thrombus tissue and their differentiation relationship with peripheral blood monocyte subsets by immunofluorescence staining. Results The results showed that the monocyte subsets in peripheral blood of CTEPH patients changed significantly, especially the proportion of CD16+ monocyte subset increased. This monocyte subset had unique functional features at the transcriptomic level, involving processes such as cell adhesion, T cell activation, coagulation response and platelet activation, which may play an important role in pulmonary artery thrombus formation and pulmonary artery intimal remodeling. In addition, we also found that the macrophage subsets in pulmonary endarterectomy tissue of CTEPH patients showed pro-inflammatory and lipid metabolism reprogramming features, which may be related to the persistence and insolubility of pulmonary artery thrombi and the development of pulmonary hypertension. Finally, we also observed that CD16+ monocyte subset in peripheral blood of CTEPH patients may be recruited to pulmonary artery intimal tissue and differentiate into macrophage subset with high expression of IL-1β, participating in disease progression. Conclusion CD16+ monocytes subset had significant gene expression changes in CTEPH patients, related to platelet activation, coagulation response and inflammatory response. And we also found that these cells could migrate to the thrombus and differentiate into macrophages with high expression of IL-1β involved in CTEPH disease progression. We believe that CD16+ monocytes are important participants in CTEPH and potential therapeutic targets.
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Affiliation(s)
- Maohe Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Qiuxia Wu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Nan Shao
- Division of Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xingyue Lai
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Huo Lin
- Department of Pulmonary and Critical Care Medicine, Shishi County Hospital, Shishi, China
| | - Min Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Yijing Wu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Jiafan Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Qinghuang Lin
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Jiahui Huang
- Department of Respiratory and Critical Care Medicine, Fuqing City Hospital Affiliated to Fujian Medical University, Fuzhou, China
| | - Xiaoyun Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Wei Yan
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
| | - Shi Chen
- Department of Respiratory and Critical Care, Wuhan No. 6 Hospital, Affiliated Hospital of Jianghan University, Wuhan, China
| | - Hongli Li
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
- Department of Respiratory and Critical Care Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Dawen Wu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
- Department of Respiratory and Critical Care Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Minxia Yang
- Division of Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Chaosheng Deng
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Institute of Respiratory Disease, Fujian Medical University, Fuzhou, China
- Department of Respiratory and Critical Care Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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13
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Ravesloot-Chávez MM, Van Dis E, Fox D, Anaya Sanchez A, Espich S, Nguyenla XH, Rawal SL, Samani H, Ballinger MA, Thomas H, Kotov D, Vance R, Nachman MW, Stanley SA. Tuberculosis susceptibility in genetically diverse mice reveals functional diversity of neutrophils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.29.547125. [PMID: 39211107 PMCID: PMC11361191 DOI: 10.1101/2023.06.29.547125] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Tuberculosis (TB) is a heterogenous disease in humans with individuals exhibiting a wide range of susceptibility. This heterogeneity is not captured by standard laboratory mouse lines. We used a new collection of 19 wild-derived inbred mouse lines collected from diverse geographic sites to identify novel phenotypes during Mycobacterium tuberculosis ( Mtb ) infection. Wild derived mice have heterogenous immune responses to infection that result in differential ability to control disease at early timepoints. Correlation analysis with multiple parameters including sex, weight, and cellular immune responses in the lungs revealed that enhanced control of infection is associated with increased numbers of CD4 T cells, CD8 T cells and B cells. Surprisingly, we did not observe strong correlations between IFN-γ production and control of infection. Although in most lines high neutrophils were associated with susceptibility, we identified a mouse line that harbors high neutrophils numbers yet controls infection. Using single-cell RNA sequencing, we identified a novel neutrophil signature associated with failure to control infection.
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14
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Cabrera LE, Jokiranta ST, Mäki S, Miettinen S, Kant R, Kareinen L, Sironen T, Pietilä JP, Kantele A, Kekäläinen E, Lindgren H, Mattila P, Kipar A, Vapalahti O, Strandin T. The assembly of neutrophil inflammasomes during COVID-19 is mediated by type I interferons. PLoS Pathog 2024; 20:e1012368. [PMID: 39172744 PMCID: PMC11340896 DOI: 10.1371/journal.ppat.1012368] [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: 02/08/2024] [Accepted: 06/24/2024] [Indexed: 08/24/2024] Open
Abstract
The severity of COVID-19 is linked to excessive inflammation. Neutrophils represent a critical arm of the innate immune response and are major mediators of inflammation, but their role in COVID-19 pathophysiology remains poorly understood. We conducted transcriptomic profiling of neutrophils obtained from patients with mild and severe COVID-19, as well as from SARS-CoV-2 infected mice, in comparison to non-infected healthy controls. In addition, we investigated the inflammasome formation potential in neutrophils from patients and mice upon SARS-CoV-2 infection. Transcriptomic analysis of polymorphonuclear cells (PMNs), consisting mainly of mature neutrophils, revealed a striking type I interferon (IFN-I) gene signature in severe COVID-19 patients, contrasting with mild COVID-19 and healthy controls. Notably, low-density granulocytes (LDGs) from severe COVID-19 patients exhibited an immature neutrophil phenotype and lacked this IFN-I signature. Moreover, PMNs from severe COVID-19 patients showed heightened nigericin-induced caspase1 activation, but reduced responsiveness to exogenous inflammasome priming. Furthermore, IFN-I emerged as a priming stimulus for neutrophil inflammasomes. These findings suggest a potential role for neutrophil inflammasomes in driving inflammation during severe COVID-19. Altogether, these findings open promising avenues for targeted therapeutic interventions to mitigate the pathological processes associated with the disease.
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Affiliation(s)
- Luz E. Cabrera
- Viral Zoonosis Research Unit, Medicum, Department of Virology, University of Helsinki, Helsinki, Finland
| | - Suvi T. Jokiranta
- Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
- Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sanna Mäki
- Viral Zoonosis Research Unit, Medicum, Department of Virology, University of Helsinki, Helsinki, Finland
| | - Simo Miettinen
- Viral Zoonosis Research Unit, Medicum, Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Viral Zoonosis Research Unit, Medicum, Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdynia, Poland
| | - Lauri Kareinen
- Viral Zoonosis Research Unit, Medicum, Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Viral Zoonosis Research Unit, Medicum, Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jukka-Pekka Pietilä
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Meilahti Vaccine Research Center MeVac, Department of Infectious Diseases, Inflammation Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Anu Kantele
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Meilahti Vaccine Research Center MeVac, Department of Infectious Diseases, Inflammation Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Eliisa Kekäläinen
- Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
- Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Virology and Immunology, HUSLAB Clinical Microbiology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Hanna Lindgren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Pirkko Mattila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Anja Kipar
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Olli Vapalahti
- Viral Zoonosis Research Unit, Medicum, Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Division of Virology and Immunology, HUSLAB Clinical Microbiology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Tomas Strandin
- Viral Zoonosis Research Unit, Medicum, Department of Virology, University of Helsinki, Helsinki, Finland
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15
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Janssen LLG, van Leeuwen-Kerkhoff N, Westers TM, de Gruijl TD, van de Loosdrecht AA. The immunoregulatory role of monocytes and thrombomodulin in myelodysplastic neoplasms. Front Oncol 2024; 14:1414102. [PMID: 39132505 PMCID: PMC11310157 DOI: 10.3389/fonc.2024.1414102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/12/2024] [Indexed: 08/13/2024] Open
Abstract
Myelodysplastic neoplasms (MDS) are clonal disorders of the myeloid lineage leading to peripheral blood cytopenias. Dysregulation of innate immunity is hypothesized to be a potent driver of MDS. A recent study revealed increased thrombomodulin (TM) expression on classical monocytes in MDS, which was associated with prolonged survival. TM is a receptor with immunoregulatory capacities, however, its exact role in MDS development remains to be elucidated. In this review we focus on normal monocyte biology and report on the involvement of monocytes in myeloid disease entities with a special focus on MDS. Furthermore, we delve into the current knowledge on TM and its function in monocytes in health and disease and explore the role of TM-expressing monocytes as driver, supporter or epiphenomenon in the MDS bone marrow environment.
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Affiliation(s)
- Luca L. G. Janssen
- Department of Hematology, Amsterdam University Medical Center (UMC), Vrije Universiteit, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, Netherlands
| | - Nathalie van Leeuwen-Kerkhoff
- Department of Hematology, Amsterdam University Medical Center (UMC), Vrije Universiteit, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, Netherlands
| | - Theresia M. Westers
- Department of Hematology, Amsterdam University Medical Center (UMC), Vrije Universiteit, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, Netherlands
| | - Tanja D. de Gruijl
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, Netherlands
- Department of Medical Oncology, Amsterdam University Medical Center (UMC), Vrije Universiteit, Amsterdam, Netherlands
- Amsterdam Institute for Immunity and Infectious Diseases, Amsterdam, Netherlands
| | - Arjan A. van de Loosdrecht
- Department of Hematology, Amsterdam University Medical Center (UMC), Vrije Universiteit, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, Netherlands
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16
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Breisnes HW, Leeming DJ, Karsdal MA, Burke H, Freeman A, Wilkinson T, Fazleen A, Bülow Sand JM. Biomarkers of tissue remodelling are elevated in serum of COVID-19 patients who develop interstitial lung disease - an exploratory biomarker study. BMC Pulm Med 2024; 24:331. [PMID: 38982423 PMCID: PMC11234769 DOI: 10.1186/s12890-024-03144-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is a viral pneumonia that can result in serious respiratory illness. It is associated with extensive systemic inflammation, changes to the lung extracellular matrix, and long-term lung impairment such as interstitial lung disease (ILD). In this study, the aim was to investigate whether tissue remodelling, wound healing, and neutrophil activity is altered in patients with COVID-19 and how these relate to the development of post-COVID ILD. METHOD Serum samples were collected from 63 patients three months after discharge as part of the Research Evaluation Alongside Clinical Treatment study in COVID-19 (REACT COVID-19), 10 of whom developed ILD, and 16 healthy controls. Samples were quantified using neo-epitope specific biomarkers reflecting tissue stiffness and formation (PC3X, PRO-C3, and PRO-C6), tissue degradation (C1M, C3M, and C6M), wound healing (PRO-FIB and X-FIB), and neutrophil activity (CPa9-HNE and ELP-3). RESULTS Mean serum levels of PC3X (p < 0.0001), PRO-C3 (p = 0.002), C3M (p = 0.009), PRO-FIB (p < 0.0001), CPa9-HNE (p < 0.0001), and ELP-3 (p < 0.0001) were significantly elevated in patients with COVID-19 compared to healthy controls. Moreover, PC3X (p = 0.023) and PRO-C3 (p = 0.032) were significantly elevated in post-COVID ILD as compared to COVID-19. CONCLUSION Serological biomarkers reflecting type III collagen remodelling, clot formation, and neutrophil activity were significantly elevated in COVID-19 and type III collagen formation markers were further elevated in post-COVID ILD. The findings suggest an increased type III collagen remodelling in COVID-19 and warrants further investigations to assess the potential of tissue remodelling biomarkers as a tool to identify COVID-19 patients at high risk of developing ILD.
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Affiliation(s)
- Helene Wallem Breisnes
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Hepatic and Pulmonary Research, Nordic Bioscience, Herlev, Denmark.
| | | | | | - Hannah Burke
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, Hampshire, England
| | - Anna Freeman
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, Hampshire, England
| | - Tom Wilkinson
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, Hampshire, England
- CES, Faculty of Medicine, University of Southampton, Southampton, Hampshire, England
| | - Aishath Fazleen
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, Hampshire, England
- CES, Faculty of Medicine, University of Southampton, Southampton, Hampshire, England
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17
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Didriksson I, Lengquist M, Spångfors M, Leffler M, Sievert T, Lilja G, Frigyesi A, Friberg H, Schiopu A. Increasing plasma calprotectin (S100A8/A9) is associated with 12-month mortality and unfavourable functional outcome in critically ill COVID-19 patients. J Intensive Care 2024; 12:26. [PMID: 38982551 PMCID: PMC11232228 DOI: 10.1186/s40560-024-00740-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 06/27/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Calprotectin (S100A8/A9) is a pro-inflammatory mediator primarily released from neutrophils. Previous studies have revealed associations between plasma calprotectin, disease severity and in-hospital mortality in unselected COVID-19 patients. OBJECTIVE We aimed to assess whether plasma calprotectin dynamics during the first week of intensive care are associated with mortality and functional outcome in critically ill COVID-19 patients. METHODS This prospective study included 498 COVID-19 patients admitted to six intensive care units (ICUs) in Sweden between May 2020 and May 2021. Blood samples were collected on ICU admission and on day 7. The primary outcome was 12-month mortality. Secondary outcomes were functional outcome of survivors at 3 and 12 months, and the need for invasive mechanical ventilation (IMV) or continuous renal replacement therapy (CRRT) during the ICU stay. Functional outcome was assessed by the Glasgow Outcome Scale Extended (GOSE, range 1-8, with < 5 representing an unfavourable outcome). Associations between plasma calprotectin and outcomes were examined in binary logistic regression analyses adjusted for age, sex, BMI, hypertension, smoking, and creatinine. RESULTS High plasma calprotectin on admission and day 7 was independently associated with increased 12-month mortality. Increasing calprotectin from admission to day 7 was independently associated with higher mortality at 12 months [OR 2.10 (95% CI 1.18-3.74), p = 0.012], unfavourable functional outcome at 3 months [OR 2.53 (95% CI 1.07-6.10), p = 0.036], and the use of IMV [OR 2.23 (95% CI 1.10-4.53), p = 0.027)] and CRRT [OR 2.07 (95% CI 1.07-4.00), p = 0.031)]. A receiver operator characteristic (ROC) model including day 7 calprotectin and age was a good predictor of 12-month mortality [AUC 0.79 (95% CI 0.74-0.84), p < 0.001]. Day 7 calprotectin alone predicted an unfavourable functional outcome at 3 months [AUC 0.67 (95% CI 0.58-0.76), p < 0.001]. CONCLUSION In critically ill COVID-19 patients, increasing calprotectin levels after admission to the ICU are associated with 12-month mortality and unfavourable functional outcome in survivors. Monitoring plasma calprotectin dynamics in the ICU may be considered to evaluate prognosis in critical COVID-19. STUDY REGISTRATION ClinicalTrials.gov Identifier: NCT04974775, registered April 28, 2020.
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Affiliation(s)
- Ingrid Didriksson
- Department of Clinical Sciences, Anaesthesiology and Intensive Care, Lund University, Lund, Sweden.
- Intensive and Perioperative Care Unit, Skåne University Hospital, Malmö, Sweden.
| | - Maria Lengquist
- Department of Clinical Sciences, Anaesthesiology and Intensive Care, Lund University, Lund, Sweden
- Intensive and Perioperative Care Unit, Skåne University Hospital, Lund, Sweden
| | - Martin Spångfors
- Department of Clinical Sciences, Anaesthesiology and Intensive Care, Lund University, Lund, Sweden
- Anaesthesia, and Intensive Care Unit, Kristianstad Hospital, Kristianstad, Sweden
| | - Märta Leffler
- Department of Clinical Sciences, Anaesthesiology and Intensive Care, Lund University, Lund, Sweden
- Intensive and Perioperative Care Unit, Skåne University Hospital, Malmö, Sweden
| | - Theodor Sievert
- Department of Clinical Sciences, Anaesthesiology and Intensive Care, Lund University, Lund, Sweden
| | - Gisela Lilja
- Department of Neurology, Skåne University Hospital, Lund, Sweden
| | - Attila Frigyesi
- Department of Clinical Sciences, Anaesthesiology and Intensive Care, Lund University, Lund, Sweden
- Intensive and Perioperative Care Unit, Skåne University Hospital, Lund, Sweden
| | - Hans Friberg
- Department of Clinical Sciences, Anaesthesiology and Intensive Care, Lund University, Lund, Sweden
- Intensive and Perioperative Care Unit, Skåne University Hospital, Malmö, Sweden
| | - Alexandru Schiopu
- Department of Translational Medicine, Lund University, Malmö, Sweden
- Department of Internal Medicine, Skåne University Hospital, Lund, Sweden
- Nicolae Simionescu Institute of Cellular Biology and Pathology, Bucharest, Romania
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18
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Q.B. Alenzi F. Survivin: A key apoptosis inhibitor in COVID-19 infection and its implication for treatment protocol. Saudi J Biol Sci 2024; 31:104021. [PMID: 38831893 PMCID: PMC11145386 DOI: 10.1016/j.sjbs.2024.104021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 06/05/2024] Open
Abstract
While the relationship between cellular apoptosis and proliferation rates in COVID patients remains underexplored in existing literature, various viruses are known to impact these fundamental process to modulate response to infection. This paper aims to assess apoptosis and proliferation rates in individuals recently infected with Coronavirus, both before and after vaccination, comparing them with healthy controls. Peripheral blood cells from newly diagnosed COVID-19 patients revealed a significant increase in proliferation and apoptosis levels in fresh lymphocytes and granulocytes compared to healthy donors. Notably, as none of the patients were under corticosteroid therapy or cytotoxic drugs, the study underscores the critical role of white blood (WBC) apoptosis in viral pathogenesis, potentially contributing significantly to COVID-19's pathogenicity. Elevated levels of soluble Fas ligand (FaSL) and the pro-inflatmmatory cytokine IL-38 were identified in COVID-19 patients, indicating potential immune dysregulation. Furthermore, individual who received the vaccine or recovered from COVID-19 exhibited higher survivin rates, suggesting a protective role for survivin in migitating lung damage. These findings suggest the prospect of developing a strategy to prevent WBC apoptosis, offering potential benefits in averting lymphopenia associated with severe COVID-19 ouctomes.
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Affiliation(s)
- Faris Q.B. Alenzi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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19
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Shao J, Ma J, Yu Y, Zhang S, Wang W, Li W, Wang C. A multimodal integration pipeline for accurate diagnosis, pathogen identification, and prognosis prediction of pulmonary infections. Innovation (N Y) 2024; 5:100648. [PMID: 39021525 PMCID: PMC11253137 DOI: 10.1016/j.xinn.2024.100648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/19/2024] [Indexed: 07/20/2024] Open
Abstract
Pulmonary infections pose formidable challenges in clinical settings with high mortality rates across all age groups worldwide. Accurate diagnosis and early intervention are crucial to improve patient outcomes. Artificial intelligence (AI) has the capability to mine imaging features specific to different pathogens and fuse multimodal features to reach a synergistic diagnosis, enabling more precise investigation and individualized clinical management. In this study, we successfully developed a multimodal integration (MMI) pipeline to differentiate among bacterial, fungal, and viral pneumonia and pulmonary tuberculosis based on a real-world dataset of 24,107 patients. The area under the curve (AUC) of the MMI system comprising clinical text and computed tomography (CT) image scans yielded 0.910 (95% confidence interval [CI]: 0.904-0.916) and 0.887 (95% CI: 0.867-0.909) in the internal and external testing datasets respectively, which were comparable to those of experienced physicians. Furthermore, the MMI system was utilized to rapidly differentiate between viral subtypes with a mean AUC of 0.822 (95% CI: 0.805-0.837) and bacterial subtypes with a mean AUC of 0.803 (95% CI: 0.775-0.830). Here, the MMI system harbors the potential to guide tailored medication recommendations, thus mitigating the risk of antibiotic misuse. Additionally, the integration of multimodal factors in the AI-driven system also provided an evident advantage in predicting risks of developing critical illness, contributing to more informed clinical decision-making. To revolutionize medical care, embracing multimodal AI tools in pulmonary infections will pave the way to further facilitate early intervention and precise management in the foreseeable future.
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Affiliation(s)
- Jun Shao
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, West China School of Medicine, Sichuan University, Chengdu 610041, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610213, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu 610213, China
| | - Jiechao Ma
- AI Lab, Deepwise Healthcare, Beijing 100080, China
| | - Yizhou Yu
- Department of Computer Science, The University of Hong Kong, Hong Kong SAR, China
| | - Shu Zhang
- AI Lab, Deepwise Healthcare, Beijing 100080, China
| | - Wenyang Wang
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, West China School of Medicine, Sichuan University, Chengdu 610041, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610213, China
| | - Weimin Li
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, West China School of Medicine, Sichuan University, Chengdu 610041, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610213, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu 610213, China
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, West China School of Medicine, Sichuan University, Chengdu 610041, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610213, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu 610213, China
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20
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Gutierrez-Chavez C, Aperrigue-Lira S, Ortiz-Saavedra B, Paz I. Chemokine receptors in COVID-19 infection. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 388:53-94. [PMID: 39260938 DOI: 10.1016/bs.ircmb.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Chemokine receptors play diverse roles in the immune response against pathogens by recruiting innate and adaptive immune cells to sites of infection. However, their involvement could also be detrimental, causing tissue damage and exacerbating respiratory diseases by triggering histological alterations such as fibrosis and remodeling. This chapter reviews the role of chemokine receptors in the immune defense against SARS-CoV-2 infection. In COVID-19, CXCR3 is expressed mainly in T cells, and its upregulation is related to an increase in SARS-CoV-2-specific antibodies but also to COVID-19 severity. CCR5 is a key player in T-cell recruitment, and its suppression leads to reduced inflammation and viremia levels. Conversely, CXCR6 is implicated in the aberrant migration of memory T cells within airways. On the other hand, increased CCR4+ cells in the blood and decreased CCR4+ cells in lung cells are associated with severe COVID-19. Additionally, CCR2 is associated with an increase in macrophage recruitment to lung tissues. Elevated levels of CXCR1 and CXCR2, which are predominantly expressed in neutrophils, are associated with the severity of the disease, and finally, the expression of CX3CR1 in cytotoxic T lymphocytes affects the retention of these cells in lung tissues, thereby impacting the severity of COVID-19. Despite the efforts of many clinical trials to find effective therapies for COVID-19 using chemokine receptor inhibitors, no conclusive results have been found due to the small number of patients, redundancy, and co-expression of chemokine receptors by immune cells, which explains the difficulty in finding a single therapeutic target or effective treatment.
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Affiliation(s)
| | - Shalom Aperrigue-Lira
- Universidad Nacional de San Agustín de Arequipa, Arequipa, Peru; Grupo de Investigación en Inmunología-GII, UNSA, Arequipa, Peru
| | - Brando Ortiz-Saavedra
- Universidad Nacional de San Agustín de Arequipa, Arequipa, Peru; Grupo de Investigación en Inmunología-GII, UNSA, Arequipa, Peru
| | - Irmia Paz
- Universidad Nacional de San Agustín de Arequipa, Arequipa, Peru.
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21
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Fang C, Selega A, Campbell KR. Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance. Genome Biol 2024; 25:159. [PMID: 38886757 PMCID: PMC11184819 DOI: 10.1186/s13059-024-03304-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND The advent of single-cell RNA-sequencing (scRNA-seq) has driven significant computational methods development for all steps in the scRNA-seq data analysis pipeline, including filtering, normalization, and clustering. The large number of methods and their resulting parameter combinations has created a combinatorial set of possible pipelines to analyze scRNA-seq data, which leads to the obvious question: which is best? Several benchmarking studies compare methods but frequently find variable performance depending on dataset and pipeline characteristics. Alternatively, the large number of scRNA-seq datasets along with advances in supervised machine learning raise a tantalizing possibility: could the optimal pipeline be predicted for a given dataset? RESULTS Here, we begin to answer this question by applying 288 scRNA-seq analysis pipelines to 86 datasets and quantifying pipeline success via a range of measures evaluating cluster purity and biological plausibility. We build supervised machine learning models to predict pipeline success given a range of dataset and pipeline characteristics. We find that prediction performance is significantly better than random and that in many cases pipelines predicted to perform well provide clustering outputs similar to expert-annotated cell type labels. We identify characteristics of datasets that correlate with strong prediction performance that could guide when such prediction models may be useful. CONCLUSIONS Supervised machine learning models have utility for recommending analysis pipelines and therefore the potential to alleviate the burden of choosing from the near-infinite number of possibilities. Different aspects of datasets influence the predictive performance of such models which will further guide users.
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Affiliation(s)
- Cindy Fang
- Lunenfeld-Tanenbaum Research Institute, Toronto, Canada
- Program in Bioinformatics and Computational Biology, University of Toronto, Toronto, Canada
- Present address: Department of Biostatistics, Johns Hopkins University, Baltimore, USA
| | - Alina Selega
- Lunenfeld-Tanenbaum Research Institute, Toronto, Canada
- Vector Institute, Toronto, Canada
| | - Kieran R Campbell
- Lunenfeld-Tanenbaum Research Institute, Toronto, Canada.
- Vector Institute, Toronto, Canada.
- Departments of Molecular Genetics, Statistical Sciences, Computer Science, University of Toronto, Toronto, Canada.
- Ontario Institute for Cancer Research, Toronto, Canada.
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22
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Ferreté-Bonastre AG, Martínez-Gallo M, Morante-Palacios O, Calvillo CL, Calafell-Segura J, Rodríguez-Ubreva J, Esteller M, Cortés-Hernández J, Ballestar E. Disease activity drives divergent epigenetic and transcriptomic reprogramming of monocyte subpopulations in systemic lupus erythematosus. Ann Rheum Dis 2024; 83:865-878. [PMID: 38413168 DOI: 10.1136/ard-2023-225433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is characterised by systemic inflammation involving various immune cell types. Monocytes, pivotal in promoting and regulating inflammation in SLE, differentiate from classic monocytes into intermediate and non-classic monocytes, assuming diverse roles and changing their proportions in inflammation. In this study, we investigated the epigenetic and transcriptomic profiles of these and novel monocyte subsets in SLE in relation to activity and progression. METHODS We obtained the DNA methylomes and transcriptomes of classic, intermediate, non-classic monocytes in patients with SLE (at first and follow-up visits) and healthy donors. We integrated these data with single-cell transcriptomics of SLE and healthy donors and interrogated their relationships with activity and progression. RESULTS In addition to shared DNA methylation and transcriptomic alterations associated with a strong interferon signature, we identified monocyte subset-specific alterations, especially in DNA methylation, which reflect an impact of SLE on monocyte differentiation. SLE classic monocytes exhibited a proinflammatory profile and were primed for macrophage differentiation. SLE non-classic monocytes displayed a T cell differentiation-related phenotype, with Th17-regulating features. Changes in monocyte proportions, DNA methylation and expression occurred in relation to disease activity and involved the STAT pathway. Integration of bulk with single-cell RNA sequencing datasets revealed disease activity-dependent expansion of SLE-specific monocyte subsets, further supported the interferon signature for classic monocytes, and associated intermediate and non-classic populations with exacerbated complement activation. CONCLUSIONS Disease activity in SLE drives a subversion of the epigenome and transcriptome programme in monocyte differentiation, impacting the function of different subsets and allowing to generate predictive methods for activity and progression.
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Affiliation(s)
| | - Mónica Martínez-Gallo
- Immunology Division, Vall d'Hebron University Hospital and Diagnostic Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | | | - Celia Lourdes Calvillo
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Josep Calafell-Segura
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Cancer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Josefina Cortés-Hernández
- Rheumatology Department, Hospital Vall d'Hebron and Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, China
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23
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Zhou D, Zhao S, He K, Liu Q, Zhang F, Pu Z, Xiao L, Zhang L, Chen S, Qian X, Wu X, Shen Y, Yu L, Zhang H, Jin J, Xu M, Wang X, Zhu D, Xie Z, Xu X. Longitudinal dynamic single-cell mass cytometry analysis of peripheral blood mononuclear cells in COVID-19 patients within 6 months after viral RNA clearance. BMC Infect Dis 2024; 24:567. [PMID: 38844850 PMCID: PMC11157885 DOI: 10.1186/s12879-024-09464-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
This study investigates the longitudinal dynamic changes in immune cells in COVID-19 patients over an extended period after recovery, as well as the interplay between immune cells and antibodies. Leveraging single-cell mass spectrometry, we selected six COVID-19 patients and four healthy controls, dissecting the evolving landscape within six months post-viral RNA clearance, alongside the levels of anti-spike protein antibodies. The T cell immunophenotype ascertained via single-cell mass spectrometry underwent validation through flow cytometry in 37 samples. Our findings illuminate that CD8 + T cells, gamma-delta (gd) T cells, and NK cells witnessed an increase, in contrast to the reduction observed in monocytes, B cells, and double-negative T (DNT) cells over time. The proportion of monocytes remained significantly elevated in COVID-19 patients compared to controls even after six-month. Subpopulation-wise, an upsurge manifested within various T effector memory subsets, CD45RA + T effector memory, gdT, and NK cells, whereas declines marked the populations of DNT, naive and memory B cells, and classical as well as non-classical monocytes. Noteworthy associations surfaced between DNT, gdT, CD4 + T, NK cells, and the anti-S antibody titer. This study reveals the changes in peripheral blood mononuclear cells of COVID-19 patients within 6 months after viral RNA clearance and sheds light on the interactions between immune cells and antibodies. The findings from this research contribute to a better understanding of immune transformations during the recovery from COVID-19 and offer guidance for protective measures against reinfection in the context of viral variants.
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Affiliation(s)
- Diwenxin Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Shuai Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Keting He
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Qiuhong Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Fen Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Zhangya Pu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Lanlan Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Lingjian Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Shangci Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Xiaohan Qian
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Xiaoxin Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Yangfan Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Ling Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Huafen Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Jiandi Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Min Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Xiaoyan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Danhua Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China
| | - Zhongyang Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China.
| | - Xiaowei Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City, 310003, China.
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24
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Malireddi RKS, Sharma BR, Kanneganti TD. Innate Immunity in Protection and Pathogenesis During Coronavirus Infections and COVID-19. Annu Rev Immunol 2024; 42:615-645. [PMID: 38941608 PMCID: PMC11373870 DOI: 10.1146/annurev-immunol-083122-043545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
The COVID-19 pandemic was caused by the recently emerged β-coronavirus SARS-CoV-2. SARS-CoV-2 has had a catastrophic impact, resulting in nearly 7 million fatalities worldwide to date. The innate immune system is the first line of defense against infections, including the detection and response to SARS-CoV-2. Here, we discuss the innate immune mechanisms that sense coronaviruses, with a focus on SARS-CoV-2 infection and how these protective responses can become detrimental in severe cases of COVID-19, contributing to cytokine storm, inflammation, long-COVID, and other complications. We also highlight the complex cross talk among cytokines and the cellular components of the innate immune system, which can aid in viral clearance but also contribute to inflammatory cell death, cytokine storm, and organ damage in severe COVID-19 pathogenesis. Furthermore, we discuss how SARS-CoV-2 evades key protective innate immune mechanisms to enhance its virulence and pathogenicity, as well as how innate immunity can be therapeutically targeted as part of the vaccination and treatment strategy. Overall, we highlight how a comprehensive understanding of innate immune mechanisms has been crucial in the fight against SARS-CoV-2 infections and the development of novel host-directed immunotherapeutic strategies for various diseases.
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Affiliation(s)
- R K Subbarao Malireddi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
| | - Bhesh Raj Sharma
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
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25
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Lafon T, Chapuis N, Guerin E, Daix T, Otranto M, Boumediene A, Jeannet R, Fontenay M, Henri Hani K, Vignon P, Monneret G, François B, Jean-Philippe J, Feuillard J. Along with PaO2/FiO2 ratio and lymphopenia, low HLA-DR monocytes are the only additional parameter that independently predicts the clinical course of undifferentiated SARS-CoV-2 patients in emergency departments. J Leukoc Biol 2024; 115:1131-1142. [PMID: 38366559 DOI: 10.1093/jleuko/qiae022] [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: 09/30/2023] [Revised: 12/28/2023] [Accepted: 01/01/2024] [Indexed: 02/18/2024] Open
Abstract
Because one-third of patients deteriorate after their admission to the emergency department, assessing the prognosis of COVID-19 patients is of great importance. However, to date, only lymphopenia and the partial pressure of oxygen/fraction of inspired oxygen (PaO2/FiO2) ratio have been reported as partly predictive of COVID-19-related further deterioration, and their association has not been evaluated. We asked whether other key biomarkers of SARS-CoV-2 immunologic defects-increase in circulating immature granulocytes, loss of monocyte HLA-DR (mHLA-DR) expression, and monocyte differentiation blockade-could also predict further COVID-19 deterioration. A series of 284 consecutive COVID-19 patients, with the sole inclusion criterion of being an adult, were prospectively enrolled at emergency department admission (day 0) of 2 different hospitals: 1 for the exploratory cohort (180 patients) and 1 for the confirmatory cohort (104 patients). Deterioration was assessed over the next 7 days. Neither increased immature granulocyte levels nor monocyte differentiation blockade predicted patient worsening. Among more than 30 clinical, biological, and radiological parameters, the value of decreased P/F ratio and lymphopenia for prediction of further COVID-19 deterioration was strongly confirmed, and the loss of mHLA-DR was the only additional independent marker. Combined together in a simple OxyLymphoMono score, the 3 variables perfectly predicted patients who did not worsen and correctly predicted worsening in 59% of cases. By highlighting lymphocyte and monocyte defects as preceding COVID-19 deterioration, these results point on early immunosuppression in COVID-19 deterioration. Combining P/F ratio, lymphopenia, and loss of mHLA-DR together in a simple and robust score could offer a pragmatic method for COVID-19 patient stratification.
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Affiliation(s)
- Thomas Lafon
- Emergency Department, University Hospital Center of Limoges, 2 avenue Martin Luther King, 87042 Limoges, France
- Institut National de la Santé et de la Recherche Médicale Centre d'Investigation Clinique 1435, Centre Hospitalier Universitaire Dupuytren, 2 avenue Martin Luther King, 87042 Limoges, France
| | - Nicolas Chapuis
- Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut Cochin, Université Paris Cité, 27 Rue du Faubourg Saint-Jacques, 75014 Paris, France
- Service d'Hématologie Biologique, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Centre-Université Paris Cité, 27 Rue du Faubourg Saint-Jacques, 75014 Paris, France
| | - Estelle Guerin
- Laboratoire d'Hématologie Biologique, Centre Hospitalier Universitaire de Limoges, Centre de Biologie et de Recherche en Santé, rue Bernard Descottes, 87042 Limoges, France
| | - Thomas Daix
- Institut National de la Santé et de la Recherche Médicale Centre d'Investigation Clinique 1435, Centre Hospitalier Universitaire Dupuytren, 2 avenue Martin Luther King, 87042 Limoges, France
- Réanimation Polyvalente, Centre Hospitalier Universitaire de Limoges, 2 avenue Martin Luther King, 87042 Limoges, France
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1092, Centre Hospitalier Universitaire Dupuytren, 2 avenue Martin Luther King, 87042 Limoges, France
| | - Marcela Otranto
- Emergency Department, University Hospital Center of Limoges, 2 avenue Martin Luther King, 87042 Limoges, France
| | - Ahmed Boumediene
- Laboratoire Immunologie, Centre Hospitalier Universitaire de Limoges, Centre de Biologie et de Recherche en Santé, rue Bernard Descottes, 87042 Limoges, France
| | - Robin Jeannet
- Institut National de la Santé et de la Recherche Médicale Centre d'Investigation Clinique 1435, Centre Hospitalier Universitaire Dupuytren, 2 avenue Martin Luther King, 87042 Limoges, France
- Unité Mixte de Recherche Centre National de Recherche Scientifique 7276/Institut National de la Santé et de la Recherche Médicale U1262, Contrôle de la Réponse Immune B et Lymphoproliférations, Centre de Biologie et de Recherche en Santé, rue Bernard Descottes, 87025 Limoges, France
| | - Michaela Fontenay
- Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut Cochin, Université Paris Cité, 27 Rue du Faubourg Saint-Jacques, 75014 Paris, France
- Service d'Hématologie Biologique, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Centre-Université Paris Cité, 27 Rue du Faubourg Saint-Jacques, 75014 Paris, France
| | - Karam Henri Hani
- Emergency Department, University Hospital Center of Limoges, 2 avenue Martin Luther King, 87042 Limoges, France
| | - Philippe Vignon
- Institut National de la Santé et de la Recherche Médicale Centre d'Investigation Clinique 1435, Centre Hospitalier Universitaire Dupuytren, 2 avenue Martin Luther King, 87042 Limoges, France
- Réanimation Polyvalente, Centre Hospitalier Universitaire de Limoges, 2 avenue Martin Luther King, 87042 Limoges, France
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1092, Centre Hospitalier Universitaire Dupuytren, 2 avenue Martin Luther King, 87042 Limoges, France
| | - Guillaume Monneret
- Laboratoire d'Immunologie, Hôpital E. Herriot, Hospices Civils de Lyon, 5 Pl. d'Arsonval, 69003 Lyon, France
| | - Bruno François
- Institut National de la Santé et de la Recherche Médicale Centre d'Investigation Clinique 1435, Centre Hospitalier Universitaire Dupuytren, 2 avenue Martin Luther King, 87042 Limoges, France
- Réanimation Polyvalente, Centre Hospitalier Universitaire de Limoges, 2 avenue Martin Luther King, 87042 Limoges, France
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1092, Centre Hospitalier Universitaire Dupuytren, 2 avenue Martin Luther King, 87042 Limoges, France
| | - Jais Jean-Philippe
- Imagine Institute, Université Paris Cité, 24 Bd du Montparnasse, 75015 Paris, France
- Biostatistic Unit, Necker University Hospital, Assistance Publique-Hôpitaux de Paris, 149 rue de Sèvre, 75015 Paris, France
- Human Genetics of Infectious Diseases: Complex Predisposition, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1163, 24 Bd du Montparnasse, 75015 Paris, France
| | - Jean Feuillard
- Laboratoire d'Hématologie Biologique, Centre Hospitalier Universitaire de Limoges, Centre de Biologie et de Recherche en Santé, rue Bernard Descottes, 87042 Limoges, France
- Unité Mixte de Recherche Centre National de Recherche Scientifique 7276/Institut National de la Santé et de la Recherche Médicale U1262, Contrôle de la Réponse Immune B et Lymphoproliférations, Centre de Biologie et de Recherche en Santé, rue Bernard Descottes, 87025 Limoges, France
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26
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Starshinova A, Borozinets A, Kulpina A, Sereda V, Rubinstein A, Kudryavtsev I, Kudlay D. Bronchial Asthma and COVID-19: Etiology, Pathological Triggers, and Therapeutic Considerations. PATHOPHYSIOLOGY 2024; 31:269-287. [PMID: 38921725 PMCID: PMC11206645 DOI: 10.3390/pathophysiology31020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024] Open
Abstract
Bronchial asthma (BA) continues to be a difficult disease to diagnose. Various factors have been described in the development of BA, but to date, there is no clear evidence for the etiology of this chronic disease. The emergence of COVID-19 has contributed to the pandemic course of asthma and immunologic features. However, there are no unambiguous data on asthma on the background and after COVID-19. There is correlation between various trigger factors that provoke the development of bronchial asthma. It is now obvious that the SARS-CoV-2 virus is one of the provoking factors. COVID-19 has affected the course of asthma. Currently, there is no clear understanding of whether asthma progresses during or after COVID-19 infection. According to the results of some studies, a significant difference was identified between the development of asthma in people after COVID-19. Mild asthma and moderate asthma do not increase the severity of COVID-19 infection. Nevertheless, oral steroid treatment and hospitalization for severe BA were associated with higher COVID-19 severity. The influence of SARS-CoV-2 infection is one of the protective factors. It causes the development of severe bronchial asthma. The accumulated experience with omalizumab in patients with severe asthma during COVID-19, who received omalizumab during the pandemic, has strongly suggested that continued treatment with omalizumab is safe and may help prevent the severe course of COVID-19. Targeted therapy for asthma with the use of omalizumab may also help to reduce severe asthma associated with COVID-19. However, further studies are needed to prove the effect of omalizumab. Data analysis should persist, based on the results of the course of asthma after COVID-19 with varying degrees of severity.
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Affiliation(s)
- Anna Starshinova
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia;
| | - Anastasia Borozinets
- Medical Department, I.M. Sechenov First Moscow State Medical University, 197022 Moscow, Russia
| | - Anastasia Kulpina
- Medical Department, Saint Petersburg State Pediatric Medical University, 194100 St. Petersburg, Russia;
| | - Vitaliy Sereda
- Medical Department, Saint Petersburg State University, 199034 St. Petersburg, Russia;
| | - Artem Rubinstein
- Department of immunology, Institution of Experimental Medicine, 197376 St. Petersburg, Russia;
| | - Igor Kudryavtsev
- Almazov National Medical Research Centre, 197341 St. Petersburg, Russia;
- Department of immunology, Institution of Experimental Medicine, 197376 St. Petersburg, Russia;
| | - Dmitry Kudlay
- Institute of Immunology FMBA of Russia, 115478 Moscow, Russia;
- Department of Pharmacognosy and Industrial Pharmacy, Faculty of Fundamental Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia
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27
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Moreno E, Ciordia S, Fátima SM, Jiménez D, Martínez-Sanz J, Vizcarra P, Ron R, Sánchez-Conde M, Bargiela R, Sanchez-Carrillo S, Moreno S, Corrales F, Ferrer M, Serrano-Villar S. Proteomic snapshot of saliva samples predicts new pathways implicated in SARS-CoV-2 pathogenesis. Clin Proteomics 2024; 21:37. [PMID: 38778280 PMCID: PMC11112864 DOI: 10.1186/s12014-024-09482-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Information on the microbiome's human pathways and active members that can affect SARS-CoV-2 susceptibility and pathogenesis in the salivary proteome is very scarce. Here, we studied a unique collection of samples harvested from April to June 2020 from unvaccinated patients. METHODS We compared 10 infected and hospitalized patients with severe (n = 5) and moderate (n = 5) coronavirus disease (COVID-19) with 10 uninfected individuals, including non-COVID-19 but susceptible individuals (n = 5) and non-COVID-19 and nonsusceptible healthcare workers with repeated high-risk exposures (n = 5). RESULTS By performing high-throughput proteomic profiling in saliva samples, we detected 226 unique differentially expressed (DE) human proteins between groups (q-value ≤ 0.05) out of 3376 unambiguously identified proteins (false discovery rate ≤ 1%). Major differences were observed between the non-COVID-19 and nonsusceptible groups. Bioinformatics analysis of DE proteins revealed human proteomic signatures related to inflammatory responses, central cellular processes, and antiviral activity associated with the saliva of SARS-CoV-2-infected patients (p-value ≤ 0.0004). Discriminatory biomarker signatures from human saliva include cystatins, protective molecules present in the oral cavity, calprotectins, involved in cell cycle progression, and histones, related to nucleosome functions. The expression levels of two human proteins related to protein transport in the cytoplasm, DYNC1 (p-value, 0.0021) and MAPRE1 (p-value, 0.047), correlated with angiotensin-converting enzyme 2 (ACE2) plasma activity. Finally, the proteomes of microorganisms present in the saliva samples showed 4 main microbial functional features related to ribosome functioning that were overrepresented in the infected group. CONCLUSION Our study explores potential candidates involved in pathways implicated in SARS-CoV-2 susceptibility, although further studies in larger cohorts will be necessary.
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Affiliation(s)
- Elena Moreno
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain.
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Sergio Ciordia
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Santos Milhano Fátima
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Daniel Jiménez
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
| | - Javier Martínez-Sanz
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Pilar Vizcarra
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Raquel Ron
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Matilde Sánchez-Conde
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Rafael Bargiela
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Sergio Sanchez-Carrillo
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049, Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, 28049, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Facultad de Medicina, Universidad de Alcalá de Henares, 28801, Alcalá de Henares, Madrid, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049, Madrid, Spain
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
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28
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Gaudin C, Born-Bony M, Villeret B, Jaillet M, Faille D, Timsit JF, Tran-Dinh A, Montravers P, Crestani B, Garcia-Verdugo I, Sallenave JM. COVID-19 PBMCs are doubly harmful, through LDN-mediated lung epithelial damage and monocytic impaired responsiveness to live Pseudomonas aeruginosa exposure. Front Immunol 2024; 15:1398369. [PMID: 38835759 PMCID: PMC11148249 DOI: 10.3389/fimmu.2024.1398369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024] Open
Abstract
Introduction Although many studies have underscored the importance of T cells, phenotypically and functionally, fewer have studied the functions of myeloid cells in COVID disease. In particular, the potential role of myeloid cells such as monocytes and low-density neutrophils (LDNs) in innate responses and particular in the defense against secondary bacterial infections has been much less documented. Methods Here, we compared, in a longitudinal study, healthy subjects, idiopathic fibrosis patients, COVID patients who were either hospitalized/moderate (M-) or admitted to ICU (COV-ICU) and patients in ICU hospitalized for other reasons (non-COV-ICU). Results We show that COVID patients have an increased proportion of low-density neutrophils (LDNs), which produce high levels of proteases (particularly, NE, MMP-8 and MMP-9) (unlike non-COV-ICU patients), which are partly responsible for causing type II alveolar cell damage in co-culture experiments. In addition, we showed that M- and ICU-COVID monocytes had reduced responsiveness towards further live Pseudomonas aeruginosa (PAO1 strain) infection, an important pathogen colonizing COVID patients in ICU, as assessed by an impaired secretion of myeloid cytokines (IL-1, TNF, IL-8,…). By contrast, lymphoid cytokines (in particular type 2/type 3) levels remained high, both basally and post PAO1 infection, as reflected by the unimpaired capacity of T cells to proliferate, when stimulated with anti-CD3/CD28 beads. Discussion Overall, our results demonstrate that COVID circulatory T cells have a biased type 2/3 phenotype, unconducive to proper anti-viral responses and that myeloid cells have a dual deleterious phenotype, through their LDN-mediated damaging effect on alveolar cells and their impaired responsiveness (monocyte-mediated) towards bacterial pathogens such as P. aeruginosa.
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Affiliation(s)
- Clémence Gaudin
- Laboratoire d'Excellence Inflamex, Institut National de la Santé et de la Recherche Medicale U1152, Physiopathologie et Épidémiologie des Maladies Respiratoires, Université de Paris-Cité, Paris, France
| | - Maëlys Born-Bony
- Laboratoire d'Excellence Inflamex, Institut National de la Santé et de la Recherche Medicale U1152, Physiopathologie et Épidémiologie des Maladies Respiratoires, Université de Paris-Cité, Paris, France
| | - Bérengère Villeret
- Laboratoire d'Excellence Inflamex, Institut National de la Santé et de la Recherche Medicale U1152, Physiopathologie et Épidémiologie des Maladies Respiratoires, Université de Paris-Cité, Paris, France
| | - Madeleine Jaillet
- Laboratoire d'Excellence Inflamex, Institut National de la Santé et de la Recherche Medicale U1152, Physiopathologie et Épidémiologie des Maladies Respiratoires, Université de Paris-Cité, Paris, France
| | - Dorothée Faille
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, LVTS, Paris, France
- Laboratoire d'Hématologie, AP-HP, Hôpital Bichat, Paris, France
| | - Jean-François Timsit
- Réanimation Médicale et des Maladies Infectieuses, Centre Hospitalier Universitaire Bichat-Claude Bernard, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alexy Tran-Dinh
- Inserm UMR1148, Laboratory for Vascular Translational Science Bichat Hospital, Paris, France
- AP-HP Nord, Anesthesiology and Intensive Care Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Philippe Montravers
- Laboratoire d'Excellence Inflamex, Institut National de la Santé et de la Recherche Medicale U1152, Physiopathologie et Épidémiologie des Maladies Respiratoires, Université de Paris-Cité, Paris, France
- AP-HP Nord, Anesthesiology and Intensive Care Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Bruno Crestani
- Laboratoire d'Excellence Inflamex, Institut National de la Santé et de la Recherche Medicale U1152, Physiopathologie et Épidémiologie des Maladies Respiratoires, Université de Paris-Cité, Paris, France
- Service de Pneumologie A, Hôpital Bichat, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Ignacio Garcia-Verdugo
- Laboratoire d'Excellence Inflamex, Institut National de la Santé et de la Recherche Medicale U1152, Physiopathologie et Épidémiologie des Maladies Respiratoires, Université de Paris-Cité, Paris, France
| | - Jean-Michel Sallenave
- Laboratoire d'Excellence Inflamex, Institut National de la Santé et de la Recherche Medicale U1152, Physiopathologie et Épidémiologie des Maladies Respiratoires, Université de Paris-Cité, Paris, France
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29
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Aminu M, Hong L, Vokes N, Schmidt ST, Saad M, Zhu B, Le X, Tina C, Sheshadri A, Wang B, Jaffray D, Futreal A, Lee JJ, Byers LA, Gibbons D, Heymach J, Chen K, Cheng C, Zhang J, Wu J. Joint multi-omics discriminant analysis with consistent representation learning using PANDA. RESEARCH SQUARE 2024:rs.3.rs-4353037. [PMID: 38798352 PMCID: PMC11118856 DOI: 10.21203/rs.3.rs-4353037/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Integrative multi-omics analysis provides deeper insight and enables better and more realistic modeling of the underlying biology and causes of diseases than does single omics analysis. Although several integrative multi-omics analysis methods have been proposed and demonstrated promising results in integrating distinct omics datasets, inconsistent distribution of the different omics data, which is caused by technology variations, poses a challenge for paired integrative multi-omics methods. In addition, the existing discriminant analysis-based integrative methods do not effectively exploit correlation and consistent discriminant structures, necessitating a compromise between correlation and discrimination in using these methods. Herein we present PAN-omics Discriminant Analysis (PANDA), a joint discriminant analysis method that seeks omics-specific discriminant common spaces by jointly learning consistent discriminant latent representations for each omics. PANDA jointly maximizes between-class and minimizes within-class omics variations in a common space and simultaneously models the relationships among omics at the consistency representation and cross-omics correlation levels, overcoming the need for compromise between discrimination and correlation as with the existing integrative multi-omics methods. Because of the consistency representation learning incorporated into the objective function of PANDA, this method seeks a common discriminant space to minimize the differences in distributions among omics, can lead to a more robust latent representations than other methods, and is against the inconsistency of the different omics. We compared PANDA to 10 other state-of-the-art multi-omics data integration methods using both simulated and real-world multi-omics datasets and found that PANDA consistently outperformed them while providing meaningful discriminant latent representations. PANDA is implemented using both R and MATLAB, with codes available at https://github.com/WuLabMDA/PANDA.
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Affiliation(s)
- Muhammad Aminu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lingzhi Hong
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Natalie Vokes
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie T. Schmidt
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maliazurina Saad
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bo Zhu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cascone Tina
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ajay Sheshadri
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bo Wang
- Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - David Jaffray
- Office of the Chief Technology and Digital Officer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J. Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren A. Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Don Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chao Cheng
- Department of Medicine, Institution of Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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30
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Diehl-Wiesenecker E, Galtung N, Dickescheid J, Prpic M, Somasundaram R, Kappert K, Bauer W. Blood calprotectin as a biomarker for infection and sepsis - the prospective CASCADE trial. BMC Infect Dis 2024; 24:496. [PMID: 38755564 PMCID: PMC11100246 DOI: 10.1186/s12879-024-09394-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: 02/07/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Early in the host-response to infection, neutrophils release calprotectin, triggering several immune signalling cascades. In acute infection management, identifying infected patients and stratifying these by risk of deterioration into sepsis, are crucial tasks. Recruiting a heterogenous population of patients with suspected infections from the emergency department, early in the care-path, the CASCADE trial aimed to evaluate the accuracy of blood calprotectin for detecting bacterial infections, estimating disease severity, and predicting clinical deterioration. METHODS In a prospective, observational trial from February 2021 to August 2022, 395 patients (n = 194 clinically suspected infection; n = 201 controls) were enrolled. Blood samples were collected at enrolment. The accuracy of calprotectin to identify bacterial infections, and to predict and identify sepsis and mortality was analysed. These endpoints were determined by a panel of experts. RESULTS The Area Under the Receiver Operating Characteristic (AUROC) of calprotectin for detecting bacterial infections was 0.90. For sepsis within 72 h, calprotectin's AUROC was 0.83. For 30-day mortality it was 0.78. In patients with diabetes, calprotectin had an AUROC of 0.94 for identifying bacterial infection. CONCLUSIONS Calprotectin showed notable accuracy for all endpoints. Using calprotectin in the emergency department could improve diagnosis and management of severe infections, in combination with current biomarkers. CLINICAL TRIAL REGISTRATION NUMBER DRKS00020521.
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Affiliation(s)
- Eva Diehl-Wiesenecker
- Department of Emergency Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Benjamin Franklin Campus, Zentrale Notaufnahme und Aufnahmestation, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Noa Galtung
- Department of Emergency Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Benjamin Franklin Campus, Zentrale Notaufnahme und Aufnahmestation, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Johannes Dickescheid
- Department of Emergency Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Benjamin Franklin Campus, Zentrale Notaufnahme und Aufnahmestation, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Monika Prpic
- Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Rajan Somasundaram
- Department of Emergency Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Benjamin Franklin Campus, Zentrale Notaufnahme und Aufnahmestation, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Kai Kappert
- Institute of Diagnostic Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Labor Berlin - Charité Vivantes GmbH, Berlin, Germany
| | - Wolfgang Bauer
- Department of Emergency Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Benjamin Franklin Campus, Zentrale Notaufnahme und Aufnahmestation, Hindenburgdamm 30, 12203, Berlin, Germany.
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31
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Poisson J, El-Sissy C, Serret-Larmande A, Smith N, Lebraud M, Augy JL, Conti C, Gonnin C, Planquette B, Arlet JB, Hermann B, Charbit B, Pastre J, Devaux F, Ladavière C, Lim L, Ober P, Cannovas J, Biard L, Gulczynski MC, Blumenthal N, Péré H, Knosp C, Gey A, Benhamouda N, Murris J, Veyer D, Tartour E, Diehl JL, Duffy D, Paillaud E, Granier C. Increased levels of GM-CSF and CXCL10 and low CD8 + memory stem T Cell count are markers of immunosenescence and severe COVID-19 in older people. Immun Ageing 2024; 21:28. [PMID: 38715114 PMCID: PMC11075216 DOI: 10.1186/s12979-024-00430-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Ageing leads to altered immune responses, resulting in higher susceptibility to certain infections in the elderly. Immune ageing is a heterogeneous process also associated with inflammaging, a low-grade chronic inflammation. Altered cytotoxic T cell responses and cytokine storm have previously been described in severe COVID-19 cases, however the parameters responsible for such immune response failures are not well known. The aim of our study was to characterize CD8+ T cells and cytokines associated with ageing, in a cohort of patients aged over 70 years stratified by COVID-19 severity. RESULTS One hundred and four patients were included in the study. We found that, in older people, COVID-19 severity was associated with (i) higher level of GM-CSF, CXCL10 (IP-10), VEGF, IL-1β, CCL2 (MCP-1) and the neutrophil to lymphocyte ratio (NLR), (ii) increased terminally differentiated CD8+T cells, and (ii) decreased early precursors CD8+ T stem cell-like memory cells (TSCM) and CD27+CD28+. The cytokines mentioned above were found at higher concentrations in the COVID-19+ older cohort compared to a younger cohort in which they were not associated with disease severity. CONCLUSIONS Our results highlight the particular importance of the myeloid lineage in COVID-19 severity among older people. As GM-CSF and CXCL10 were not associated with COVID-19 severity in younger patients, they may represent disease severity specific markers of ageing and should be considered in older people care.
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Affiliation(s)
- Johanne Poisson
- Université Paris Cité, Paris, France
- Department of Geriatric Medicine, Hôpital Europeen Georges Pompidou, AP-HP, Paris, France
- Inserm U1149, Center for Research on Inflammation, Paris, France
| | - Carine El-Sissy
- INSERM, Laboratory of Integrative Cancer Immunology, Paris, France
- Cordeliers Research Center, Sorbonne University, University Paris Cité, Paris, France
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Paris, France
| | - Arnaud Serret-Larmande
- ECSTRRA Team, UMR-1153, Université Paris Cité, INSERM, AP-HP, Saint Louis Hospital, Paris, France
| | - Nikaïa Smith
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Morgane Lebraud
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Paris, France
| | - Jean-Loup Augy
- Medical intensive care unit, Hopital Delafontaine, 2 rue du Dr Delafontaine, Saint-Denis, 93200, France
| | - Catherine Conti
- Université Paris Cité, Paris, France
- Department of Geriatric Medicine, Hôpital Europeen Georges Pompidou, AP-HP, Paris, France
| | - Cécile Gonnin
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Paris, France
- Université Paris Cité, INSERM, PARCC, Paris, France
| | - Benjamin Planquette
- Service de Pneumologie Et Soins Intensifs, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Jean-Benoît Arlet
- Internal Medicine Department, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Faculty of Medicine, Université Paris Cité, Paris, 75006, France
| | - Bertrand Hermann
- Medical Intensive Care Unit, AP-HP. Centre Université Paris Cité, Georges Pompidou European Hospital, Paris, 75015, France
- INSERM UMR 1266, Institut de Psychiatrie Et Neurosciences de Paris (IPNP), Université Paris Cité, Paris, France
| | - Bruno Charbit
- Institute of Ophthalmology, University College London (UCL), London, UK
| | - Jean Pastre
- Service de Pneumologie Et Soins Intensifs, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Floriane Devaux
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Paris, France
| | - Cyrielle Ladavière
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Paris, France
| | - Lydie Lim
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Paris, France
| | - Pauline Ober
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Paris, France
| | - Johanna Cannovas
- Department of Geriatric Medicine, Hôpital Europeen Georges Pompidou, AP-HP, Paris, France
| | - Lucie Biard
- ECSTRRA Team, UMR-1153, Université Paris Cité, INSERM, AP-HP, Saint Louis Hospital, Paris, France
| | - Marie-Christelle Gulczynski
- Gérontologie 1, GHU AP-HP. Centre Université Paris Cité, Corentin Celton Hospital, Issy-Les-Moulineaux, 92130, France
| | - Noémie Blumenthal
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Paris, France
| | - Hélène Péré
- Virology Laboratory, Hôpital Européen Georges-Pompidou, APHP.Centre - Université Paris Cité, Paris, France
- Centre de Recherche Des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Functional Genomics of Solid Tumors Laboratory, Équipe Labellisée Ligue Nationale Contre Le Cancer, Labex OncoImmunology, Paris, France
- Université Paris Cité, Faculté de Santé, UFR de Médecine, Paris, France
| | | | - Alain Gey
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Paris, France
| | - Nadine Benhamouda
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Paris, France
| | - Juliette Murris
- HeKA, Inria Paris, Inserm, Université Paris Cité, Paris, France
| | - David Veyer
- Virology Laboratory, Hôpital Européen Georges-Pompidou, APHP.Centre - Université Paris Cité, Paris, France
- Centre de Recherche Des Cordeliers, Sorbonne Université, Inserm, Université de Paris, Functional Genomics of Solid Tumors Laboratory, Équipe Labellisée Ligue Nationale Contre Le Cancer, Labex OncoImmunology, Paris, France
| | - Eric Tartour
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Paris, France
| | - Jean-Luc Diehl
- Medical Intensive Care Unit, AP-HP. Centre Université Paris Cité, Georges Pompidou European Hospital, Paris, 75015, France
- University Paris Cité, Innovative Therapies in Hemostasis, INSERM, Paris, 75006, France
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Elena Paillaud
- Université Paris Cité, Paris, France.
- Department of Geriatric Medicine, Hôpital Europeen Georges Pompidou, AP-HP, Paris, France.
- Univ. Paris Est Créteil, Inserm U955, IMRB, Créteil, France.
| | - Clémence Granier
- Department of Immunology, APHP, Hôpital Européen Georges Pompidou (HEGP), Paris, France.
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Tarfi S, Kern W, Goulas E, Selimoglu-Buet D, Wagner-Ballon O. Technical, gating and interpretation recommendations for the partitioning of circulating monocyte subsets assessed by flow cytometry. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2024; 106:203-215. [PMID: 38656036 DOI: 10.1002/cyto.b.22176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/24/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
The monocyte subset partitioning by flow cytometry, known as "monocyte assay," is now integrated into the new classifications as a supporting criterion for CMML diagnosis, if a relative accumulation of classical monocytes above 94% of total circulating monocytes is observed. Here we provide clinical flow cytometry laboratories with technical support adapted for the most commonly used cytometers. Step-by-step explanations of the gating strategy developed on whole peripheral blood are presented while underlining the most common difficulties. In a second part, interpretation recommendations of circulating monocyte partitioning from the dedicated French working group "CytHem-LMMC" are shared as well as the main pitfalls, including false positive and false negative cases. The particular flow-defined inflammatory profile is described and the usefulness of the nonclassical monocyte specific marker, namely slan, highlighted. Examples of reporting to the physician with frequent situations encountered when using the monocyte assay are also presented.
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Affiliation(s)
- Sihem Tarfi
- Département d'Hématologie et Immunologie Biologiques, AP-HP, Hôpital Henri Mondor, Créteil, France
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, GmbH, Munich, Germany
| | - Elodie Goulas
- Département d'Hématologie et Immunologie Biologiques, AP-HP, Hôpital Henri Mondor, Créteil, France
| | - Dorothée Selimoglu-Buet
- INSERM Unité Mixte de Recherche (UMR) 1287, Faculté de Médecine, Université Paris-Sud, Villejuif, France
| | - Orianne Wagner-Ballon
- Département d'Hématologie et Immunologie Biologiques, AP-HP, Hôpital Henri Mondor, Créteil, France
- INSERM, IMRB, Univ Paris Est Créteil, Créteil, France
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33
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Li Y, Jiang L, Chen Y, Li Y, Yuan J, Lu J, Zhang Z, Liu S, Feng X, Xiong J, Jiang Y, Zhang X, Li J, Shen L. Specific lineage transition of tumor-associated macrophages elicits immune evasion of ascitic tumor cells in gastric cancer with peritoneal metastasis. Gastric Cancer 2024; 27:519-538. [PMID: 38460015 PMCID: PMC11016508 DOI: 10.1007/s10120-024-01486-6] [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: 11/30/2023] [Accepted: 02/23/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Gastric cancer with peritoneal metastasis (PM-GC), recognized as one of the deadliest cancers. However, whether and how the tumor cell-extrinsic tumor microenvironment (TME) is involved in the therapeutic failure remains unknown. Thus, this study systematically assessed the immunosuppressive tumor microenvironment in ascites from patients with PM-GC, and its contribution to dissemination and immune evasion of ascites-disseminated tumor cells (aDTCs). METHODS Sixty-three ascites and 43 peripheral blood (PB) samples from 51 patients with PM-GC were included in this study. aDTCs in ascites and circulating tumor cells (CTCs) in paired PB were immunophenotypically profiled. Using single-cell RNA transcriptional sequencing (scRNA-seq), crosstalk between aDTCs and the TME features of ascites was inspected. Further studies on the mechanism underlying aDTCs-immune cells crosstalk were performed on in vitro cultured aDTCs. RESULTS Immune cells in ascites interact with aDTCs, prompting their immune evasion. Specifically, we found that the tumor-associated macrophages (TAMs) in ascites underwent a continuum lineage transition from cathepsinhigh (CTShigh) to complement 1qhigh (C1Qhigh) TAM. CTShigh TAM initially attracted the metastatic tumor cells to ascites, thereafter, transitioning terminally to C1Qhigh TAM to trigger overproliferation and immune escape of aDTCs. Mechanistically, we demonstrated that C1Qhigh TAMs significantly enhanced the expression of PD-L1 and NECTIN2 on aDTCs, which was driven by the activation of the C1q-mediated complement pathway. CONCLUSIONS For the first time, we identified an immunosuppressive macrophage transition from CTShigh to C1Qhigh TAM in ascites from patients with PM-GC. This may contribute to developing potential TAM-targeted immunotherapies for PM-GC.
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Affiliation(s)
- Yilin Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Lei Jiang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Yang Chen
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Yanyan Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jiajia Yuan
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jialin Lu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Zizhen Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Shengde Liu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xujiao Feng
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | | | - Yan Jiang
- Singleron Biotechnologies, Nanjing, China
| | - Xiaotian Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jian Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Lin Shen
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
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34
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Albert MC, Uranga-Murillo I, Arias M, De Miguel D, Peña N, Montinaro A, Varanda AB, Theobald SJ, Areso I, Saggau J, Koch M, Liccardi G, Peltzer N, Rybniker J, Hurtado-Guerrero R, Merino P, Monzón M, Badiola JJ, Reindl-Schwaighofer R, Sanz-Pamplona R, Cebollada-Solanas A, Megyesfalvi Z, Dome B, Secrier M, Hartmann B, Bergmann M, Pardo J, Walczak H. Identification of FasL as a crucial host factor driving COVID-19 pathology and lethality. Cell Death Differ 2024; 31:544-557. [PMID: 38514848 PMCID: PMC11093991 DOI: 10.1038/s41418-024-01278-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
The dysregulated immune response and inflammation resulting in severe COVID-19 are still incompletely understood. Having recently determined that aberrant death-ligand-induced cell death can cause lethal inflammation, we hypothesized that this process might also cause or contribute to inflammatory disease and lung failure following SARS-CoV-2 infection. To test this hypothesis, we developed a novel mouse-adapted SARS-CoV-2 model (MA20) that recapitulates key pathological features of COVID-19. Concomitantly with occurrence of cell death and inflammation, FasL expression was significantly increased on inflammatory monocytic macrophages and NK cells in the lungs of MA20-infected mice. Importantly, therapeutic FasL inhibition markedly increased survival of both, young and old MA20-infected mice coincident with substantially reduced cell death and inflammation in their lungs. Intriguingly, FasL was also increased in the bronchoalveolar lavage fluid of critically-ill COVID-19 patients. Together, these results identify FasL as a crucial host factor driving the immuno-pathology that underlies COVID-19 severity and lethality, and imply that patients with severe COVID-19 may significantly benefit from therapeutic inhibition of FasL.
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Affiliation(s)
- Marie-Christine Albert
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany
- Cell death, inflammation and immunity laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
| | - Iratxe Uranga-Murillo
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, 28029, Spain
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
- Department of Microbiology, Paediatrics, Radiology and Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, 50009, Spain
| | - Maykel Arias
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, 28029, Spain
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
- Department of Microbiology, Paediatrics, Radiology and Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, 50009, Spain
| | - Diego De Miguel
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
| | - Natacha Peña
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
| | - Antonella Montinaro
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Ana Beatriz Varanda
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany
- Cell death, inflammation and immunity laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
| | - Sebastian J Theobald
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, 50931, Germany
- Faculty of Medicine and University Hospital of Cologne, Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, 50931, Germany
| | - Itziar Areso
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Julia Saggau
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany
- Cell death, inflammation and immunity laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
- Genome instability, inflammation and cell death laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
| | - Manuel Koch
- Institue for Dental Research and Oral Musculoskeletal Biology, Faculty of Medicine and University Hospital Cologne, Cologne, 50931, Germany
| | - Gianmaria Liccardi
- Genome instability, inflammation and cell death laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
| | - Nieves Peltzer
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany
- Faculty of Medicine and University Hospital of Cologne, Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
- Department of Translational Genomics, University of Cologne, Cologne, 50931, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, 50931, Germany
- Faculty of Medicine and University Hospital of Cologne, Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, 50931, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, 50931, Germany
| | - Ramón Hurtado-Guerrero
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), University of Zaragoza, Zaragoza, 50018, Spain
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, 2200, Denmark
- Fundación ARAID, Zaragoza, 50018, Spain
| | - Pedro Merino
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), University of Zaragoza, Zaragoza, 50018, Spain
| | - Marta Monzón
- Research Centre for Encephalopaties and Transmissible Emerging Diseases, Institute for Health Research Aragón (IIS), University of Zaragoza, Zaragoza, 50013, Spain
- Department of Human Anatomy and Histology, University of Zaragoza, Zaragoza, 50009, Spain
| | - Juan J Badiola
- Research Centre for Encephalopaties and Transmissible Emerging Diseases, Institute for Health Research Aragón (IIS), University of Zaragoza, Zaragoza, 50013, Spain
| | | | - Rebeca Sanz-Pamplona
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
- Fundación ARAID, Zaragoza, 50018, Spain
- CIBER de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Alberto Cebollada-Solanas
- Aragon Biomedical Research Center (CIBA), Instituto Aragonés de Ciencias de la Salud (IACS), Unidad de Biocomputación, Zaragoza, 50018, Spain
| | - Zsolt Megyesfalvi
- Deparment of Thoracic Surgery, Medical University of Vienna, Vienna, 1090, Austria
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, 1122, Hungary
- National Koranyi Institute of Pulmonology, Budapest, 1121, Hungary
| | - Balazs Dome
- Deparment of Thoracic Surgery, Medical University of Vienna, Vienna, 1090, Austria
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, 1122, Hungary
- National Koranyi Institute of Pulmonology, Budapest, 1121, Hungary
- Department of Translational Medicine, Lund University, Lund, SE-22100, Sweden
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
| | - Boris Hartmann
- Virology Group, Institute for Veterinary Disease Control at AGES, Moedling, 2340, Austria
| | - Michael Bergmann
- Div. of Visceral Surgery, Dept. of General Surgery, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, 1090, Austria
| | - Julián Pardo
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, 28029, Spain
- Aragón Health Research Institute (IIS Aragón), San Juan Bosco 13, Zaragoza, 50009, Spain
- Department of Microbiology, Paediatrics, Radiology and Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, 50009, Spain
| | - Henning Walczak
- Cell death, inflammation and immunity laboratory, CECAD Cluster of Excellence, University of Cologne, Cologne, 50931, Germany.
- Cell death, inflammation and immunity laboratory, Institute of Biochemistry I, Centre for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, 50931, Germany.
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, WC1E 6DD, UK.
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35
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Baronaitė I, Šulskis D, Kopu̅stas A, Tutkus M, Smirnovas V. Formation of Calprotectin Inhibits Amyloid Aggregation of S100A8 and S100A9 Proteins. ACS Chem Neurosci 2024; 15:1915-1925. [PMID: 38634811 PMCID: PMC11066842 DOI: 10.1021/acschemneuro.4c00093] [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: 02/09/2024] [Revised: 03/31/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
Calcium-binding S100A8 and S100A9 proteins play a significant role in various disorders due to their pro-inflammatory functions. Substantially, they are also relevant in neurodegenerative disorders via the delivery of signals for the immune response. However, at the same time, they can aggregate and accelerate the progression of diseases. Natively, S100A8 and S100A9 exist as homo- and heterodimers, but upon aggregation, they form amyloid-like oligomers, fibrils, or amorphous aggregates. In this study, we aimed to elucidate the aggregation propensities of S100A8, S100A9, and their heterodimer calprotectin by investigating aggregation kinetics, secondary structures, and morphologies of the aggregates. For the first time, we followed the in vitro aggregation of S100A8, which formed spherical aggregates, unlike the fibrillar structures of S100A9 under the same conditions. The aggregates were sensitive to amyloid-specific ThT and ThS dyes and had a secondary structure composed of β-sheets. Similarly to S100A9, S100A8 protein was stabilized by calcium ions, resulting in aggregation inhibition. Finally, the formation of S100A8 and S100A9 heterodimers stabilized the proteins in the absence of calcium ions and prevented their aggregation.
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Affiliation(s)
- Ieva Baronaitė
- Institute
of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Darius Šulskis
- Institute
of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Aurimas Kopu̅stas
- Institute
of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
- Department
of Molecular Compound Physics, Center for
Physical Sciences and Technology, LT- 10257 Vilnius, Lithuania
| | - Marijonas Tutkus
- Institute
of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
- Department
of Molecular Compound Physics, Center for
Physical Sciences and Technology, LT- 10257 Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute
of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
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36
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Drury RE, Camara S, Chelysheva I, Bibi S, Sanders K, Felle S, Emary K, Phillips D, Voysey M, Ferreira DM, Klenerman P, Gilbert SC, Lambe T, Pollard AJ, O'Connor D. Multi-omics analysis reveals COVID-19 vaccine induced attenuation of inflammatory responses during breakthrough disease. Nat Commun 2024; 15:3402. [PMID: 38649734 PMCID: PMC11035709 DOI: 10.1038/s41467-024-47463-6] [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: 06/18/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
The immune mechanisms mediating COVID-19 vaccine attenuation of COVID-19 remain undescribed. We conducted comprehensive analyses detailing immune responses to SARS-CoV-2 virus in blood post-vaccination with ChAdOx1 nCoV-19 or a placebo. Samples from randomised placebo-controlled trials (NCT04324606 and NCT04400838) were taken at baseline, onset of COVID-19-like symptoms, and 7 days later, confirming COVID-19 using nucleic amplification test (NAAT test) via real-time PCR (RT-PCR). Serum cytokines were measured with multiplexed immunoassays. The transcriptome was analysed with long, short and small RNA sequencing. We found attenuation of RNA inflammatory signatures in ChAdOx1 nCoV-19 compared with placebo vaccinees and reduced levels of serum proteins associated with COVID-19 severity. KREMEN1, a putative alternative SARS-CoV-2 receptor, was downregulated in placebo compared with ChAdOx1 nCoV-19 vaccinees. Vaccination ameliorates reductions in cell counts across leukocyte populations and platelets noted at COVID-19 onset, without inducing potentially deleterious Th2-skewed immune responses. Multi-omics integration links a global reduction in miRNA expression at COVID-19 onset to increased pro-inflammatory responses at the mRNA level. This study reveals insights into the role of COVID-19 vaccines in mitigating disease severity by abrogating pro-inflammatory responses associated with severe COVID-19, affirming vaccine-mediated benefit in breakthrough infection, and highlighting the importance of clinically relevant endpoints in vaccine evaluation.
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Affiliation(s)
- Ruth E Drury
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susana Camara
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Irina Chelysheva
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Katherine Sanders
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Salle Felle
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Katherine Emary
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel Phillips
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniela M Ferreira
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah C Gilbert
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
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Li C, Wu K, Yang R, Liao M, Li J, Zhu Q, Zhang J, Zhang X. Comprehensive analysis of immunogenic cell death-related gene and construction of prediction model based on WGCNA and multiple machine learning in severe COVID-19. Sci Rep 2024; 14:8450. [PMID: 38600309 PMCID: PMC11006847 DOI: 10.1038/s41598-024-59117-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/08/2024] [Indexed: 04/12/2024] Open
Abstract
The death of coronavirus disease 2019 (COVID-19) is primarily due to from critically ill patients, especially from ARDS complications caused by SARS-CoV-2. Therefore, it is essential to contribute an in-depth understanding of the pathogenesis of the disease and to identify biomarkers for predicting critically ill patients at the molecular level. Immunogenic cell death (ICD), as a specific variant of regulatory cell death driven by stress, can induce adaptive immune responses against cell death antigens in the host. Studies have confirmed that both innate and adaptive immune pathways are involved in the pathogenesis of SARS-CoV-2 infection. However, the role of ICD in the pathogenesis of severe COVID-19 has rarely been explored. In this study, we systematically evaluated the role of ICD-related genes in COVID-19. We conducted consensus clustering, immune infiltration analysis, and functional enrichment analysis based on ICD differentially expressed genes. The results showed that immune infiltration characteristics were altered in severe and non-severe COVID-19. In addition, we used multiple machine learning methods to screen for five risk genes (KLF5, NSUN7, APH1B, GRB10 and CD4), which are used to predict COVID-19 severity. Finally, we constructed a nomogram to predict the risk of severe COVID-19 based on the classification and recognition model, and validated the model with external data sets. This study provides a valuable direction for the exploration of the pathogenesis and progress of COVID-19, and helps in the early identification of severe cases of COVID-19 to reduce mortality.
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Affiliation(s)
- Chunyu Li
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Ke Wu
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Rui Yang
- Department of Internal Medicine, Guiyang First People's Hospital, Guiyang, 550004, Guizhou, China
| | - Minghua Liao
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jun Li
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Qian Zhu
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jiayi Zhang
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xianming Zhang
- Department of Respiratory and Critical Medicine, the Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China.
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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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Cadore NA, Lord VO, Recamonde-Mendoza M, Kowalski TW, Vianna FSL. Meta-analysis of Transcriptomic Data from Lung Autopsy and Cellular Models of SARS-CoV-2 Infection. Biochem Genet 2024; 62:892-914. [PMID: 37486510 DOI: 10.1007/s10528-023-10453-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023]
Abstract
Severe COVID-19 is a systemic disorder involving excessive inflammatory response, metabolic dysfunction, multi-organ damage, and several clinical features. Here, we performed a transcriptome meta-analysis investigating genes and molecular mechanisms related to COVID-19 severity and outcomes. First, transcriptomic data of cellular models of SARS-CoV-2 infection were compiled to understand the first response to the infection. Then, transcriptomic data from lung autopsies of patients deceased due to COVID-19 were compiled to analyze altered genes of damaged lung tissue. These analyses were followed by functional enrichment analyses and gene-phenotype association. A biological network was constructed using the disturbed genes in the lung autopsy meta-analysis. Central genes were defined considering closeness and betweenness centrality degrees. A sub-network phenotype-gene interaction analysis was performed. The meta-analysis of cellular models found genes mainly associated with cytokine signaling and other pathogen response pathways. The meta-analysis of lung autopsy tissue found genes associated with coagulopathy, lung fibrosis, multi-organ damage, and long COVID-19. Only genes DNAH9 and FAM216B were found perturbed in both meta-analyses. BLNK, FABP4, GRIA1, ATF3, TREM2, TPPP, TPPP3, FOS, ALB, JUNB, LMNA, ADRB2, PPARG, TNNC1, and EGR1 were identified as central elements among perturbed genes in lung autopsy and were found associated with several clinical features of severe COVID-19. Central elements were suggested as interesting targets to investigate the relation with features of COVID-19 severity, such as coagulopathy, lung fibrosis, and organ damage.
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Affiliation(s)
- Nathan Araujo Cadore
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Post-Graduation Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Vinicius Oliveira Lord
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Centro Universitário CESUCA, Cachoeirinha, Brazil
| | - Mariana Recamonde-Mendoza
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Institute of Informatics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Thayne Woycinck Kowalski
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Post-Graduation Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Centro Universitário CESUCA, Cachoeirinha, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
- Post-Graduation Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
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40
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Gatselis NK, Lyberopoulou A, Lygoura V, Giannoulis G, Samakidou A, Vaiou A, Antoniou K, Triantafyllou K, Stefos A, Georgiadou S, Sagris D, Sveroni D, Gabeta S, Ntaios G, Norman GL, Dalekos GN. Calprotectin serum levels on admission and during follow-up predict severity and outcome of patients with COVID-19: A prospective study. Eur J Intern Med 2024; 122:78-85. [PMID: 37953124 DOI: 10.1016/j.ejim.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/02/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND & AIMS Calprotectin reflects neutrophil activation and is increased in various inflammatory conditions including severe COVID-19. However, serial serum calprotectin measurements in COVID-19 patients are limited. We assessed prospectively, calprotectin levels as biomarker of severity/outcome of the disease and a COVID-19 monitoring parameter in a large cohort of consecutive COVID-19 patients. METHODS Calprotectin serum levels were measured in 736 patients (58.2 % males; median age 63-years; moderate disease, n = 292; severe, n = 444, intubated and/or died, n = 50). Patients were treated with combined immunotherapies according to our published local algorithm. The endpoint was the composite event of intubation due to severe respiratory failure (SRF)/COVID-19-related mortality. RESULTS Median (interquartile range) calprotectin levels were significantly higher in patients with severe disease [7(8.2) vs. 6.1(8.1)μg/mL, p = 0.015]. Calprotectin on admission was the only independent risk factor for intubation/death (HR=1.473, 95 %CI=1.003-2.165, p = 0.048) even after adjustment for age, sex, body mass index, comorbidities, neutrophils, lymphocytes, neutrophil to lymphocytes ratio, ferritin, and CRP. The area under the curve (AUC, 95 %CI) of calprotectin for prediction of intubation/death was 0.619 (0.531-0.708), with an optimal cut-off at 13 μg/mL (sensitivity: 44 %, specificity: 79 %, positive and negative predictive values: 13 % and 95 %, respectively). For intubated/died patients, paired comparisons from baseline to middle of hospitalization and subsequently to intubation/death showed significant increase of calprotectin (p = 0.009 and p < 0.001, respectively). Calprotectin alteration had the higher predictive ability for intubation/death [AUC (95 %CI):0.803 (0.664-0.943), p < 0.001]. CONCLUSIONS Calprotectin levels on admission and their subsequent dynamic alterations could serve as indicator of COVID-19 severity and predict the occurrence of SRF and mortality.
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Affiliation(s)
- Nikolaos K Gatselis
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Aggeliki Lyberopoulou
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Vasiliki Lygoura
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - George Giannoulis
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Anna Samakidou
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Antonia Vaiou
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Katerina Antoniou
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Katerina Triantafyllou
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Aggelos Stefos
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Sarah Georgiadou
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Dimitrios Sagris
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Dafni Sveroni
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Stella Gabeta
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - George Ntaios
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Gary L Norman
- Research and Development, Headquarters & Technology Center Autoimmunity, Werfen, San Diego, CA 92131, USA
| | - George N Dalekos
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa, Larissa, Greece; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece.
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Flora C, Olesnavich M, Zuo Y, Sandford E, Madhukar R, Rozwadowski M, Sugur K, Ly A, Canbaz AA, Shedeck A, Li G, Geer MJ, Yanik GA, Ghosh M, Frame DG, Bonifant CL, Jain T, Knight JS, Choi SW, Tewari M. Longitudinal plasma proteomics in CAR T-cell therapy patients implicates neutrophils and NETosis in the genesis of CRS. Blood Adv 2024; 8:1422-1426. [PMID: 38266157 PMCID: PMC10950819 DOI: 10.1182/bloodadvances.2023010728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024] Open
Affiliation(s)
- Christopher Flora
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI
| | - Mary Olesnavich
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI
| | - Yu Zuo
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI
| | - Erin Sandford
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI
| | - Rashmi Madhukar
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI
| | - Michelle Rozwadowski
- Department of Pediatrics, Division of Pediatric Hematology Oncology, University of Michigan, Ann Arbor, MI
| | - Kavya Sugur
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI
| | - Andrew Ly
- Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ata Alpay Canbaz
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Audra Shedeck
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Gen Li
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Marcus J. Geer
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI
| | - Gregory A. Yanik
- Department of Pediatrics, Division of Pediatric Hematology Oncology, University of Michigan, Ann Arbor, MI
| | - Monalisa Ghosh
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI
| | - David G. Frame
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI
| | - Challice L. Bonifant
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Tania Jain
- Johns Hopkins University School of Medicine, Baltimore, MD
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jason S. Knight
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI
| | - Sung Won Choi
- Department of Pediatrics, Division of Pediatric Hematology Oncology, University of Michigan, Ann Arbor, MI
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
- VA Ann Arbor Healthcare System, Ann Arbor, MI
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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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Lin Y, Yang Y, Xiang N, Wang L, Zheng T, Zhuo X, Shi R, Su X, Liu Y, Liao G, Du L, Huang J. Characterization and trajectories of hematological parameters prior to severe COVID-19 based on a large-scale prospective health checkup cohort in western China: a longitudinal study of 13-year follow-up. BMC Med 2024; 22:105. [PMID: 38454462 PMCID: PMC10921814 DOI: 10.1186/s12916-024-03326-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND The relaxation of the "zero-COVID" policy on Dec. 7, 2022, in China posed a major public health threat recently. Complete blood count test was discovered to have complicated relationships with COVID-19 after the infection, while very few studies could track long-term monitoring of the health status and identify the characterization of hematological parameters prior to COVID-19. METHODS Based on a 13-year longitudinal prospective health checkup cohort of ~ 480,000 participants in West China Hospital, the largest medical center in western China, we documented 998 participants with a laboratory-confirmed diagnosis of COVID-19 during the 1 month after the policy. We performed a time-to-event analysis to explore the associations of severe COVID-19 patients diagnosed, with 34 different hematological parameters at the baseline level prior to COVID-19, including the whole and the subtypes of white and red blood cells. RESULTS A total of 998 participants with a positive SARS-CoV-2 test were documented in the cohort, 42 of which were severe cases. For white blood cell-related parameters, a higher level of basophil percentage (HR = 6.164, 95% CI = 2.066-18.393, P = 0.001) and monocyte percentage (HR = 1.283, 95% CI = 1.046-1.573, P = 0.017) were found associated with the severe COVID-19. For lymphocyte-related parameters, a lower level of lymphocyte count (HR = 0.571, 95% CI = 0.341-0.955, P = 0.033), and a higher CD4/CD8 ratio (HR = 2.473, 95% CI = 1.009-6.059, P = 0.048) were found related to the risk of severe COVID-19. We also observed that abnormality of red cell distribution width (RDW), mean corpuscular hemoglobin concentration (MCHC), and hemoglobin might also be involved in the development of severe COVID-19. The different trajectory patterns of RDW-SD and white blood cell count, including lymphocyte and neutrophil, prior to the infection were also discovered to have significant associations with the risk of severe COVID-19 (all P < 0.05). CONCLUSIONS Our findings might help decision-makers and clinicians to classify different risk groups of population due to outbreaks including COVID-19. They could not only optimize the allocation of medical resources, but also help them be more proactive instead of reactive to long COVID-19 or even other outbreaks in the future.
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Affiliation(s)
- Yifei Lin
- Department of Urology, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Yong Yang
- Health Management Center, General Practice Medical Center, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Nanyan Xiang
- Department of Urology, Innovation Institute for Integration of Medicine and Engineering, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Le Wang
- Department of Urology, Innovation Institute for Integration of Medicine and Engineering, Frontiers Science Center for Disease-Related Molecular Network, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Tao Zheng
- Engineering Research Center of Medical Information Technology, Ministry of Education, West China Hospital of Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Xuejun Zhuo
- Engineering Research Center of Medical Information Technology, Ministry of Education, West China Hospital of Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Rui Shi
- Engineering Research Center of Medical Information Technology, Ministry of Education, West China Hospital of Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Xiaoyi Su
- Department of Urology, Innovation Institute for Integration of Medicine and Engineering, Chinese Evidence-Based Medicine Center, West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Yan Liu
- Department of Neurosurgery, Innovation Institute for Integration of Medicine and Engineering, Ministry of Education, West China Hospital of Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Ga Liao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Liang Du
- Department of Urology, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
| | - Jin Huang
- Department of Urology, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
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Ciurea A, Stanomir A, Șurlin P, Micu IC, Pamfil C, Leucuța DC, Rednic S, Rasperini G, Soancă A, Țigu AB, Roman A, Picoș A, Delean AG. Insights into the Relationship between Periodontitis and Systemic Sclerosis Based on the New Periodontitis Classification (2018): A Cross-Sectional Study. Diagnostics (Basel) 2024; 14:540. [PMID: 38473012 DOI: 10.3390/diagnostics14050540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
(1) Background: This study aimed to assess the periodontitis burden in systemic sclerosis patients and the possible association between them, and the degree to which some potential risk factors and two potential diagnostic biomarkers may account for this association. (2) Methods: This cross-sectional study included a test group (systemic sclerosis patients) and a control group (non-systemic sclerosis patients). Both groups benefited from medical, periodontal examination and saliva sampling to determine the salivary flow rate and two inflammatory biomarkers (calprotectin, psoriasin). A systemic sclerosis severity scale was established. (3) Results: In the studied groups, comparable periodontitis rates of 88.68% and 85.85%, respectively, were identified. There were no significant differences in the severity of periodontitis among different systemic sclerosis severity, or in the positivity for anti-centromere and anti-SCL70 antibodies. Musculoskeletal lesions were significantly more common in stage III/IV periodontitis (n = 33, 86.84%) than in those in stage I/II (n = 1, 100%, and n = 3, 37.5%, respectively) (p = 0.007). Comparable levels of the inflammatory mediators were displayed by the two groups. There were no significant differences in calprotectin and psoriasin levels between diffuse and limited forms of systemic sclerosis. (4) Conclusions: Within the limitations of the current study, no associations between systemic sclerosis and periodontitis, or between their risk factors, could be proven.
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Affiliation(s)
- Andreea Ciurea
- Department of Periodontology, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Emergency County Clinical Hospital Cluj, 400006 Cluj-Napoca, Romania
| | - Alina Stanomir
- Department of Periodontology, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Petra Șurlin
- Department of Periodontology, Faculty of Dental Medicine, University of Medicine and Pharmacy Craiova, 200349 Craiova, Romania
| | - Iulia Cristina Micu
- Department of Periodontology, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Cristina Pamfil
- Emergency County Clinical Hospital Cluj, 400006 Cluj-Napoca, Romania
- Department of Rheumatology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
| | - Daniel Corneliu Leucuța
- Department of Medical Informatics and Biostatistics, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400347 Cluj-Napoca, Romania
| | - Simona Rednic
- Emergency County Clinical Hospital Cluj, 400006 Cluj-Napoca, Romania
- Department of Rheumatology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
| | - Giulio Rasperini
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Foundation IRCCS Ca' Granda Policlinic, 20122 Milan, Italy
| | - Andrada Soancă
- Department of Periodontology, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Emergency County Clinical Hospital Cluj, 400006 Cluj-Napoca, Romania
| | - Adrian Bogdan Țigu
- Research Centre for Advanced Medicine (MEDFUTURE), Iuliu Hatieganu University of Medicine and Pharmacy, 400347 Cluj-Napoca, Romania
| | - Alexandra Roman
- Department of Periodontology, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Emergency County Clinical Hospital Cluj, 400006 Cluj-Napoca, Romania
| | - Andrei Picoș
- Department of Prevention in Dental Medicine, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400083 Cluj-Napoca, Romania
| | - Ada Gabriela Delean
- Department of Odontology and Endodontics, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400001 Cluj-Napoca, Romania
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Lignier G, Camaré C, Jamme T, Combis MS, Tayac D, Maupas-Schwalm F. Assessment of the predictive value of plasma calprotectin in the evolution of SARS-Cov-2 primo-infection. Infect Dis Now 2024; 54:104860. [PMID: 38309645 DOI: 10.1016/j.idnow.2024.104860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 01/29/2024] [Indexed: 02/05/2024]
Abstract
BACKGROUND The COVID-19 epidemic still calls for anticipation aimed at preventing the overloading of critical care services. With this in mind, the predictive value of easily accessible biomarkers is to be assessed. OBJECTIVE Secretion of calprotectin is stimulated during an inflammatory process, especially in the cytokine storm. We tried to determine whether early plasma concentration of calprotectin in patients with primary SARS-CoV-2 infection could predict an adverse outcome in cases of COVID-19. METHODS We included 308 patients with a primary diagnosis of SARS-CoV-2 confirmed by PCR. Heparinized tube samples, collected within the first 24 h of hospitalization, were used for biomarker assays, in which plasma calprotectin was included. Data from the patients' medical records and severity groups established subsequent to diagnosis at the end of hospitalization were collected. RESULTS Early plasma calprotectin concentration is significantly associated with progression to a severe form of COVID-19 in patients with primary infection (Relative Risk: 2.2 [1.6-2.7]). In multivariate analysis, however, it does not appear to provide additional information compared to other parameters (age, GFR, CRP…). CONCLUSION Our study shows that while an early single blood test for calprotectin could help to predict the progression of a primary SARS-CoV-2 infection, it is not superior to the other parameters currently used in emergency medicine. However, it paves the way for future considerations, such as the interest of this biomarker for high-risk infected patients (immunocompromised individuals…). Finally, the usefulness of early serial measurements of plasma calprotectin to assess progression towards severity of COVID-19 requires further assessment.
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Affiliation(s)
- Gauthier Lignier
- Faculty of Pharmacy, Toulouse III university, France; Medical biochemistry laboratory, CHU Toulouse, France
| | - Caroline Camaré
- Medical biochemistry laboratory, CHU Toulouse, France; Faculty of Medicine, Toulouse III university, France
| | - Thibaut Jamme
- Medical biochemistry laboratory, CHU Toulouse, France
| | | | - Didier Tayac
- Medical biochemistry laboratory, CHU Toulouse, France
| | - Françoise Maupas-Schwalm
- Medical biochemistry laboratory, CHU Toulouse, France; Faculty of Medicine, Toulouse III university, France.
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Mahmoodi M, Mohammadi Henjeroei F, Hassanshahi G, Nosratabadi R. Do chemokine/chemokine receptor axes play paramount parts in trafficking and oriented locomotion of monocytes/macrophages toward the lungs of COVID-19 infected patients? A systematic review. Cytokine 2024; 175:156497. [PMID: 38190792 DOI: 10.1016/j.cyto.2023.156497] [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: 07/25/2023] [Revised: 12/19/2023] [Accepted: 12/31/2023] [Indexed: 01/10/2024]
Abstract
The COVID-19 (coronavirus disease 2019) is a well-defined viral infection, resulting from SARS-CoV-2 (severe acute respiratory syndrome- coronavirus-2). The innate immune system serves as the first line of defense to limit viral spreading and subsequently stimulate adaptive immune responses by the prominent aids of its cellular and molecular arms. Monocytes are defined as the most prominent innate immune cells (IICs) that are reactive against invading pathogens. These cells support host protection against the virus that is mediated by several non-specific mechanisms such as phagocytosis, producing antiviral enzymes, and recruitment of immune cells toward and into the infected tissues. They have the ability to egress from blood and migrate to the SARS-CoV-2 infected regions by the aid of some defense-related functions like chemotaxis, which is mediated by chemical compounds, e.g., chemokines. Chemokines, in addition to their related ligands are categorized within the most important and deserved agents involved in oriented trafficking of monocytes/macrophages towards and within the lung parenchyma in both steady state and pathological circumstances, including COVID-19-raised infection. However, the overexpression of chemokines could have deleterious effects on various organs through the induction of cytokine storm and may be the most important leading mechanisms in the pathogenesis of COVID-19. Authors have aimed the current review article to describe present knowledge about the interplay between monocytes/macrophages and SARS-CoV-2 with a focus on the ability of IICs to migrate and home into the lung of COVID-19 patients through various chemokine-chemokine receptor axes to promote our understanding regarding this disease.
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Affiliation(s)
- Merat Mahmoodi
- Department of Medical Immunology, Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Fatemeh Mohammadi Henjeroei
- Department of Medical Immunology, Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Gholamhossein Hassanshahi
- Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, RafsanjanUniversity of Medical Sciences, Rafsanjan, Iran
| | - Reza Nosratabadi
- Department of Medical Immunology, Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran; Gastroenterology and Hepatology Research Center, Kerman University of Medical Sciences, Kerman, Iran.
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Zhang H, Zhang Q, Liu K, Yuan Z, Xu X, Dong J. Elevated level of circulating calprotectin correlates with severity and high mortality in patients with COVID-19. Immun Inflamm Dis 2024; 12:e1212. [PMID: 38477671 DOI: 10.1002/iid3.1212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/22/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Patients with coronavirus disease-2019 (COVID-19) are characterized by hyperinflammation. Calprotectin (S100A8/S100A9) is a calcium- and zinc-binding protein mainly secreted by neutrophilic granulocytes or macrophages and has been suggested to be correlated with the severity and prognosis of COVID-19. AIM To thoroughly evaluate the diagnostic and prognostic utility of calprotectin in patients with COVID-19 by analyzing relevant studies. METHODS PubMed, Web of Science, and Cochrane Library were comprehensively searched from inception to August 1, 2023 to retrieve studies about the application of calprotectin in COVID-19. Useful data such as the level of calprotectin in different groups and the diagnostic efficacy of this biomarker for severe COVID-19 were extracted and aggregated by using Stata 16.0 software. RESULTS Fifteen studies were brought into this meta-analysis. First, the pooled standardized mean differences (SMDs) were used to estimate the differences in the levels of circulating calprotectin between patients with severe and non-severe COVID-19. The results showed an overall estimate of 1.84 (95% confidence interval [CI]: 1.09-2.60). Diagnostic information was extracted from 11 studies, and the pooled sensitivity and specificity of calprotectin for diagnosing severe COVID-19 were 0.75 (95% CI: 0.64-0.84) and 0.88 (95% CI: 0.79-0.94), respectively. The AUC was 0.89 and the pooled DOR was 18.44 (95% CI: 9.07-37.51). Furthermore, there was a strong correlation between elevated levels of circulating calprotectin and a higher risk of mortality outcomes in COVID-19 patients (odds ratio: 8.60, 95% CI: 2.17-34.12; p < 0.1). CONCLUSION This meta-analysis showed that calprotectin was elevated in patients with severe COVID-19, and this atypical inflammatory cytokine might serve as a useful biomarker to distinguish the severity of COVID-19 and predict the prognosis.
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Affiliation(s)
- Haoran Zhang
- Department of Orthopaedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, China
| | - Qingyu Zhang
- Department of Orthopaedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, China
| | - Kun Liu
- Graduate School of Education, Shandong Sport University, Jinan, Shandong Province, China
| | - Zenong Yuan
- Department of Orthopaedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, China
| | - Xiqiang Xu
- Department of Orthopaedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, China
| | - Jun Dong
- Department of Orthopaedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, China
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Gu X, Huang L, Li X, Zhou Y, Zhang H, Wang Y, Cui D, Yu T, Wang Y, Cao B. Association of Monocyte Count With Lung Function and Exercise Capacity Among Hospitalized COVID-19 Survivors: A 2-Year Cohort Study. Influenza Other Respir Viruses 2024; 18:e13263. [PMID: 38503498 PMCID: PMC10950557 DOI: 10.1111/irv.13263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/17/2024] [Accepted: 01/27/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Abnormal changes of monocytes have been observed in acute COVID-19, whereas associations of monocyte count with long COVID were not sufficiently elucidated. METHODS A cohort study was conducted among COVID-19 survivors discharged from hospital. The primary outcomes were core symptoms of long COVID, distance walked in 6 min, and lung function, and the secondary outcomes were health-related quality of life and healthcare use after discharge. Latent variable mixture modeling was used to classify individuals into groups with similar trajectory of monocyte count from discharge to 2-year after symptom onset. Multivariable adjusted generalized linear regression models and logistic regression models were used to estimate the associations of monocyte count trajectories and monocyte count at discharge with outcomes. RESULTS In total, 1389 study participants were included in this study. Two monocyte count trajectories including high to normal high and normal trajectory were identified. After multivariable adjustment, participants in high to normal high trajectory group had an odds ratio (OR) of 2.52 (95% CI, 1.44-4.42) for smell disorder, 2.27 (1.27-4.04) for 6-min walking distance less than lower limit of normal range, 2.45 (1.08-5.57) for total lung capacity (TLC) < 80% of predicted, 3.37 (1.16-9.76) for personal care problem, and 1.70 (1.12-2.58) for rehospitalization after discharge at 2-year follow-up compared with those in normal trajectory group. Monocyte count at discharge showed similar results, which was associated with smell disorder, TLC < 80% of predicted, diffusion impairment, and rehospitalization. CONCLUSIONS Monocyte count may serve as an easily accessible marker for long-term management of people recovering from COVID-19.
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Affiliation(s)
- Xiaoying Gu
- National Center for Respiratory MedicineBeijingChina
- State Key Laboratory of Respiratory Health and MultimorbidityBeijingChina
- National Clinical Research Center for Respiratory DiseasesBeijingChina
- Institute of Respiratory MedicineChinese Academy of Medical SciencesBeijingChina
- Department of Clinical Research and Data Management, Center of Respiratory MedicineChina‐Japan Friendship HospitalBeijingChina
| | - Lixue Huang
- Department of Respiratory and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Xia Li
- Hubei Provincial Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and TreatmentChinese Academy of Medical SciencesWuhanChina
| | - Yuting Zhou
- Department of Pulmonary and Critical Care Medicine, Hubei Provincial Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and TreatmentChinese Academy of Medical SciencesWuhanChina
| | - Hui Zhang
- National Center for Respiratory MedicineBeijingChina
- State Key Laboratory of Respiratory Health and MultimorbidityBeijingChina
- National Clinical Research Center for Respiratory DiseasesBeijingChina
- Institute of Respiratory MedicineChinese Academy of Medical SciencesBeijingChina
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory MedicineChina‐Japan Friendship HospitalBeijingChina
- Department of Pulmonary and Critical Care MedicineCapital Medical UniversityBeijingChina
| | - Yeming Wang
- National Center for Respiratory MedicineBeijingChina
- State Key Laboratory of Respiratory Health and MultimorbidityBeijingChina
- National Clinical Research Center for Respiratory DiseasesBeijingChina
- Institute of Respiratory MedicineChinese Academy of Medical SciencesBeijingChina
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory MedicineChina‐Japan Friendship HospitalBeijingChina
| | - Dan Cui
- Department of Pulmonary and Critical Care MedicineThe 2nd Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Ting Yu
- Department of Pulmonary and Critical Care Medicine, Hubei Provincial Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and TreatmentChinese Academy of Medical SciencesWuhanChina
| | - Yimin Wang
- National Center for Respiratory MedicineBeijingChina
- State Key Laboratory of Respiratory Health and MultimorbidityBeijingChina
- National Clinical Research Center for Respiratory DiseasesBeijingChina
- Institute of Respiratory MedicineChinese Academy of Medical SciencesBeijingChina
- Department of Pulmonary and Critical Care Medicine, Hubei Provincial Clinical Research Center for Infectious Diseases, Wuhan Research Center for Communicable Disease Diagnosis and TreatmentChinese Academy of Medical SciencesWuhanChina
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory MedicineChina‐Japan Friendship HospitalBeijingChina
| | - Bin Cao
- National Center for Respiratory MedicineBeijingChina
- State Key Laboratory of Respiratory Health and MultimorbidityBeijingChina
- National Clinical Research Center for Respiratory DiseasesBeijingChina
- Institute of Respiratory MedicineChinese Academy of Medical SciencesBeijingChina
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory MedicineChina‐Japan Friendship HospitalBeijingChina
- Department of Pulmonary and Critical Care MedicineCapital Medical UniversityBeijingChina
- Tsinghua University‐Peking University Joint Center for Life SciencesBeijingChina
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Long MB, Howden AJM, Keir HR, Rollings CM, Giam YH, Pembridge T, Delgado L, Abo-Leyah H, Lloyd AF, Sollberger G, Hull R, Gilmour A, Hughes C, New BJM, Cassidy D, Shoemark A, Richardson H, Lamond AI, Cantrell DA, Chalmers JD, Brenes AJ. Extensive acute and sustained changes to neutrophil proteomes post-SARS-CoV-2 infection. Eur Respir J 2024; 63:2300787. [PMID: 38097207 PMCID: PMC10918319 DOI: 10.1183/13993003.00787-2023] [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: 05/14/2023] [Accepted: 11/23/2023] [Indexed: 02/15/2024]
Abstract
BACKGROUND Neutrophils are important in the pathophysiology of coronavirus disease 2019 (COVID-19), but the molecular changes contributing to altered neutrophil phenotypes following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are not fully understood. We used quantitative mass spectrometry-based proteomics to explore neutrophil phenotypes immediately following acute SARS-CoV-2 infection and during recovery. METHODS Prospective observational study of hospitalised patients with PCR-confirmed SARS-CoV-2 infection (May to December 2020). Patients were enrolled within 96 h of admission, with longitudinal sampling up to 29 days. Control groups comprised non-COVID-19 acute lower respiratory tract infection (LRTI) and age-matched noninfected controls. Neutrophils were isolated from peripheral blood and analysed using mass spectrometry. COVID-19 severity and recovery were defined using the World Health Organization ordinal scale. RESULTS Neutrophil proteomes from 84 COVID-19 patients were compared to those from 91 LRTI and 42 control participants. 5800 neutrophil proteins were identified, with >1700 proteins significantly changed in neutrophils from COVID-19 patients compared to noninfected controls. Neutrophils from COVID-19 patients initially all demonstrated a strong interferon signature, but this signature rapidly declined in patients with severe disease. Severe disease was associated with increased abundance of proteins involved in metabolism, immunosuppression and pattern recognition, while delayed recovery from COVID-19 was associated with decreased granule components and reduced abundance of metabolic proteins, chemokine and leukotriene receptors, integrins and inhibitory receptors. CONCLUSIONS SARS-CoV-2 infection results in the sustained presence of circulating neutrophils with distinct proteomes suggesting altered metabolic and immunosuppressive profiles and altered capacities to respond to migratory signals and cues from other immune cells, pathogens or cytokines.
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Affiliation(s)
- Merete B Long
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
- Indicates equal contribution
| | - Andrew J M Howden
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Indicates equal contribution
| | - Holly R Keir
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
- Indicates equal contribution
| | - Christina M Rollings
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Indicates equal contribution
| | - Yan Hui Giam
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Thomas Pembridge
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Lilia Delgado
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Hani Abo-Leyah
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Amy F Lloyd
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Gabriel Sollberger
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Rebecca Hull
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Amy Gilmour
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Chloe Hughes
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Benjamin J M New
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Diane Cassidy
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Amelia Shoemark
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Hollian Richardson
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Angus I Lamond
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Doreen A Cantrell
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
- Indicates joint senior authorship
| | - Alejandro J Brenes
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
- Indicates joint senior authorship
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Andrejčinová I, Blažková G, Papatheodorou I, Bendíčková K, Bosáková V, Skotáková M, Panovský R, Opatřil L, Vymazal O, Kovačovicová P, Šrámek V, Helán M, Hortová-Kohoutková M, Frič J. Persisting IL-18 levels after COVID-19 correlate with markers of cardiovascular inflammation reflecting potential risk of CVDs development. Heliyon 2024; 10:e25938. [PMID: 38404862 PMCID: PMC10884808 DOI: 10.1016/j.heliyon.2024.e25938] [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: 11/10/2023] [Revised: 02/04/2024] [Accepted: 02/05/2024] [Indexed: 02/27/2024] Open
Abstract
COVID-19 manifestation is associated with a strong immune system activation leading to inflammation and subsequently affecting the cardiovascular system. The objective of the study was to reveal possible interconnection between prolongated inflammation and the development or exacerbation of long-term cardiovascular complications after COVID-19. We investigated correlations between humoral and cellular immune system markers together with markers of cardiovascular inflammation/dysfunction during COVID-19 onset and subsequent recovery. We analyzed 22 hospitalized patients with severe COVID-19 within three timepoints (acute, 1 and 6 months after COVID-19) in order to track the impact of COVID-19 on the long-term decline of the cardiovascular system fitness and eventual development of CVDs. Among the cytokines dysregulated during COVID-19 changes, we showed significant correlations of IL-18 as a key driver of several pathophysiological changes with markers of cardiovascular inflammation/dysfunction. Our findings established novel immune-related markers, which can be used for the stratification of patients at high risk of CVDs for further therapy.
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Affiliation(s)
- Ivana Andrejčinová
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Gabriela Blažková
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Ioanna Papatheodorou
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Kamila Bendíčková
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- International Clinical Research Center, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Veronika Bosáková
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Monika Skotáková
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Roman Panovský
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- 1st Department of Internal Medicine/Cardioangiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lukáš Opatřil
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- 1st Department of Internal Medicine/Cardioangiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ondřej Vymazal
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Petra Kovačovicová
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Vladimír Šrámek
- Department of Anesthesiology and Intensive Care, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Martin Helán
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- Department of Anesthesiology and Intensive Care, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marcela Hortová-Kohoutková
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- International Clinical Research Center, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Frič
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
- International Clinical Research Center, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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