151
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Wang H, Ji Z. T-cell receptor sequences correlate with and predict gene expression levels in T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568912. [PMID: 38076860 PMCID: PMC10705237 DOI: 10.1101/2023.11.27.568912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
T cells exhibit high heterogeneity in both their gene expression profiles and antigen specificities. We analyzed fifteen single-cell immune profiling datasets to systematically investigate the association between T-cell receptor (TCR) sequences and the gene expression profiles of T cells. Our findings reveal that T cells sharing identical or similar TCR sequences tend to have highly similar gene expression profiles. Additionally, we developed a foundational model that leverages TCR information to predict gene expression levels in T cells.
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Affiliation(s)
- Hao Wang
- Department of Statistical Science, Duke University, Durham, NC, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
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152
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Chauhan NR, Kundu S, Bal R, Chattopadhyay D, Sahu R, Mehto S, Yadav R, Krishna S, Jena KK, Satapathy S, Pv A, Murmu KC, Singh B, Patnaik S, Jena S, Harshan KH, Syed GH, Idris MM, Prasad P, Chauhan S. Transgenic mouse models support a protective role of type I IFN response in SARS-CoV-2 infection-related lung immunopathology and neuroinvasion. Cell Rep 2023; 42:113275. [PMID: 37874678 DOI: 10.1016/j.celrep.2023.113275] [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: 04/07/2023] [Revised: 08/14/2023] [Accepted: 09/28/2023] [Indexed: 10/26/2023] Open
Abstract
Type I interferon (IFN-I) response is the first line of host defense against invading viruses. In the absence of definite mouse models, the role of IFN-I in SARS-CoV-2 infection remains perplexing. Here, we develop two mouse models, one with constitutively high IFN-I response (hACE2; Irgm1-/-) and the other with dampened IFN-I response (hACE2; Ifnar1-/-), to comprehend the role of IFN-I response. We report that hACE2; Irgm1-/- mice are resistant to lethal SARS-CoV-2 infection. In contrast, a severe SARS-CoV-2 infection along with immune cell infiltration, cytokine storm, and enhanced pathology is observed in the lungs and brain of hACE2; Ifnar1-/- mice. The hACE2; Irgm1-/-Ifnar1-/- double-knockout mice display loss of the protective phenotype observed in hACE2; Irgm1-/- mice, suggesting that heightened IFN-I response accounts for the observed immunity. Taking the results together, we demonstrate that IFN-I protects from lethal SARS-CoV-2 infection, and Irgm1 (IRGM) could be an excellent therapeutic target against SARS-CoV-2.
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Affiliation(s)
- Nishant Ranjan Chauhan
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India.
| | - Soumya Kundu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Ramyasingh Bal
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Diya Chattopadhyay
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Rinku Sahu
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Subhash Mehto
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Rina Yadav
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Sivaram Krishna
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Kautilya Kumar Jena
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Sameekshya Satapathy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Anusha Pv
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Krushna C Murmu
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Bharati Singh
- Virus-Host Interactions Lab, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | | | - Sarita Jena
- Experimental Animal Facility, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Krishnan H Harshan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Gulam Hussain Syed
- Virus-Host Interactions Lab, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Mohammed M Idris
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Punit Prasad
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Santosh Chauhan
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India.
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153
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Wang L, Nicols A, Turtle L, Richter A, Duncan CJA, Dunachie SJ, Klenerman P, Payne RP. T cell immune memory after covid-19 and vaccination. BMJ MEDICINE 2023; 2:e000468. [PMID: 38027416 PMCID: PMC10668147 DOI: 10.1136/bmjmed-2022-000468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The T cell memory response is a crucial component of adaptive immunity responsible for limiting or preventing viral reinfection. T cell memory after infection with the SARS-CoV-2 virus or vaccination is broad, and spans multiple viral proteins and epitopes, about 20 in each individual. So far the T cell memory response is long lasting and provides a high level of cross reactivity and hence resistance to viral escape by variants of the SARS-CoV-2 virus, such as the omicron variant. All current vaccine regimens tested produce robust T cell memory responses, and heterologous regimens will probably enhance protective responses through increased breadth. T cell memory could have a major role in protecting against severe covid-19 disease through rapid viral clearance and early presentation of epitopes, and the presence of cross reactive T cells might enhance this protection. T cell memory is likely to provide ongoing protection against admission to hospital and death, and the development of a pan-coronovirus vaccine might future proof against new pandemic strains.
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Affiliation(s)
- Lulu Wang
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Alex Nicols
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Alex Richter
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Christopher JA Duncan
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Susanna J Dunachie
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University Faculty of Science, Bangkok, Thailand
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, Oxfordshire, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
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154
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Morrell ED, Holton SE, Lawrance M, Orlov M, Franklin Z, Mitchem MA, DeBerg H, Gersuk VH, Garay A, Barnes E, Liu T, Peltan ID, Rogers A, Ziegler S, Wurfel MM, Mikacenic C. The transcriptional and phenotypic characteristics that define alveolar macrophage subsets in acute hypoxemic respiratory failure. Nat Commun 2023; 14:7443. [PMID: 37978185 PMCID: PMC10656558 DOI: 10.1038/s41467-023-43223-0] [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: 05/06/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
The transcriptional and phenotypic characteristics that define alveolar monocyte and macrophage subsets in acute hypoxemic respiratory failure (AHRF) are poorly understood. Here, we apply CITE-seq (single-cell RNA-sequencing and cell-surface protein quantification) to bronchoalveolar lavage and blood specimens longitudinally collected from participants with AHRF to identify alveolar myeloid subsets, and then validate their identity in an external cohort using flow cytometry. We identify alveolar myeloid subsets with transcriptional profiles that differ from other lung diseases as well as several subsets with similar transcriptional profiles as reported in healthy participants (Metallothionein) or patients with COVID-19 (CD163/LGMN). We use information from CITE-seq to determine cell-surface proteins that distinguish transcriptional subsets (CD14, CD163, CD123, CD71, CD48, CD86 and CD44). In the external cohort, we find a higher proportion of CD163/LGMN alveolar macrophages are associated with mortality in AHRF. We report a parsimonious set of cell-surface proteins that distinguish alveolar myeloid subsets using scalable approaches that can be applied to clinical cohorts.
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Affiliation(s)
- Eric D Morrell
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA.
| | - Sarah E Holton
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Matthew Lawrance
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Marika Orlov
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado, Aurora, CO, USA
| | - Zoie Franklin
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | | | - Hannah DeBerg
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Vivian H Gersuk
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Ashley Garay
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Elizabeth Barnes
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Ted Liu
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Ithan D Peltan
- Division of Pulmonary and Critical Care Medicine, Intermountain Health, Murray, UT, USA
| | - Angela Rogers
- Division of Pulmonary and Critical Care, Stanford University, Stanford, CA, USA
| | - Steven Ziegler
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Mark M Wurfel
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Carmen Mikacenic
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA.
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155
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Liang Z, Wang N, Fan C, Shang L, Zhang Y, Gao C, Luo J. Disturbance of Adaptive Immunity System Was Accompanied by a Decrease in Plasma Short-Chain Fatty Acid for Patients Hospitalized During SARS-CoV-2 Infection After COVID-19 Vaccination. J Inflamm Res 2023; 16:5261-5272. [PMID: 38026252 PMCID: PMC10656857 DOI: 10.2147/jir.s434860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can lead to disorders of immune function and a decrease in the diversity of intestinal flora. We aimed to explore the changes of circulating immune cell subsets and the plasma level of intestinal short-chain fatty acids (SCFAs) in patients with Coronavirus disease 2019 (COVID-19), further understanding the pathogenesis of COVID-19. Methods The study included 83 newly diagnosed COVID-19 patients and 39 non-COVID-19 controls. All have completed a full course of vaccination against SARS-CoV-2. The levels of peripheral lymphocyte subsets and plasma cytokines were detected by flow cytometry. Targeted metabolomics was used to explore the level of SCFAs in plasma. Results Compared with the non-COVID-19 group, COVID-19 patients showed a decrease in CD19+B cells, CD4+T cells, CD8+T cells, NK cells, CD4+CD8+T cells and CD4-CD8-T cells (all p<0.001) and concomitantly an increase in sIL-2R, IL-6 and IL-10 (all p<0.005). These alterations were more pronounced in those critical patients. In addition, COVID-19 patients had lower levels of propanoic acid (PA), butyric acid (BA), isobutyric acid (IBA) and isohexanoic acid (ICA) (all p<0.01). Among them, the level of ICA is positively correlated with the absolute number of immune cells. Conclusion Our study suggests the immune cell subsets in COVID-19 patients who had completed vaccination were still severely disturbed and concomitantly lower SCFAs, especially in severe patients with poor prognosis. Lower levels of plasma SCFAs may contribute to lymphopenia in COVID-19. The potential relationship between plasma SCFAs and immune cell reduction provides a new direction for the treatment of COVID-19.
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Affiliation(s)
- Zhaojun Liang
- Division of Rheumatology, Department of Medicine, the Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
- Shanxi Key Laboratory for Immunomicroecology, the Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Nan Wang
- Division of Rheumatology, Department of Medicine, the Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
- Shanxi Key Laboratory for Immunomicroecology, the Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Chunxue Fan
- Division of Rheumatology, Department of Medicine, the Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
- Shanxi Key Laboratory for Immunomicroecology, the Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Lili Shang
- Division of Rheumatology, Department of Medicine, the Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
- Shanxi Key Laboratory for Immunomicroecology, the Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Yaping Zhang
- Division of Rheumatology, Department of Medicine, the Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
- Shanxi Key Laboratory for Immunomicroecology, the Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Chong Gao
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jing Luo
- Division of Rheumatology, Department of Medicine, the Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
- Shanxi Key Laboratory for Immunomicroecology, the Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
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156
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Flynn J, Ahmadi MM, McFarland CT, Kubal MD, Taylor MA, Cheng Z, Torchia EC, Edwards MG. Crowdsourcing temporal transcriptomic coronavirus host infection data: Resources, guide, and novel insights. Biol Methods Protoc 2023; 8:bpad033. [PMID: 38107402 PMCID: PMC10723038 DOI: 10.1093/biomethods/bpad033] [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: 08/09/2023] [Revised: 10/07/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
The emergence of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) reawakened the need to rapidly understand the molecular etiologies, pandemic potential, and prospective treatments of infectious agents. The lack of existing data on SARS-CoV-2 hampered early attempts to treat severe forms of coronavirus disease-2019 (COVID-19) during the pandemic. This study coupled existing transcriptomic data from severe acute respiratory syndrome-related coronavirus 1 (SARS-CoV-1) lung infection animal studies with crowdsourcing statistical approaches to derive temporal meta-signatures of host responses during early viral accumulation and subsequent clearance stages. Unsupervised and supervised machine learning approaches identified top dysregulated genes and potential biomarkers (e.g. CXCL10, BEX2, and ADM). Temporal meta-signatures revealed distinct gene expression programs with biological implications to a series of host responses underlying sustained Cxcl10 expression and Stat signaling. Cell cycle switched from G1/G0 phase genes, early in infection, to a G2/M gene signature during late infection that correlated with the enrichment of DNA damage response and repair genes. The SARS-CoV-1 meta-signatures were shown to closely emulate human SARS-CoV-2 host responses from emerging RNAseq, single cell, and proteomics data with early monocyte-macrophage activation followed by lymphocyte proliferation. The circulatory hormone adrenomedullin was observed as maximally elevated in elderly patients who died from COVID-19. Stage-specific correlations to compounds with potential to treat COVID-19 and future coronavirus infections were in part validated by a subset of twenty-four that are in clinical trials to treat COVID-19. This study represents a roadmap to leverage existing data in the public domain to derive novel molecular and biological insights and potential treatments to emerging human pathogens.
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Affiliation(s)
- James Flynn
- Illumina Corporation, San Diego, CA 92122, United States
| | - Mehdi M Ahmadi
- Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | | | | | - Mark A Taylor
- Bioinfo Solutions LLC, Parker, CO 80134, United States
| | - Zhang Cheng
- Illumina Corporation, San Diego, CA 92122, United States
| | - Enrique C Torchia
- Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
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157
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Ghag R, Kaushal M, Nwanne G, Knoten A, Kiryluk K, Rosenberg A, Menez S, Bagnasco SM, Sperati CJ, Atta MG, Gaut JP, Williams JC, El-Achkar TM, Arend LJ, Parikh CR, Jain S. Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566497. [PMID: 37986991 PMCID: PMC10659401 DOI: 10.1101/2023.11.10.566497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Acute kidney injury (AKI) in COVID-19 patients is associated with high mortality and morbidity. Critically ill COVID-19 patients are at twice the risk of in-hospital mortality compared to non-COVID AKI patients. We know little about the cell-specific mechanism in the kidney that contributes to worse clinical outcomes in these patients. New generation single cell technologies have the potential to provide insights into physiological states and molecular mechanisms in COVID-AKI. One of the key limitations is that these patients are severely ill posing significant risks in procuring additional biopsy tissue. We recently generated single nucleus RNA-sequencing data using COVID-AKI patient biopsy tissue as part of the human kidney atlas. Here we describe this approach in detail and report deeper comparative analysis of snRNAseq of 4 COVID-AKI, 4 reference, and 6 non-COVID-AKI biopsies. We also generated and analyzed urine transcriptomics data to find overlapping COVID-AKI-enriched genes and their corresponding cell types in the kidney from snRNA-seq data. We identified all major and minor cell types and states by using by using less than a few cubic millimeters of leftover tissue after pathological workup in our approach. Differential expression analysis of COVID-AKI biopsies showed pathways enriched in viral response, WNT signaling, kidney development, and cytokines in several nephron epithelial cells. COVID-AKI profiles showed a much higher proportion of altered TAL cells than non-COVID AKI and the reference samples. In addition to kidney injury and fibrosis markers indicating robust remodeling we found that, 17 genes overlap between urine cell COVID-AKI transcriptome and the snRNA-seq data from COVID-AKI biopsies. A key feature was that several of the distal nephron and collecting system cell types express these markers. Some of these markers have been previously observed in COVID-19 studies suggesting a common mechanism of injury and potentially the kidney as one of the sources of soluble factors with a potential role in disease progression. Translational Statement The manuscript describes innovation, application and discovery that impact clinical care in kidney disease. First, the approach to maximize use of remnant frozen clinical biopsies to inform on clinically relevant molecular features can augment existing pathological workflow for any frozen tissue without much change in the protocol. Second, this approach is transformational in medical crises such as pandemics where mechanistic insights are needed to evaluate organ injury, targets for drug therapy and diagnostic and prognostic markers. Third, the cell type specific and soluble markers identified and validated can be used for diagnoses or prognoses in AKI due to different etiologies and in multiorgan injury.
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158
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Al Saihati HA, Hussein HAM, Thabet AA, Wardany AA, Mahmoud SY, Farrag ES, Mohamed TIA, Fathy SM, Elnosary ME, Sobhy A, Ahmed AE, El-Adly AM, El-Shenawy FS, Elsadek AA, Rayan A, Zahran ZAM, El-Badawy O, El-Naggar MGM, Afifi MM, Zahran AM. Memory T Cells Discrepancies in COVID-19 Patients. Microorganisms 2023; 11:2737. [PMID: 38004749 PMCID: PMC10673271 DOI: 10.3390/microorganisms11112737] [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: 09/18/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The immune response implicated in Coronavirus disease 2019 (COVID-19) pathogenesis remains to be fully understood. The present study aimed to clarify the alterations in CD4+ and CD8+ memory T cells' compartments in SARS-CoV-2-infected patients, with an emphasis on various comorbidities affecting COVID-19 patients. Peripheral blood samples were collected from 35 COVID-19 patients, 16 recovered individuals, and 25 healthy controls, and analyzed using flow cytometry. Significant alterations were detected in the percentage of CD8+ T cells and effector memory-expressing CD45RA CD8+ T cells (TEMRA) in COVID-19 patients compared to healthy controls. Interestingly, altered percentages of CD4+ T cells, CD8+ T cells, T effector (TEff), T naïve cells (TNs), T central memory (TCM), T effector memory (TEM), T stem cell memory (TSCM), and TEMRA T cells were significantly associated with the disease severity. Male patients had more CD8+ TSCMs and CD4+ TNs cells, while female patients had a significantly higher percentage of effector CD8+CD45RA+ T cells. Moreover, altered percentages of CD8+ TNs and memory CD8+CD45RO+ T cells were detected in diabetic and non-diabetic COVID-19 patients, respectively. In summary, this study identified alterations in memory T cells among COVID-19 patients, revealing a sex bias in the percentage of memory T cells. Moreover, COVID-19 severity and comorbidities have been linked to specific subsets of T memory cells which could be used as therapeutic, diagnostic, and protective targets for severe COVID-19.
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Affiliation(s)
- Hajir A. Al Saihati
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, University of Hafr Al Batin, P.O. Box 1803, Hafar Al Batin 31991, Saudi Arabia; (H.A.A.S.); (E.S.F.)
| | - Hosni A. M. Hussein
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Ali A. Thabet
- Department of Zoology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt;
| | - Ahmed A. Wardany
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Sabry Y. Mahmoud
- Biology Department, College of Sciences, University of Hafr Al-Batin, Hafr Al-Batin 31991, Saudi Arabia;
- Department of Microbiology, Sohag University, Sohag 82524, Egypt
| | - Eman S. Farrag
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, University of Hafr Al Batin, P.O. Box 1803, Hafar Al Batin 31991, Saudi Arabia; (H.A.A.S.); (E.S.F.)
- Department of Microbiology, South Valley University, Qena 83523, Egypt
| | - Taha I. A. Mohamed
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Samah M. Fathy
- Department of Zoology, Faculty of Science, Fayoum University, Fayoum 63514, Egypt;
| | - Mohamed E. Elnosary
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Egypt; (M.E.E.); (M.M.A.)
| | - Ali Sobhy
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, Assiut 71524, Egypt; (A.S.); (A.E.A.)
| | - Abdelazeem E. Ahmed
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, Assiut 71524, Egypt; (A.S.); (A.E.A.)
| | - Ahmed M. El-Adly
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Fareed S. El-Shenawy
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | | | - Amal Rayan
- Department of Clinical Oncology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | | | - Omnia El-Badawy
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Mohamed G. M. El-Naggar
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut 71515, Egypt; (M.G.M.E.-N.); (A.M.Z.)
| | - Magdy M. Afifi
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Egypt; (M.E.E.); (M.M.A.)
| | - Asmaa M. Zahran
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut 71515, Egypt; (M.G.M.E.-N.); (A.M.Z.)
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159
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Weeratunga P, Denney L, Bull JA, Repapi E, Sergeant M, Etherington R, Vuppussetty C, Turner GDH, Clelland C, Woo J, Cross A, Issa F, de Andrea CE, Melero Bermejo I, Sims D, McGowan S, Zurke YX, Ahern DJ, Gamez EC, Whalley J, Richards D, Klenerman P, Monaco C, Udalova IA, Dong T, Antanaviciute A, Ogg G, Knight JC, Byrne HM, Taylor S, Ho LP. Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs. Nat Commun 2023; 14:7216. [PMID: 37940670 PMCID: PMC10632491 DOI: 10.1038/s41467-023-42421-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
Single cell spatial interrogation of the immune-structural interactions in COVID -19 lungs is challenging, mainly because of the marked cellular infiltrate and architecturally distorted microstructure. To address this, we develop a suite of mathematical tools to search for statistically significant co-locations amongst immune and structural cells identified using 37-plex imaging mass cytometry. This unbiased method reveals a cellular map interleaved with an inflammatory network of immature neutrophils, cytotoxic CD8 T cells, megakaryocytes and monocytes co-located with regenerating alveolar progenitors and endothelium. Of note, a highly active cluster of immature neutrophils and CD8 T cells, is found spatially linked with alveolar progenitor cells, and temporally with the diffuse alveolar damage stage. These findings offer further insights into how immune cells interact in the lungs of severe COVID-19 disease. We provide our pipeline [Spatial Omics Oxford Pipeline (SpOOx)] and visual-analytical tool, Multi-Dimensional Viewer (MDV) software, as a resource for spatial analysis.
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Affiliation(s)
- Praveen Weeratunga
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Laura Denney
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Joshua A Bull
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Emmanouela Repapi
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Martin Sergeant
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rachel Etherington
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chaitanya Vuppussetty
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gareth D H Turner
- Department of Cellular Pathology and Radcliffe Department of Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Colin Clelland
- Anatomic Pathology, Weill Cornell Medical College, Doha, Qatar
| | - Jeongmin Woo
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Amy Cross
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Fadi Issa
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | | | - David Sims
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Simon McGowan
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - David J Ahern
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Eddie C Gamez
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Justin Whalley
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Duncan Richards
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Diseases, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Claudia Monaco
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Irina A Udalova
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Tao Dong
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Agne Antanaviciute
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Graham Ogg
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Stephen Taylor
- MRC WIMM Computational Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Ling-Pei Ho
- MRC Translational Immunology Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Respiratory Medicine Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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Joshua V, Loberg Haarhaus M, Hensvold A, Wähämaa H, Gerstner C, Hansson M, Israelsson L, Stålesen R, Sköld M, Grunewald J, Klareskog L, Grönwall C, Réthi B, Catrina A, Malmström V. Rheumatoid Arthritis-Specific Autoimmunity in the Lung Before and at the Onset of Disease. Arthritis Rheumatol 2023; 75:1910-1922. [PMID: 37192126 DOI: 10.1002/art.42549] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/14/2023] [Accepted: 04/18/2023] [Indexed: 05/18/2023]
Abstract
OBJECTIVE The lung is implicated as a site for breach of tolerance prior to onset of seropositive rheumatoid arthritis (RA). To substantiate this, we investigated lung-resident B cells in bronchoalveolar lavage (BAL) samples from untreated early RA patients and anti-citrullinated protein antibody (ACPA)-positive individuals at risk for developing RA. METHODS Single B cells (n = 7,680) were phenotyped and isolated from BAL samples from individuals at risk of RA (n = 3) and at RA diagnosis (n = 9). The immunoglobulin variable region transcripts were sequenced and selected for expression as monoclonal antibodies (n = 141). Monoclonal ACPAs were tested for reactivity patterns and binding to neutrophils. RESULTS Using our single-cell approach, we found significantly increased proportions of B lymphocytes in ACPA+ compared to ACPA- individuals. Memory and double-negative B cells were prominent in all subgroups. Upon antibody re-expression, 7 highly mutated citrulline-autoreactive clones originating from different memory B cell subsets were identified, both in individuals at risk of RA and early RA patients. Lung IgG variable gene transcripts from ACPA+ individuals carried frequent mutation-induced N-linked Fab glycosylation sites (P < 0.001), often in the framework 3 of the variable region. Two of the lung ACPAs bound to activated neutrophils, 1 from an individual at risk of RA and 1 from an early RA patient. CONCLUSION T cell-driven B cell differentiation resulting in local class switching and somatic hypermutation are evident in lungs before as well as in early stages of ACPA+ RA. Our findings add to the notion of lung mucosa being a site for initiation of citrulline autoimmunity preceding seropositive RA.
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Affiliation(s)
- Vijay Joshua
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Malena Loberg Haarhaus
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Aase Hensvold
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Heidi Wähämaa
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Christina Gerstner
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Monika Hansson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lena Israelsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ragnhild Stålesen
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Sköld
- Division of Respiratory Medicine, Department of Medicine Solna, Karolinska Institutet, and Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Grunewald
- Division of Respiratory Medicine, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lars Klareskog
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Grönwall
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Bence Réthi
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anca Catrina
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Vivianne Malmström
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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161
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Sahanic S, Hilbe R, Dünser C, Tymoszuk P, Löffler-Ragg J, Rieder D, Trajanoski Z, Krogsdam A, Demetz E, Yurchenko M, Fischer C, Schirmer M, Theurl M, Lener D, Hirsch J, Holfeld J, Gollmann-Tepeköylü C, Zinner CP, Tzankov A, Zhang SY, Casanova JL, Posch W, Wilflingseder D, Weiss G, Tancevski I. SARS-CoV-2 activates the TLR4/MyD88 pathway in human macrophages: A possible correlation with strong pro-inflammatory responses in severe COVID-19. Heliyon 2023; 9:e21893. [PMID: 38034686 PMCID: PMC10686889 DOI: 10.1016/j.heliyon.2023.e21893] [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: 02/03/2023] [Revised: 09/26/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Background Toll-like receptors (TLRs) play a pivotal role in the immunologic response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Exaggerated inflammatory response of innate immune cells, however, may drive morbidity and death in Coronavirus disease 19 (COVID-19). Objective We investigated the engagement of SARS-CoV-2 with TLR4 in order to better understand how to tackle hyperinflammation in COVID-19. Methods We combined RNA-sequencing data of human lung tissue and of bronchoalveolar lavage fluid cells derived from COVID-19 patients with functional studies in human macrophages using SARS-CoV-2 spike proteins and viable SARS-CoV-2. Pharmacological inhibitors as well as gene editing with CRISPR/Cas9 were used to delineate the signalling pathways involved. Results We found TLR4 to be the most abundantly upregulated TLR in human lung tissue irrespective of the underlying pathology. Accordingly, bronchoalveolar lavage fluid cells from patients with severe COVID-19 showed an NF-κB-pathway dominated immune response, whereas they were mostly defined by type I interferon signalling in moderate COVID-19. Mechanistically, we found the Spike ectodomain, but not receptor binding domain monomer to induce TLR4-dependent inflammation in human macrophages. By using pharmacological inhibitors as well as CRISPR/Cas9 deleted macrophages, we identify SARS-CoV-2 to engage canonical TLR4-MyD88 signalling. Importantly, we demonstrate that TLR4 blockage prevents exaggerated inflammatory responses in human macrophages infected with different SARS-CoV-2 variants, including immune escape variants B.1.1.7.-E484K and B.1.1.529 (omicron). Conclusion Our study critically extends the current knowledge on TLR-mediated hyperinflammatory responses to SARS-CoV-2 in human macrophages, paving the way for novel approaches to tackle severe COVID-19. Take-home message Our study combining human lung transcriptomics with functional studies in human macrophages clearly supports the design and development of TLR4 - directed therapeutics to mitigate hyperinflammation in severe COVID-19.
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Affiliation(s)
- Sabina Sahanic
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Richard Hilbe
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Christina Dünser
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Piotr Tymoszuk
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Judith Löffler-Ragg
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Anne Krogsdam
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Egon Demetz
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Maria Yurchenko
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
- The Central Norway Regional Health Authority, St. Olavs Hospital HF, Trondheim, Norway
| | - Christine Fischer
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Schirmer
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Theurl
- Department of Internal Medicine III, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniela Lener
- Department of Internal Medicine III, Medical University of Innsbruck, Innsbruck, Austria
| | - Jakob Hirsch
- Department of Cardiac Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Holfeld
- Department of Cardiac Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Carl P. Zinner
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, 10065, USA
| | - Wilfried Posch
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Austria
| | - Doris Wilflingseder
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Austria
| | - Guenter Weiss
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Ivan Tancevski
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
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162
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Diniz MO, Maini MK, Swadling L. T cell control of SARS-CoV-2: When, which, and where? Semin Immunol 2023; 70:101828. [PMID: 37651850 DOI: 10.1016/j.smim.2023.101828] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/13/2023] [Indexed: 09/02/2023]
Abstract
Efficient immune protection against viruses such as SARS-CoV-2 requires the coordinated activity of innate immunity, B and T cells. Accumulating data point to a critical role for T cells not only in the clearance of established infection, but also for aborting viral replication independently of humoral immunity. Here we review the evidence supporting the contribution of antiviral T cells and consider which of their qualitative features favour efficient control of infection. We highlight how studies of SARS-CoV-2 and other coronaviridae in animals and humans have provided important lessons on the optimal timing (When), functionality and specificity (Which), and location (Where) of antiviral T cells. We discuss the clinical implications, particularly for the development of next-generation vaccines, and emphasise areas requiring further study.
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Affiliation(s)
- Mariana O Diniz
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK
| | - Mala K Maini
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK.
| | - Leo Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK.
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163
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Nikitopoulou I, Vassiliou AG, Athanasiou N, Jahaj E, Akinosoglou K, Dimopoulou I, Orfanos SE, Dimakopoulou V, Schinas G, Tzouvelekis A, Aidinis V, Kotanidou A. Increased Levels of Galectin-3 in Critical COVID-19. Int J Mol Sci 2023; 24:15833. [PMID: 37958814 PMCID: PMC10650562 DOI: 10.3390/ijms242115833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Severe COVID-19 is related to hyperinflammation and multiple organ injury, including respiratory failure, thus requiring intensive care unit (ICU) admission. Galectin-3, a carbohydrate-binding protein exhibiting pleiotropic effects, has been previously recognized to participate in inflammation, the immune response to infections and fibrosis. The aim of this study was to evaluate the relationship between galectin-3 and the clinical severity of COVID-19, as well as assess the prognostic accuracy of galectin-3 for the probability of ICU mortality. The study included 235 COVID-19 patients with active disease, treated in two different Greek hospitals in total. Our results showed that median galectin-3 serum levels on admission were significantly increased in critical COVID-19 patients (7.2 ng/mL), as compared to the median levels of patients with less severe disease (2.9 ng/mL, p = 0.003). Galectin-3 levels of the non-survivors hospitalized in the ICU were significantly higher than those of the survivors (median 9.1 ng/mL versus 5.8 ng/mL, p = 0.001). The prognostic accuracy of galectin-3 for the probability of ICU mortality was studied with a receiver operating characteristic (ROC) curve and a multivariate analysis further demonstrated that galectin-3 concentration at hospital admission could be assumed as an independent risk factor associated with ICU mortality. Our results were validated with galectin-3 measurements in a second patient cohort from a different Greek university hospital. Our results, apart from strongly confirming and advancing previous knowledge with two patient cohorts, explore the possibility of predicting ICU mortality, which could provide useful information to clinicians. Therefore, galectin-3 seems to establish its involvement in the prognosis of hospitalized COVID-19 patients, suggesting that it could serve as a promising biomarker in critical COVID-19.
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Affiliation(s)
- Ioanna Nikitopoulou
- 1st Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 10676 Athens, Greece; (I.N.); (A.G.V.); (N.A.); (E.J.); (I.D.); (S.E.O.)
| | - Alice G. Vassiliou
- 1st Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 10676 Athens, Greece; (I.N.); (A.G.V.); (N.A.); (E.J.); (I.D.); (S.E.O.)
| | - Nikolaos Athanasiou
- 1st Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 10676 Athens, Greece; (I.N.); (A.G.V.); (N.A.); (E.J.); (I.D.); (S.E.O.)
| | - Edison Jahaj
- 1st Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 10676 Athens, Greece; (I.N.); (A.G.V.); (N.A.); (E.J.); (I.D.); (S.E.O.)
| | - Karolina Akinosoglou
- Division of Internal Medicine, University General Hospital of Patras, 26504 Patras, Greece; (K.A.); (V.D.); (G.S.)
| | - Ioanna Dimopoulou
- 1st Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 10676 Athens, Greece; (I.N.); (A.G.V.); (N.A.); (E.J.); (I.D.); (S.E.O.)
| | - Stylianos E. Orfanos
- 1st Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 10676 Athens, Greece; (I.N.); (A.G.V.); (N.A.); (E.J.); (I.D.); (S.E.O.)
| | - Vasiliki Dimakopoulou
- Division of Internal Medicine, University General Hospital of Patras, 26504 Patras, Greece; (K.A.); (V.D.); (G.S.)
| | - Georgios Schinas
- Division of Internal Medicine, University General Hospital of Patras, 26504 Patras, Greece; (K.A.); (V.D.); (G.S.)
| | - Argyrios Tzouvelekis
- Department of Respiratory Medicine, University General Hospital of Patras, 26504 Patras, Greece;
| | - Vassilis Aidinis
- Institute of Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, 16672 Athens, Greece;
| | - Anastasia Kotanidou
- 1st Department of Critical Care Medicine & Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, Evangelismos Hospital, 10676 Athens, Greece; (I.N.); (A.G.V.); (N.A.); (E.J.); (I.D.); (S.E.O.)
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164
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Hammer Q, Cuapio A, Bister J, Björkström NK, Ljunggren HG. NK cells in COVID-19-from disease to vaccination. J Leukoc Biol 2023; 114:507-512. [PMID: 36976012 DOI: 10.1093/jleuko/qiad031] [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: 11/21/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 03/13/2023] Open
Abstract
Natural killer cells participate in the host innate immune response to viral infection. Conversely, natural killer cell dysfunction and hyperactivation can contribute to tissue damage and immunopathology. Here, we review recent studies with respect to natural killer cell activity during infection with SARS-CoV-2. Discussed are initial reports of patients hospitalized with COVID-19, which revealed prompt natural killer cell activation during the acute disease state. Another hallmark of COVID-19, early on observed, was a decrease in numbers of natural killer cells in the circulation. Data from patients with acute SARS-CoV-2 infection as well as from in vitro models demonstrated strong anti-SARS-CoV-2 activity by natural killer cells, likely through direct cytotoxicity as well as indirectly by secreting cytokines. Additionally, we describe the molecular mechanisms underlying natural killer cell recognition of SARS-CoV-2-infected cells, which involve triggering of multiple activating receptors, including NKG2D, as well as loss of inhibition through NKG2A. Discussed is also the ability of natural killer cells to respond to SARS-CoV-2 infection via antibody-dependent cellular cytotoxicity. With respect to natural killer cells in the pathogenesis of COVID-19, we review studies demonstrating how hyperactivation and misdirected NK cell responses could contribute to disease course. Finally, while knowledge is still rather limited, we discuss current insights suggesting a contribution of an early natural killer cell activation response in the generation of immunity against SARS-CoV-2 following vaccination with anti-SARS-CoV-2 mRNA vaccines.
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Affiliation(s)
- Quirin Hammer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels allé 8, Stockholms län, 141 52 Huddinge, Sweden
| | - Angelica Cuapio
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels allé 8, Stockholms län, 141 52 Huddinge, Sweden
| | - Jonna Bister
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels allé 8, Stockholms län, 141 52 Huddinge, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels allé 8, Stockholms län, 141 52 Huddinge, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels allé 8, Stockholms län, 141 52 Huddinge, Sweden
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165
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Mitsi E, Diniz MO, Reiné J, Collins AM, Robinson RE, Hyder-Wright A, Farrar M, Liatsikos K, Hamilton J, Onyema O, Urban BC, Solórzano C, Belij-Rammerstorfer S, Sheehan E, Lambe T, Draper SJ, Weiskopf D, Sette A, Maini MK, Ferreira DM. Respiratory mucosal immune memory to SARS-CoV-2 after infection and vaccination. Nat Commun 2023; 14:6815. [PMID: 37884506 PMCID: PMC10603102 DOI: 10.1038/s41467-023-42433-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Respiratory mucosal immunity induced by vaccination is vital for protection from coronavirus infection in animal models. In humans, the capacity of peripheral vaccination to generate sustained immunity in the lung mucosa, and how this is influenced by prior SARS-CoV-2 infection, is unknown. Here we show using bronchoalveolar lavage samples that donors with history of both infection and vaccination have more airway mucosal SARS-CoV-2 antibodies and memory B cells than those only vaccinated. Infection also induces populations of airway spike-specific memory CD4+ and CD8+ T cells that are not expanded by vaccination alone. Airway mucosal T cells induced by infection have a distinct hierarchy of antigen specificity compared to the periphery. Spike-specific T cells persist in the lung mucosa for 7 months after the last immunising event. Thus, peripheral vaccination alone does not appear to induce durable lung mucosal immunity against SARS-CoV-2, supporting an argument for the need for vaccines targeting the airways.
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Affiliation(s)
- Elena Mitsi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Mariana O Diniz
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, UK
| | - Jesús Reiné
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Andrea M Collins
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ryan E Robinson
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Angela Hyder-Wright
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Madlen Farrar
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Josh Hamilton
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Onyia Onyema
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Britta C Urban
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Carla Solórzano
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Emma Sheehan
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Simon J Draper
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, USA
| | - Mala K Maini
- Division of Infection and Immunity and Institute of Immunity and Transplantation, UCL, London, UK
| | - Daniela M Ferreira
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
- Department of Clinical Science, Liverpool School of Tropical Medicine, Liverpool, UK.
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166
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Li LH, Chiu HW, Wong WT, Huang KC, Lin TW, Chen ST, Hua KF. Antrodia cinnamomea May Interfere with the Interaction Between ACE2 and SARS-CoV-2 Spike Protein in vitro and Reduces Lung Inflammation in a Hamster Model of COVID-19. J Inflamm Res 2023; 16:4867-4884. [PMID: 37908202 PMCID: PMC10614667 DOI: 10.2147/jir.s431222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/24/2023] [Indexed: 11/02/2023] Open
Abstract
Purpose Coronavirus disease 2019 (COVID-19) poses a global health challenge with widespread transmission. Growing concerns about vaccine side effects, diminishing efficacy, and religious-based hesitancy highlight the need for alternative pharmacological approaches. Our study investigates the impact of the ethanol extract of Antrodia cinnamomea (AC), a native medicinal fungus from Taiwan, on COVID-19 in both in vitro and in vivo contexts. Methods We measured the mRNA and protein levels of angiotensin-converting enzyme-2 (ACE2) in human lung cells using real-time reverse transcriptase-polymerase chain reaction and Western blotting, respectively. Additionally, we determined the enzymatic activity of ACE2 using the fluorogenic peptide substrate Mca-YVADAPK(Dnp)-OH. To assess the impact of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, we used SARS-CoV-2 pseudovirus infections in human embryonic kidney 293T cells expressing ACE2 to measure infection rates. Furthermore, we evaluated the in vivo efficacy of AC in mitigating COVID-19 by conducting experiments on hamsters infected with the Delta variant of SARS-CoV-2. Results AC effectively decreased ACE2 mRNA and protein levels, a critical host receptor for the SARS-CoV-2 spike protein, in human lung cells. It also prevented the spike protein from binding to human lung cells. Dehydrosulphurenic acid, an isolate from AC, directly inhibited ACE2 protease activity with an inhibitory constant of 1.53 µM. In vitro experiments showed that both AC and dehydrosulphurenic acid significantly reduced the infection rate of SARS-CoV-2 pseudovirus. In hamsters infected with the Delta variant of SARS-CoV-2, oral administration of AC reduced body weight loss and improved lung injury. Notably, AC also inhibited IL-1β expression in both macrophages and the lung tissues of SARS-CoV-2-infected hamsters. Conclusion AC shows potential as a nutraceutical for reducing the risk of SARS-CoV-2 infection by disrupting the interaction between ACE2 and the SARS-CoV-2 spike protein, and for preventing COVID-19-associated lung inflammation.
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Affiliation(s)
- Lan-Hui Li
- Department of Laboratory Medicine, Linsen, Chinese Medicine and Kunming Branch, Taipei City Hospital, Taipei, Taiwan
| | - Hsiao-Wen Chiu
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
| | - Wei-Ting Wong
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
| | | | | | | | - Kuo-Feng Hua
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
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167
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Khatun MS, Remcho TP, Qin X, Kolls JK. Cell-intrinsic and -extrinsic effects of SARS-CoV-2 RNA on pathogenesis: single-cell meta-analysis. mSphere 2023; 8:e0037523. [PMID: 37737611 PMCID: PMC10597400 DOI: 10.1128/msphere.00375-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 09/23/2023] Open
Abstract
Single-cell RNA-seq has been used to characterize human COVID-19. To determine if preclinical models successfully mimic the cell-intrinsic and -extrinsic effects of severe disease, we conducted a meta-analysis of single-cell data across five model species. To assess whether dissemination of viral RNA in lung cells tracks pathology and results in cell-intrinsic and -extrinsic transcriptomic changes in COVID-19. We conducted a meta-analysis by analyzing six publicly available, scRNA-seq data sets. We used dual mapping (host and virus) and differential gene expression analyses to compare viral+ and viral- cell populations. We conducted a principal component analysis to identify successful models of human COVID-19. We found expression of viral RNA in many non-epithelial cell types. Fibroblasts, macrophages, and endothelial cells exhibit clear evidence of viral-intrinsic and -extrinsic effects on host gene expression. Using viral RNA expression, we found that K18-hACE2 mice most closely modeled severe human COVID-19, followed by hamsters. Ferrets and macaques are poor models of human disease due to the low presence of viral RNA. Moreover, we found that increased transcripts of certain key inflammatory genes such as IL1B, IL18, and CXCL10 are not restricted to virally infected cells, suggesting these genes are regulated in a paracrine or autocrine fashion. These data affirm widespread dissemination of viral RNA in the lung, which may be key in the pathogenesis of severe COVID-19 and demonstrate ferrets and Rhesus macaques are poor models of human COVID-19. IMPORTANCE We conducted a high-resolution meta-analysis of scRNA-seq data from humans and five animal models of COVID-19. This study reports viral RNA dissemination in several cell types in human data as well as in some of the pre-clinical models. Using this metric, the K18-hACE2 mouse model, followed by the hamster model, most closely resembled human COVID-19. We observed clear evidence of viral-intrinsic effects within cells (e.g., IRF5 expression) as well as viral-extrinsic cytokine modulation (e.g., IL1B, IL18, CXCL10). We observed proinflammatory chemokine expression in cells devoid of viral RNA expression, suggesting autocrine/paracrine interferon regulation. This report serves as a resource-synthesizing data from COVID-19 humans and animal models and suggesting improvements for relevant pre-clinical models that may aid future diagnostic and therapeutic development projects.
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Affiliation(s)
- Mst Shamima Khatun
- Departments of Pediatrics & Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - T. Parks Remcho
- Departments of Pediatrics & Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Xuebin Qin
- Tulane National Primate Research Center, Covington, Louisiana, USA
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Jay K. Kolls
- Departments of Pediatrics & Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, Louisiana, USA
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168
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Hackney JA, Shivram H, Vander Heiden J, Overall C, Orozco L, Gao X, Kim E, West N, Qamra A, Chang D, Chakrabarti A, Choy DF, Combes AJ, Courau T, Fragiadakis GK, Rao AA, Ray A, Tsui J, Hu K, Kuhn NF, Krummel MF, Erle DJ, Kangelaris K, Sarma A, Lyon Z, Calfee CS, Woodruff PG, Ghale R, Mick E, Byrne A, Zha BS, Langelier C, Hendrickson CM, van der Wijst MG, Hartoularos GC, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Ye CJ, Ramalingam T, McBride JM, Cai F, Teterina A, Bao M, Tsai L, Rosas IO, Regev A, Kapadia SB, Bauer RN, Rosenberger CM. A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling. iScience 2023; 26:107813. [PMID: 37810211 PMCID: PMC10551843 DOI: 10.1016/j.isci.2023.107813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/12/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023] Open
Abstract
Altered myeloid inflammation and lymphopenia are hallmarks of severe infections. We identified the upregulated EN-RAGE gene program in airway and blood myeloid cells from patients with acute lung injury from SARS-CoV-2 or other causes across 7 cohorts. This program was associated with greater clinical severity and predicted future mechanical ventilation and death. EN-RAGEhi myeloid cells express features consistent with suppressor cell functionality, including low HLA-DR and high PD-L1. Sustained EN-RAGE program expression in airway and blood myeloid cells correlated with clinical severity and increasing expression of T cell dysfunction markers. IL-6 upregulated many EN-RAGE program genes in monocytes in vitro. IL-6 signaling blockade by tocilizumab in a placebo-controlled clinical trial led to rapid normalization of EN-RAGE and T cell gene expression. This identifies IL-6 as a key driver of myeloid dysregulation associated with worse clinical outcomes in COVID-19 patients and provides insights into shared pathophysiological mechanisms in non-COVID-19 ARDS.
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Affiliation(s)
| | - Haridha Shivram
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Chris Overall
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Luz Orozco
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xia Gao
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eugene Kim
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nathan West
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Aditi Qamra
- Hoffman-La Roche Limited, 7070 Mississauga Road, Mississauga, ON L5N 5M8, Canada
| | - Diana Chang
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - David F. Choy
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Tristan Courau
- University of California San Francisco, San Francisco, CA, USA
| | | | - Arjun Arkal Rao
- University of California San Francisco, San Francisco, CA, USA
| | - Arja Ray
- University of California San Francisco, San Francisco, CA, USA
| | - Jessica Tsui
- University of California San Francisco, San Francisco, CA, USA
| | - Kenneth Hu
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - David J. Erle
- University of California San Francisco, San Francisco, CA, USA
| | | | - Aartik Sarma
- University of California San Francisco, San Francisco, CA, USA
| | - Zoe Lyon
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Rajani Ghale
- University of California San Francisco, San Francisco, CA, USA
| | - Eran Mick
- University of California San Francisco, San Francisco, CA, USA
| | - Ashley Byrne
- University of California San Francisco, San Francisco, CA, USA
| | | | | | | | - Monique G.P. van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Tianna Grant
- University of California San Francisco, San Francisco, CA, USA
| | - Raymund Bueno
- University of California San Francisco, San Francisco, CA, USA
| | - David S. Lee
- University of California San Francisco, San Francisco, CA, USA
| | | | - Yang Sun
- University of California San Francisco, San Francisco, CA, USA
| | - Richard Perez
- University of California San Francisco, San Francisco, CA, USA
| | | | - Alyssa Ward
- University of California San Francisco, San Francisco, CA, USA
| | - Chun Jimmie Ye
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Fang Cai
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Anastasia Teterina
- Hoffman-La Roche Limited, 7070 Mississauga Road, Mississauga, ON L5N 5M8, Canada
| | - Min Bao
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Larry Tsai
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ivan O. Rosas
- Baylor College of Medicine, 7200 Cambridge St, Houston, TX 77030, USA
| | - Aviv Regev
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
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169
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Apte SH, Groves PL, Tan ME, Lutzky VP, de Silva T, Monteith JN, Yerkovich ST, O’Sullivan BJ, Davis RA, Chambers DC. A Methodological Approach to Identify Natural Compounds with Antifibrotic Activity and the Potential to Treat Pulmonary Fibrosis Using Single-Cell Sequencing and Primary Human Lung Macrophages. Int J Mol Sci 2023; 24:15104. [PMID: 37894784 PMCID: PMC10606775 DOI: 10.3390/ijms242015104] [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: 08/30/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is the most common and lethal form of the interstitial pneumonias. The cause of the disease is unknown, and new therapies that stop or reverse disease progression are desperately needed. Recent advances in next-generation sequencing have led to an abundance of freely available, clinically relevant, organ-and-disease-specific, single-cell transcriptomic data, including studies from patients with IPF. We mined data from published IPF data sets and identified gene signatures delineating pro-fibrotic or antifibrotic macrophages and then used the Enrichr platform to identify compounds with the potential to drive the macrophages toward the antifibrotic transcriptotype. We then began testing these compounds in a novel in vitro phenotypic drug screening assay utilising human lung macrophages recovered from whole-lung lavage of patients with silicosis. As predicted by the Enrichr tool, glitazones potently modulated macrophage gene expression towards the antifibrotic phenotype. Next, we assayed a subset of the NatureBank pure compound library and identified the cyclobutane lignan, endiandrin A, which was isolated from the roots of the endemic Australian rainforest plant, Endiandra anthropophagorum, with a similar antifibrotic potential to the glitazones. These methods open new avenues of exploration to find treatments for lung fibrosis.
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Affiliation(s)
- Simon H. Apte
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD 4032, Australia; (P.L.G.); (M.E.T.); (V.P.L.); (T.d.S.); (B.J.O.)
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (J.N.M.); (S.T.Y.)
| | - Penny L. Groves
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD 4032, Australia; (P.L.G.); (M.E.T.); (V.P.L.); (T.d.S.); (B.J.O.)
| | - Maxine E. Tan
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD 4032, Australia; (P.L.G.); (M.E.T.); (V.P.L.); (T.d.S.); (B.J.O.)
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (J.N.M.); (S.T.Y.)
| | - Viviana P. Lutzky
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD 4032, Australia; (P.L.G.); (M.E.T.); (V.P.L.); (T.d.S.); (B.J.O.)
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (J.N.M.); (S.T.Y.)
| | - Tharushi de Silva
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD 4032, Australia; (P.L.G.); (M.E.T.); (V.P.L.); (T.d.S.); (B.J.O.)
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (J.N.M.); (S.T.Y.)
| | - Joshua N. Monteith
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (J.N.M.); (S.T.Y.)
| | - Stephanie T. Yerkovich
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (J.N.M.); (S.T.Y.)
| | - Brendan J. O’Sullivan
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD 4032, Australia; (P.L.G.); (M.E.T.); (V.P.L.); (T.d.S.); (B.J.O.)
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (J.N.M.); (S.T.Y.)
| | - Rohan A. Davis
- School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia;
- NatureBank, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Daniel C. Chambers
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD 4032, Australia; (P.L.G.); (M.E.T.); (V.P.L.); (T.d.S.); (B.J.O.)
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (J.N.M.); (S.T.Y.)
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170
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Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Nat Commun 2023; 14:6245. [PMID: 37803001 PMCID: PMC10558542 DOI: 10.1038/s41467-023-41788-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/15/2023] [Indexed: 10/08/2023] Open
Abstract
Genomic and proteomic screens have identified numerous host factors of SARS-CoV-2, but efficient delineation of their molecular roles during infection remains a challenge. Here we use Perturb-seq, combining genetic perturbations with a single-cell readout, to investigate how inactivation of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. Our high-dimensional data resolve complex phenotypes such as shifts in the stages of infection and modulations of the interferon response. However, only a small percentage of host factors showed such phenotypes upon perturbation. We further identified the NF-κB inhibitor IκBα (NFKBIA), as well as the translation factors EIF4E2 and EIF4H as strong host dependency factors acting early in infection. Overall, our study provides massively parallel functional characterization of host factors of SARS-CoV-2 and quantitatively defines their roles both in virus-infected and bystander cells.
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Affiliation(s)
- Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- University of California, Berkeley-UCSF Joint Graduate Program in Bioengineering, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Janie R Byrum
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | | | - Matthew B Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Juliane Winkler
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Oren S Rosenberg
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
| | - Marco Y Hein
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Center for Medical Biochemistry, Vienna, Austria.
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171
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O'Reilly S. Pulmonary fibrosis in COVID-19: mechanisms, consequences and targets. QJM 2023; 116:750-754. [PMID: 37191984 DOI: 10.1093/qjmed/hcad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Pulmonary fibrosis is characterized by extracellular deposition in the lung primarily collagen but also other ECM molecules. The primary cell type responsible for this is the myofibroblast, and this can be induced by various stressors and signals. Infections be they bacterial or viral can cause pulmonary fibrosis (PF). In 2019, severe acute respiratory syndrome coronavirus 2 (SAR-CoV-2) originated in Wuhan, China, has led to a worldwide pandemic and can lead to acute respiratory distress and lung fibrosis. The virus itself can be cleared, but patients may develop long-term PF, which can be debilitating and life-limiting. There is a significantly perturbed immune response that shapes the fibrotic response leading to fibrosis. Given the importance of PF irrespective of cause, understanding the similarities and differences in pathogenesis caused by SARS-CoV-2-induced PF may yield new therapeutic targets. This review examines the pathology associated with the disease and discusses possible targets.
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Affiliation(s)
- S O'Reilly
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
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172
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Kawakami E, Saiki N, Yoneyama Y, Moriya C, Maezawa M, Kawamura S, Kinebuchi A, Kono T, Funata M, Sakoda A, Kondo S, Ebihara T, Matsumoto H, Togami Y, Ogura H, Sugihara F, Okuzaki D, Kojima T, Deguchi S, Vallee S, McQuade S, Islam R, Natarajan M, Ishigaki H, Nakayama M, Nguyen CT, Kitagawa Y, Wu Y, Mori K, Hishiki T, Takasaki T, Itoh Y, Takayama K, Nio Y, Takebe T. Complement factor D targeting protects endotheliopathy in organoid and monkey models of COVID-19. Cell Stem Cell 2023; 30:1315-1330.e10. [PMID: 37802037 PMCID: PMC10575686 DOI: 10.1016/j.stem.2023.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 07/04/2023] [Accepted: 09/01/2023] [Indexed: 10/08/2023]
Abstract
COVID-19 is linked to endotheliopathy and coagulopathy, which can result in multi-organ failure. The mechanisms causing endothelial damage due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain elusive. Here, we developed an infection-competent human vascular organoid from pluripotent stem cells for modeling endotheliopathy. Longitudinal serum proteome analysis identified aberrant complement signature in critically ill patients driven by the amplification cycle regulated by complement factor B and D (CFD). This deviant complement pattern initiates endothelial damage, neutrophil activation, and thrombosis specific to organoid-derived human blood vessels, as verified through intravital imaging. We examined a new long-acting, pH-sensitive (acid-switched) antibody targeting CFD. In both human and macaque COVID-19 models, this long-acting anti-CFD monoclonal antibody mitigated abnormal complement activation, protected endothelial cells, and curtailed the innate immune response post-viral exposure. Collectively, our findings suggest that the complement alternative pathway exacerbates endothelial injury and inflammation. This underscores the potential of CFD-targeted therapeutics against severe viral-induced inflammathrombotic outcomes.
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Affiliation(s)
- Eri Kawakami
- T-CiRA Discovery & Innovation, Takeda Pharmaceutical Company Ltd, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan; Organoid Medicine Project, T-CiRA Joint Program, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Norikazu Saiki
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Organoid Medicine Project, T-CiRA Joint Program, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Yosuke Yoneyama
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Chiharu Moriya
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Mari Maezawa
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Shuntaro Kawamura
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Akiko Kinebuchi
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Tamaki Kono
- T-CiRA Discovery & Innovation, Takeda Pharmaceutical Company Ltd, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan; Organoid Medicine Project, T-CiRA Joint Program, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Masaaki Funata
- T-CiRA Discovery & Innovation, Takeda Pharmaceutical Company Ltd, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan; Organoid Medicine Project, T-CiRA Joint Program, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Ayaka Sakoda
- T-CiRA Discovery & Innovation, Takeda Pharmaceutical Company Ltd, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Shigeru Kondo
- T-CiRA Discovery & Innovation, Takeda Pharmaceutical Company Ltd, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Takeshi Ebihara
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, 2-15, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hisatake Matsumoto
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, 2-15, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yuki Togami
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, 2-15, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Ogura
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, 2-15, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center and Research Institute for Microbial Diseases, Osaka University, 3-3-1, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Disease, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Takashi Kojima
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, 2-15, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Sebastien Vallee
- Rare Disease DDU, Takeda Pharmaceutical Company Ltd, 125 Binney Street, Cambridge, MA 02139, USA
| | - Susan McQuade
- Rare Disease DDU, Takeda Pharmaceutical Company Ltd, 125 Binney Street, Cambridge, MA 02139, USA; BPS Biosciences Inc., 6405 Mira Mesa Blvd. Suite 100, San Diego, CA 92121, USA
| | - Rizwana Islam
- Rare Disease DDU, Takeda Pharmaceutical Company Ltd, 125 Binney Street, Cambridge, MA 02139, USA
| | - Madhusudan Natarajan
- Rare Disease DDU, Takeda Pharmaceutical Company Ltd, 125 Binney Street, Cambridge, MA 02139, USA
| | - Hirohito Ishigaki
- Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Otsu, Shiga 520-2192, Japan
| | - Misako Nakayama
- Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Otsu, Shiga 520-2192, Japan
| | - Cong Thanh Nguyen
- Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Otsu, Shiga 520-2192, Japan
| | - Yoshinori Kitagawa
- Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Otsu, Shiga 520-2192, Japan
| | - Yunheng Wu
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kensaku Mori
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Information Technology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Research Center for Medical Bigdata, National Institute of Informatics, Tokyo 100-0003, Japan
| | - Takayuki Hishiki
- Kanagawa Prefectural Institute of Public Health, 1-3-1, Shimomachiya, Chigasaki, Kanagawa 253-0087, Japan; Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tomohiko Takasaki
- Kanagawa Prefectural Institute of Public Health, 1-3-1, Shimomachiya, Chigasaki, Kanagawa 253-0087, Japan; Advanced Technology and Development Division, BML, INC, 1361-1, Matoba, Kawagoe-shi, Saitama 350-1101, Japan
| | - Yasushi Itoh
- Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Otsu, Shiga 520-2192, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Yasunori Nio
- T-CiRA Discovery & Innovation, Takeda Pharmaceutical Company Ltd, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan; Organoid Medicine Project, T-CiRA Joint Program, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan.
| | - Takanori Takebe
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Organoid Medicine Project, T-CiRA Joint Program, 2-26-1, Muraoka-higashi, Fujisawa, Kanagawa 251-8555, Japan; Division of Gastroenterology, Hepatology and Nutrition & Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA; The Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA; Communication Design Center, Advanced Medical Research Center, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe) and Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.
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173
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Kam NW, Lau CY, Che CM, Lee VHF. Nasopharynx Battlefield: Cellular Immune Responses Mediated by Midkine in Nasopharyngeal Carcinoma and COVID-19. Cancers (Basel) 2023; 15:4850. [PMID: 37835544 PMCID: PMC10571800 DOI: 10.3390/cancers15194850] [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: 06/19/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Clinical evidence suggests that the severe respiratory illness coronavirus disease 2019 (COVID-19) is often associated with a cytokine storm that results in dysregulated immune responses. Prolonged COVID-19 positivity is thought to disproportionately affect cancer patients. With COVID-19 disrupting the delivery of cancer care, it is crucial to gain momentum and awareness of the mechanistic intersection between these two diseases. This review discusses the role of the cytokine midkine (MK) as an immunomodulator in patients with COVID-19 and nasopharyngeal carcinoma (NPC), both of which affect the nasal cavity. We conducted a review and analysis of immunocellular similarities and differences based on clinical studies, research articles, and published transcriptomic datasets. We specifically focused on ligand-receptor pairs that could be used to infer intercellular communication, as well as the current medications used for each disease, including NPC patients who have contracted COVID-19. Based on our findings, we recommend close monitoring of the MK axis to maintain the desirable effects of therapeutic regimens in fighting both NPC and COVID-19 infections.
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Affiliation(s)
- Ngar-Woon Kam
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.-W.K.); (C.-Y.L.)
- Laboratory for Synthetic Chemistry and Chemical Biology Ltd., Hong Kong Science Park, New Territories, Hong Kong 999077, China;
| | - Cho-Yiu Lau
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.-W.K.); (C.-Y.L.)
- Laboratory for Synthetic Chemistry and Chemical Biology Ltd., Hong Kong Science Park, New Territories, Hong Kong 999077, China;
| | - Chi-Ming Che
- Laboratory for Synthetic Chemistry and Chemical Biology Ltd., Hong Kong Science Park, New Territories, Hong Kong 999077, China;
- Department of Chemistry, Faculty of Science, The University of Hong Kong, Hong Kong 999077, China
| | - Victor Ho-Fun Lee
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.-W.K.); (C.-Y.L.)
- Clinical Oncology Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China
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174
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Narasimhan M, Muthukumar A, Sataranatarajan K, Mahimainathan L, Mahan L, Timofte I, Bollineni S, Joerns J, Zhang S, Gorman A, Banga A, Mohanka M, Torres F, Lawrence A, Thalachallour M, Kaza V. Crossroads between Autoimmunity and COVID-19 in Lung Transplant Recipients. Viruses 2023; 15:2045. [PMID: 37896822 PMCID: PMC10612071 DOI: 10.3390/v15102045] [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: 08/22/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
The presence of a certain group of auto-antibodies (AAbs) is known to correlate with the severity of COVID-19. It is, however, unknown if such AAbs are prevalent and impact COVID-19-related outcomes in lung transplant recipients (LTRs) who are immunosuppressed. We performed a retrospective study of LTRs with COVID-19 and analyzed samples before and after COVID-19 for IgG AAbs. AAbs analysis was carried out using autoimmune and coronavirus microarray and the resulting cross-sectional differences in Ab-scores and clinical variables were analyzed using Fischer's Exact test for categorical variables and a paired t-test for continuous variables. Linear regression was used to analyze the differences in Ab-scores and COVID-19 severity. LTRs with non-severe [NS gp (n = 10)], and severe [S gp (n = 8)] COVID-19 disease were included. Ferritin and acute respiratory failure were higher in the S group (p = 0.03; p < 0.0001). Among the AAbs analyzed, interferon-related AAbs (IFN-alpha2, IFN-beta, IFN lamba, IFN-epsilon), eight interleukin-related AAbs, and several tissue-related AAbs were also found to be changed significantly from pre- to post-COVID-19 (p < 0.05). IFN-lambda (p = 0.03) and IL-22 (p = 0.002) were significantly associated with COVID-19 severity and remained significant in linear regression analysis while controlling for other variables. AAbs are common in LTRs, and certain groups of antibodies are particularly enhanced in LTRs with severe COVID-19. Preliminary observations of this study need to be confirmed by a larger sample size.
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Affiliation(s)
- Madhusudhanan Narasimhan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (M.N.); (A.M.); (K.S.); (L.M.)
| | - Alagarraju Muthukumar
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (M.N.); (A.M.); (K.S.); (L.M.)
| | - Kavithalakshmi Sataranatarajan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (M.N.); (A.M.); (K.S.); (L.M.)
| | - Lenin Mahimainathan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (M.N.); (A.M.); (K.S.); (L.M.)
| | - Luke Mahan
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.M.); (I.T.); (S.B.); (J.J.); (A.B.); (M.M.); (F.T.); (A.L.)
| | - Irina Timofte
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.M.); (I.T.); (S.B.); (J.J.); (A.B.); (M.M.); (F.T.); (A.L.)
| | - Srinivas Bollineni
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.M.); (I.T.); (S.B.); (J.J.); (A.B.); (M.M.); (F.T.); (A.L.)
| | - John Joerns
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.M.); (I.T.); (S.B.); (J.J.); (A.B.); (M.M.); (F.T.); (A.L.)
| | - Song Zhang
- Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (S.Z.); (A.G.)
| | - April Gorman
- Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (S.Z.); (A.G.)
| | - Amit Banga
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.M.); (I.T.); (S.B.); (J.J.); (A.B.); (M.M.); (F.T.); (A.L.)
| | - Manish Mohanka
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.M.); (I.T.); (S.B.); (J.J.); (A.B.); (M.M.); (F.T.); (A.L.)
| | - Fernando Torres
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.M.); (I.T.); (S.B.); (J.J.); (A.B.); (M.M.); (F.T.); (A.L.)
| | - Adrian Lawrence
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.M.); (I.T.); (S.B.); (J.J.); (A.B.); (M.M.); (F.T.); (A.L.)
| | | | - Vaidehi Kaza
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.M.); (I.T.); (S.B.); (J.J.); (A.B.); (M.M.); (F.T.); (A.L.)
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175
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Malainou C, Abdin SM, Lachmann N, Matt U, Herold S. Alveolar macrophages in tissue homeostasis, inflammation, and infection: evolving concepts of therapeutic targeting. J Clin Invest 2023; 133:e170501. [PMID: 37781922 PMCID: PMC10541196 DOI: 10.1172/jci170501] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
Alveolar macrophages (AMs) are the sentinel cells of the alveolar space, maintaining homeostasis, fending off pathogens, and controlling lung inflammation. During acute lung injury, AMs orchestrate the initiation and resolution of inflammation in order to ultimately restore homeostasis. This central role in acute lung inflammation makes AMs attractive targets for therapeutic interventions. Single-cell RNA-Seq and spatial omics approaches, together with methodological advances such as the generation of human macrophages from pluripotent stem cells, have increased understanding of the ontogeny, function, and plasticity of AMs during infectious and sterile lung inflammation, which could move the field closer to clinical application. However, proresolution phenotypes might conflict with proinflammatory and antibacterial responses. Therefore, therapeutic targeting of AMs at vulnerable time points over the course of infectious lung injury might harbor the risk of serious side effects, such as loss of antibacterial host defense capacity. Thus, the identification of key signaling hubs that determine functional fate decisions in AMs is of the utmost importance to harness their therapeutic potential.
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Affiliation(s)
- Christina Malainou
- Department of Internal Medicine V, Universities of Giessen and Marburg Lung Center, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany
- Institute for Lung Health, Justus Liebig University Giessen, Giessen, Germany
- Excellence Cluster Cardio-Pulmonary Institute, Giessen, Germany
- German Center for Lung Research (DZL), Heidelberg, Germany
| | - Shifaa M. Abdin
- German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Pediatric Pneumology, Allergology and Neonatology and
- REBIRTH Center for Translational and Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Nico Lachmann
- German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Pediatric Pneumology, Allergology and Neonatology and
- REBIRTH Center for Translational and Regenerative Medicine, Hannover Medical School, Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- RESIST (Resolving Infection Susceptibility), Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Ulrich Matt
- Department of Internal Medicine V, Universities of Giessen and Marburg Lung Center, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany
- Institute for Lung Health, Justus Liebig University Giessen, Giessen, Germany
- Excellence Cluster Cardio-Pulmonary Institute, Giessen, Germany
- German Center for Lung Research (DZL), Heidelberg, Germany
| | - Susanne Herold
- Department of Internal Medicine V, Universities of Giessen and Marburg Lung Center, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany
- Institute for Lung Health, Justus Liebig University Giessen, Giessen, Germany
- Excellence Cluster Cardio-Pulmonary Institute, Giessen, Germany
- German Center for Lung Research (DZL), Heidelberg, Germany
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176
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Yanagihara T, Hata K, Matsubara K, Kunimura K, Suzuki K, Tsubouchi K, Ikegame S, Baba Y, Fukui Y, Okamoto I. Mass cytometry analysis of B-cell populations in extranodal marginal-zone lymphoma of mucosa-associated lymphoid tissue of the lung. Ann Hematol 2023; 102:2959-2961. [PMID: 37522968 DOI: 10.1007/s00277-023-05391-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023]
Affiliation(s)
- Toyoshi Yanagihara
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
- Department of Respiratory Medicine, National Hospital Organization Fukuoka National Hospital, Fukuoka, Japan.
| | - Kentaro Hata
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keisuke Matsubara
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kazufumi Kunimura
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kunihiro Suzuki
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuya Tsubouchi
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoshi Ikegame
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Baba
- Division of Immunology and Genome Biology, Department of Molecular Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshinori Fukui
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Isamu Okamoto
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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177
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Jahankhani K, Ahangari F, Adcock IM, Mortaz E. Possible cancer-causing capacity of COVID-19: Is SARS-CoV-2 an oncogenic agent? Biochimie 2023; 213:130-138. [PMID: 37230238 PMCID: PMC10202899 DOI: 10.1016/j.biochi.2023.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 04/24/2023] [Accepted: 05/22/2023] [Indexed: 05/27/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown diverse life-threatening effects, most of which are considered short-term. In addition to its short-term effects, which has claimed many millions of lives since 2019, the long-term complications of this virus are still under investigation. Similar to many oncogenic viruses, it has been hypothesized that SARS-CoV-2 employs various strategies to cause cancer in different organs. These include leveraging the renin angiotensin system, altering tumor suppressing pathways by means of its nonstructural proteins, and triggering inflammatory cascades by enhancing cytokine production in the form of a "cytokine storm" paving the way for the emergence of cancer stem cells in target organs. Since infection with SARS-CoV-2 occurs in several organs either directly or indirectly, it is expected that cancer stem cells may develop in multiple organs. Thus, we have reviewed the impact of coronavirus disease 2019 (COVID-19) on the vulnerability and susceptibility of specific organs to cancer development. It is important to note that the cancer-related effects of SARS-CoV-2 proposed in this article are based on the ability of the virus and its proteins to cause cancer but that the long-term consequences of this infection will only be illustrated in the long run.
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Affiliation(s)
- Kasra Jahankhani
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Ahangari
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ian M Adcock
- Airways Disease, National Heart and Lung Institute, Imperial College London, London, United Kingdom; Immune Health Program at Hunter Medical Research Institute and the College of Health and Medicine at the University of Newcastle, Australia
| | - Esmaeil Mortaz
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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178
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Meng R, Yin S, Sun J, Hu H, Zhao Q. scAAGA: Single cell data analysis framework using asymmetric autoencoder with gene attention. Comput Biol Med 2023; 165:107414. [PMID: 37660567 DOI: 10.1016/j.compbiomed.2023.107414] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/02/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
In recent years, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating cellular heterogeneity and structure. However, analyzing scRNA-seq data remains challenging, especially in the context of COVID-19 research. Single-cell clustering is a key step in analyzing scRNA-seq data, and deep learning methods have shown great potential in this area. In this work, we propose a novel scRNA-seq analysis framework called scAAGA. Specifically, we utilize an asymmetric autoencoder with a gene attention module to learn important gene features adaptively from scRNA-seq data, with the aim of improving the clustering effect. We apply scAAGA to COVID-19 peripheral blood mononuclear cell (PBMC) scRNA-seq data and compare its performance with state-of-the-art methods. Our results consistently demonstrate that scAAGA outperforms existing methods in terms of adjusted rand index (ARI), normalized mutual information (NMI), and adjusted mutual information (AMI) scores, achieving improvements ranging from 2.8% to 27.8% in NMI scores. Additionally, we discuss a data augmentation technology to expand the datasets and improve the accuracy of scAAGA. Overall, scAAGA presents a robust tool for scRNA-seq data analysis, enhancing the accuracy and reliability of clustering results in COVID-19 research.
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Affiliation(s)
- Rui Meng
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Shuaidong Yin
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Jianqiang Sun
- School of Information Science and Engineering, Linyi University, Linyi, 276000, China
| | - Huan Hu
- Institute of Applied Genomics, Fuzhou University, Fuzhou, 350108, China.
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China.
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179
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Cui P, Li J, Tao H, Li X, Wu L, Ma J, Wang H, Liu T, Zhang M, Hu Y. Deciphering pathogenic cellular module at single-cell resolution in checkpoint inhibitor-related pneumonitis. Oncogene 2023; 42:3098-3112. [PMID: 37653115 PMCID: PMC10575783 DOI: 10.1038/s41388-023-02805-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/26/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023]
Abstract
Checkpoint inhibitor pneumonitis (CIP) is the most common fatal immune-related adverse event; however, its pathophysiology remains largely unknown. Comprehensively dissecting the key cellular players and molecular pathways associated with CIP pathobiology is critical for precision diagnosis and develop novel therapy strategy of CIP. Herein, we performed a comprehensive single-cell transcriptome analysis to dissect the complexity of the immunological response in the bronchoalveolar lavage fluid (BALF) microenvironment. CIP was characterized by a dramatic accumulation of CXCL13+ T cells and hyperinflammatory CXCL9+ monocytes. T-cell receptor (TCR) analysis revealed that CXCL13+ T cells exhibited hyperexpanded- TCR clonotypes, and pseudotime analysis revealed a potential differentiation trajectory from naïve to cytotoxic effector status. Monocyte trajectories showed that LAMP3+ DCs derived from CXCL9+ monocytes possessed the potential to migrate from tumors to the BALF, whereas the differentiation trajectory to anti-inflammatory macrophages was blocked. Intercellular crosstalk analysis revealed the signaling pathways such as CXCL9/10/11-CXCR3, FASLG-FAS, and IFNGR1/2-IFNG were activated in CIP+ samples. We also proposed a novel immune signature with high diagnostic power to distinguish CIP+ from CIP- samples (AUC = 0.755). Our data highlighted key cellular players, signatures, and interactions involved in CIP pathogenesis.
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Affiliation(s)
- Pengfei Cui
- Department of Oncology, the Second Medical Center of Chinese PLA General Hospital, 100853, Beijing, China
- Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Jinfeng Li
- Institute of oncology, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Haitao Tao
- Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Xiaoyan Li
- Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Liangliang Wu
- Institute of oncology, Senior Department of Oncology, the First Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Junxun Ma
- Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Huanhuan Wang
- Institute of oncology, Senior Department of Oncology, the First Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Tingting Liu
- Department of Pulmonary and Critical Care Medicine, the Second Medical Center of Chinese PLA General Hospital, 100853, Beijing, China
| | - Min Zhang
- State Key Laboratory of Kidney Diseases, Department of Nephrology, the First Medical Center of Chinese PLA General Hospital, 100853, Beijing, China.
| | - Yi Hu
- Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, 100853, Beijing, China.
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180
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Hu Z, Jin X, Hong W, Sui Q, Zhao M, Huang Y, Li M, Wang Q, Zhan C, Chen Z. Dissecting the single-cell transcriptome network of macrophage and identifies a signature to predict prognosis in lung adenocarcinoma. Cell Oncol (Dordr) 2023; 46:1351-1368. [PMID: 37079186 PMCID: PMC10116118 DOI: 10.1007/s13402-023-00816-7] [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] [Accepted: 04/13/2023] [Indexed: 04/21/2023] Open
Abstract
PURPOSE The tumor immune microenvironment (TME) plays a vital role in tumorigenesis, progression, and treatment. Macrophages, as an important component of the tumor microenvironment, play an essential role in antitumor immunity and TME remodeling. In this study, we aimed to explore the different functions of different origins macrophages in TME and their value as potential predictive markers of prognosis and treatment. METHODS We performed single-cell analysis using 21 lung adenocarcinoma (LUAD), 12 normal, and four peripheral blood samples from our data and public databases. A prognostic prediction model was then constructed using 502 TCGA patients and explored the potential factors affecting prognosis. The model was validated using data from 4 different GEO datasets with 544 patients after integration. RESULTS According to the source of macrophages, we classified macrophages into alveolar macrophages (AMs) and interstitial macrophages (IMs). AMs mainly infiltrated in normal lung tissue and expressed proliferative, antigen-presenting, scavenger receptors genes, while IMs occupied the majority in TME and expressed anti-inflammatory, lipid metabolism-related genes. Trajectory analysis revealed that AMs rely on self-renew, whereas IMs originated from monocytes in the blood. Cell-to-cell communication showed that AMs interacted mainly with T cells through the MHC I/II signaling pathway, while IMs mostly interacted with tumor-associated fibrocytes and tumor cells. We then constructed a risk model based on macrophage infiltration and showed an excellent predictive power. We further revealed the possible reasons for its potential prognosis prediction by differential genes, immune cell infiltration, and mutational differences. CONCLUSION In conclusion, we investigated the composition, expression differences, and phenotypic changes of macrophages from different origins in lung adenocarcinoma. In addition, we developed a prognostic prediction model based on different macrophage subtype infiltration, which can be used as a valid prognostic biomarker. New insights were provided into the role of macrophages in the prognosis and potential treatment of LUAD patients.
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Affiliation(s)
- Zhengyang Hu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Xing Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Weifeng Hong
- Department of Radiotherapy, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Qihai Sui
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Mengnan Zhao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Yiwei Huang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Ming Li
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China.
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China.
| | - Zhencong Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180, Fenglin Road, Shanghai, 200032, China.
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Lee MJ, Blish CA. Defining the role of natural killer cells in COVID-19. Nat Immunol 2023; 24:1628-1638. [PMID: 37460639 PMCID: PMC10538371 DOI: 10.1038/s41590-023-01560-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/08/2023] [Indexed: 09/20/2023]
Abstract
Natural killer (NK) cells are critical effectors of antiviral immunity. Researchers have therefore sought to characterize the NK cell response to coronavirus disease 2019 (COVID-19) and the virus that causes it, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The NK cells of patients with severe COVID-19 undergo extensive phenotypic and functional changes. For example, the NK cells from critically ill patients with COVID-19 are highly activated and exhausted, with poor cytotoxic function and cytokine production upon stimulation. The NK cell response to SARS-CoV-2 is also modulated by changes induced in virally infected cells, including the ability of a viral peptide to bind HLA-E, preventing NK cells from receiving inhibitory signals, and the downregulation of major histocompatibility complex class I and ligands for the activating receptor NKG2D. These changes have important implications for the ability of infected cells to escape NK cell killing. The implications of these findings for antibody-dependent NK cell activity in COVID-19 are also reviewed. Despite these advances in the understanding of the NK cell response to SARS-CoV-2, there remain critical gaps in our current understanding and a wealth of avenues for future research on this topic.
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Affiliation(s)
- Madeline J Lee
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA.
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182
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Lepretre F, Gras D, Chanez P, Duez C. Natural killer cells in the lung: potential role in asthma and virus-induced exacerbation? Eur Respir Rev 2023; 32:230036. [PMID: 37437915 DOI: 10.1183/16000617.0036-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/23/2023] [Indexed: 07/14/2023] Open
Abstract
Asthma is a chronic inflammatory airway disorder whose pathophysiological and immunological mechanisms are not completely understood. Asthma exacerbations are mostly driven by respiratory viral infections and characterised by worsening of symptoms. Despite current therapies, asthma exacerbations can still be life-threatening. Natural killer (NK) cells are innate lymphoid cells well known for their antiviral activity and are present in the lung as circulating and resident cells. However, their functions in asthma and its exacerbations are still unclear. In this review, we will address NK cell activation and functions, which are particularly relevant for asthma and virus-induced asthma exacerbations. Then, the role of NK cells in the lungs at homeostasis in healthy individuals will be described, as well as their functions during pulmonary viral infections, with an emphasis on those associated with asthma exacerbations. Finally, we will discuss the involvement of NK cells in asthma and virus-induced exacerbations and examine the effect of asthma treatments on NK cells.
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Affiliation(s)
- Florian Lepretre
- Aix-Marseille Université, INSERM, INRAE, C2VN, Marseille, France
| | - Delphine Gras
- Aix-Marseille Université, INSERM, INRAE, C2VN, Marseille, France
| | - Pascal Chanez
- Aix-Marseille Université, INSERM, INRAE, C2VN, Marseille, France
- APHM, Hôpital Nord, Clinique des Bronches, de l'allergie et du sommeil, Marseille, France
| | - Catherine Duez
- Aix-Marseille Université, INSERM, INRAE, C2VN, Marseille, France
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183
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Booysen P, Wilkinson KA, Sheerin D, Waters R, Coussens AK, Wilkinson RJ. Immune interaction between SARS-CoV-2 and Mycobacterium tuberculosis. Front Immunol 2023; 14:1254206. [PMID: 37841282 PMCID: PMC10569495 DOI: 10.3389/fimmu.2023.1254206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
SARS-CoV-2 and Mycobacterium tuberculosis (Mtb) are major infectious causes of death, with meta-analyses and population-based studies finding increased mortality in co-infected patients simultaneously diagnosed with COVID-19 and tuberculosis (TB). There is a need to understand the immune interaction between SARS-CoV-2 and Mtb which impacts poor outcomes for those co-infected. We performed a PubMed and preprint search using keywords [SARS-CoV-2] AND [tuberculosis] AND [Immune response], including publications after January 2020, excluding reviews or opinions. Abstracts were evaluated by authors for inclusion of data specifically investigating the innate and/or acquired immune responses to SARS-CoV-2 and Mtb in humans and animal models, immunopathological responses in co-infection and both trials and investigations of potential protection against SARS-CoV-2 by Bacille Calmette Guérin (BCG). Of the 248 articles identified, 39 were included. Incidence of co-infection is discussed, considering in areas with a high burden of TB, where reported co-infection is likely underestimated. We evaluated evidence of the clinical association between COVID-19 and TB, discuss differences and similarities in immune responses in humans and in murine studies, and the implications of co-infection. SARS-CoV-2 and Mtb have both been shown to modulate immune responses, particularly of monocytes, macrophages, neutrophils, and T cells. Co-infection may result in impaired immunity to SARS-CoV-2, with an exacerbated inflammatory response, while T cell responses to Mtb may be modulated by SARS-CoV-2. Furthermore, there has been no proven potential COVID-19 clinical benefit of BCG despite numerous large-scale clinical trials.
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Affiliation(s)
- Petro Booysen
- Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Katalin A. Wilkinson
- Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
- Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Dylan Sheerin
- Infectious Diseases and Immune Defence Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Robyn Waters
- Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Anna K. Coussens
- Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Infectious Diseases and Immune Defence Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Robert J. Wilkinson
- Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
- Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Diseases, Imperial College, London, United Kingdom
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Mansoor S, Butt AR, Bibi A, Mushtaq S, Ullah I, Alshahrani F, Khan A, Mansoor A. Expression of IFN-Gamma is significantly reduced during severity of covid-19 infection in hospitalized patients. PLoS One 2023; 18:e0291332. [PMID: 37756264 PMCID: PMC10530045 DOI: 10.1371/journal.pone.0291332] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Cytokines play an important role in SARS-CoV-2 infection progression and severity. A number of inflammatory cytokines have been directly associated with disease severity including IL-6 (interleukin-6), IL-10, TNF-α (tumor necrosis factor alpha), IFN-γ (interferon-gamma). Here, in this study, the aim was to better understand the interplay between host immune response mediated by cytokines and severity of SARS-CoV-2 infection by assessing cytokine expression. Therefore, we measured expression levels of a total of 12 genes (IFNA-1, IFN-γ, IL-1α, IL-1β, IL-4, IL-6, IL-7, IL-10, IL-11, IL-13, IL-15, and IL-27) encoding inflammatory, anti-inflammatory and regulatory cytokines using QRT-PCR in hospitalized patients with severe infection compared to mildly infected. IFN-γ was identified as a potent marker of disease severity as indicated previously. Moreover, levels of IL-7 were also found to be partially reduced in patients compared to the healthy controls and linked negatively to disease severity. Identification of these cytokines may be helpful in not only understanding disease pathogenesis but also in better management of the patients after covid infection.
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Affiliation(s)
- Sajid Mansoor
- Department of Microbiology, Faculty of Science & Technology, University of Central Punjab, Lahore, Pakistan
| | - Ayesha Raza Butt
- Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Asima Bibi
- Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Saima Mushtaq
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Inayat Ullah
- Department of Pediatrics, General Hospital, Islamabad, Pakistan
| | | | - Amjad Khan
- Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Atika Mansoor
- Institute of Biomedical & Genetic Engineering (IB&GE), Islamabad, Pakistan
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185
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Shafqat A, Omer MH, Albalkhi I, Alabdul Razzak G, Abdulkader H, Abdul Rab S, Sabbah BN, Alkattan K, Yaqinuddin A. Neutrophil extracellular traps and long COVID. Front Immunol 2023; 14:1254310. [PMID: 37828990 PMCID: PMC10565006 DOI: 10.3389/fimmu.2023.1254310] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023] Open
Abstract
Post-acute COVID-19 sequelae, commonly known as long COVID, encompasses a range of systemic symptoms experienced by a significant number of COVID-19 survivors. The underlying pathophysiology of long COVID has become a topic of intense research discussion. While chronic inflammation in long COVID has received considerable attention, the role of neutrophils, which are the most abundant of all immune cells and primary responders to inflammation, has been unfortunately overlooked, perhaps due to their short lifespan. In this review, we discuss the emerging role of neutrophil extracellular traps (NETs) in the persistent inflammatory response observed in long COVID patients. We present early evidence linking the persistence of NETs to pulmonary fibrosis, cardiovascular abnormalities, and neurological dysfunction in long COVID. Several uncertainties require investigation in future studies. These include the mechanisms by which SARS-CoV-2 brings about sustained neutrophil activation phenotypes after infection resolution; whether the heterogeneity of neutrophils seen in acute SARS-CoV-2 infection persists into the chronic phase; whether the presence of autoantibodies in long COVID can induce NETs and protect them from degradation; whether NETs exert differential, organ-specific effects; specifically which NET components contribute to organ-specific pathologies, such as pulmonary fibrosis; and whether senescent cells can drive NET formation through their pro-inflammatory secretome in long COVID. Answering these questions may pave the way for the development of clinically applicable strategies targeting NETs, providing relief for this emerging health crisis.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Mohamed H. Omer
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | | | | | | | | | | | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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186
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Imbiakha B, Ezzatpour S, Buchholz DW, Sahler J, Ye C, Olarte-Castillo XA, Zou A, Kwas C, O’Hare K, Choi A, Adeleke RA, Khomandiak S, Goodman L, Jager MC, Whittaker GR, Martinez-Sobrido L, August A, Aguilar HC. Age-dependent acquisition of pathogenicity by SARS-CoV-2 Omicron BA.5. SCIENCE ADVANCES 2023; 9:eadj1736. [PMID: 37738347 PMCID: PMC10516498 DOI: 10.1126/sciadv.adj1736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/23/2023] [Indexed: 09/24/2023]
Abstract
Pathology studies of SARS-CoV-2 Omicron variants of concern (VOC) are challenged by the lack of pathogenic animal models. While Omicron BA.1 and BA.2 replicate in K18-hACE2 transgenic mice, they cause minimal to negligible morbidity and mortality, and less is known about more recent Omicron VOC. Here, we show that in contrast to Omicron BA.1, BA.5-infected mice exhibited high levels of morbidity and mortality, correlating with higher early viral loads. Neither Omicron BA.1 nor BA.5 replicated in brains, unlike most prior VOC. Only Omicron BA.5-infected mice exhibited substantial weight loss, high pathology scores in lungs, and high levels of inflammatory cells and cytokines in bronchoalveolar lavage fluid, and 5- to 8-month-old mice exhibited 100% fatality. These results identify a rodent model for pathogenesis or antiviral countermeasure studies for circulating SARS-CoV-2 Omicron BA.5. Further, differences in morbidity and mortality between Omicron BA.1 and BA.5 provide a model for understanding viral determinants of pathogenicity.
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Affiliation(s)
- Brian Imbiakha
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Shahrzad Ezzatpour
- Department of Microbiology, Cornell University, College of Agriculture and Life Sciences, Ithaca, NY, 14853, USA
| | - David W. Buchholz
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Julie Sahler
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Ximena A. Olarte-Castillo
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- James A. Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Anna Zou
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Cole Kwas
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Katelyn O’Hare
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Annette Choi
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Richard Ayomide Adeleke
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Solomiia Khomandiak
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Laura Goodman
- James A. Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public & Ecosystem Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Mason C. Jager
- Department of Population Medicine and Diagnostic Sciences, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public & Ecosystem Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | | | - Avery August
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Hector C. Aguilar
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Microbiology, Cornell University, College of Agriculture and Life Sciences, Ithaca, NY, 14853, USA
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Mahalingam SS, Jayaraman S, Arunkumar A, Dudley HM, Anthony DD, Shive CL, Jacobson JM, Pandiyan P. Distinct SARS-CoV-2 specific NLRP3 and IL-1β responses in T cells of aging patients during acute COVID-19 infection. Front Immunol 2023; 14:1231087. [PMID: 37799713 PMCID: PMC10548880 DOI: 10.3389/fimmu.2023.1231087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/31/2023] [Indexed: 10/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19) that presents with varied clinical manifestations ranging from asymptomatic or mild infections and pneumonia to severe cases associated with cytokine storm, acute respiratory distress syndrome (ARDS), and even death. The underlying mechanisms contributing to these differences are unclear, although exacerbated inflammatory sequelae resulting from infection have been implicated. While advanced aging is a known risk factor, the precise immune parameters that determine the outcome of SARS-CoV-2 infection in elderly individuals are not understood. Here, we found aging-associated (age ≥61) intrinsic changes in T cell responses when compared to those from individuals aged ≤ 60, even among COVID-positive patients with mild symptoms. Specifically, when stimulated with SARS-CoV-2 peptides in vitro, peripheral blood mononuclear cell (PBMC) CD4+ and CD8+ T cells from individuals aged ≥61 showed a diminished capacity to produce IFN-γ and IL-1β. Although they did not have severe disease, aged individuals also showed a higher frequency of PD-1+ cells and significantly diminished IFN-γ/PD-1 ratios among T lymphocytes upon SARS-CoV-2 peptide stimulation. Impaired T cell IL-1β expression coincided with reduced NLRP3 levels in T lymphocytes. However, the expression of these molecules was not affected in the monocytes of individuals aged ≥61. Together, these data reveal SARS-CoV-2-specific CD4+ and CD8+ T-cell intrinsic cytokine alterations in the individuals older than 61 and may provide new insights into dysregulated COVID-directed immune responses in the elderly.
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Affiliation(s)
- Shanmuga Sundaram Mahalingam
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Sangeetha Jayaraman
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Adhvika Arunkumar
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Holly M. Dudley
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Donald D. Anthony
- Department of Rheumatology, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, United States
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
- Center for AIDS Research, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Medicine, School of Medicine, University Hospitals, Case Western Reserve University, Cleveland, OH, United States
| | - Carey L. Shive
- Department of Rheumatology, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, United States
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Jeffrey M. Jacobson
- Center for AIDS Research, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Medicine, School of Medicine, University Hospitals, Case Western Reserve University, Cleveland, OH, United States
| | - Pushpa Pandiyan
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Rheumatology, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, United States
- Center for AIDS Research, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
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188
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Doaei S, Mardi A, Zare M. Role of micronutrients in the modulation of immune system and platelet activating factor in patients with COVID-19; a narrative review. Front Nutr 2023; 10:1207237. [PMID: 37781112 PMCID: PMC10540693 DOI: 10.3389/fnut.2023.1207237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Background Dietary micronutrients may play important roles in the improvement of the immune responses against SARS-CoV-2. This study aimed to assess the effect of micronutrients on platelet activating factor (PAF) and immunity with a special focus on the coronavirus disease 2019 (COVID-19). Methods All paper published in English on the effects of micronutrients including fat soluble vitamins, water soluble vitamins, and minerals on PAF, immunity, and COVID-19 were collected from online valid databases. Results Vitamin A may modulate the expression of PAF-receptor gene in patients with COVID-19. Vitamin D may modulate inflammatory response through influencing PAF pathway. Vitamin E may improve COVID-19 related heart injuries by exert anti-PAF activities. Vitamin C status may have PAF related anti-inflammatory and micro-thrombotic effects in SARS-CoV-2 patients. Furthermore, some trace elements such as copper, selenium, and iron may have key roles in strengthens immunity by inactivate PAF acetyl hydrolase. Conclusion This narrative review study highlighted the importance of micronutrients in the improvement of immune function through modulation of PAF in patients with COVID-19. Further longitudinal studies are warranted.
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Affiliation(s)
- Saeid Doaei
- Department of Community Nutrition, Faculty of Nutrition Sciences and Food Technology, National Nutrition and Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afrouz Mardi
- Department of Public Health, School of Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Maryam Zare
- Department of Nutrition, Khalkhal University of Medical Sciences, Khalkhal, Iran
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189
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Johnston J, Dorrian D, Linden D, Stanel SC, Rivera-Ortega P, Chaudhuri N. Pulmonary Sequelae of COVID-19: Focus on Interstitial Lung Disease. Cells 2023; 12:2238. [PMID: 37759460 PMCID: PMC10527752 DOI: 10.3390/cells12182238] [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: 07/07/2023] [Revised: 08/28/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
As the world transitions from the acute phase of the COVID-19 pandemic, a novel concern has arisen-interstitial lung disease (ILD) as a consequence of SARS-CoV-2 infection. This review discusses what we have learned about its epidemiology, radiological, and pulmonary function findings, risk factors, and possible management strategies. Notably, the prevailing radiological pattern observed is organising pneumonia, with ground-glass opacities and reticulation frequently reported. Longitudinal studies reveal a complex trajectory, with some demonstrating improvement in lung function and radiographic abnormalities over time, whereas others show more static fibrotic changes. Age, disease severity, and male sex are emerging as risk factors for residual lung abnormalities. The intricate relationship between post-COVID ILD and idiopathic pulmonary fibrosis (IPF) genetics underscores the need for further research and elucidation of shared pathways. As this new disease entity unfolds, continued research is vital to guide clinical decision making and improve outcomes for patients with post-COVID ILD.
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Affiliation(s)
- Janet Johnston
- Interstitial Lung Diseases Unit, North West Lung Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester M23 9LT, UK (P.R.-O.)
| | - Delia Dorrian
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Dermot Linden
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
- Mater Hospital, Belfast Health and Social Care Trust, Belfast BT14 6AB, UK
| | - Stefan Cristian Stanel
- Interstitial Lung Diseases Unit, North West Lung Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester M23 9LT, UK (P.R.-O.)
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Pilar Rivera-Ortega
- Interstitial Lung Diseases Unit, North West Lung Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester M23 9LT, UK (P.R.-O.)
| | - Nazia Chaudhuri
- School of Medicine, Magee Campus, University of Ulster, Northlands Road, Londonderry BT48 7JL, UK;
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Uvarova AN, Stasevich EM, Ustiugova AS, Mitkin NA, Zheremyan EA, Sheetikov SA, Zornikova KV, Bogolyubova AV, Rubtsov MA, Kulakovskiy IV, Kuprash DV, Korneev KV, Schwartz AM. rs71327024 Associated with COVID-19 Hospitalization Reduces CXCR6 Promoter Activity in Human CD4 + T Cells via Disruption of c-Myb Binding. Int J Mol Sci 2023; 24:13790. [PMID: 37762093 PMCID: PMC10530726 DOI: 10.3390/ijms241813790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/11/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Single-nucleotide polymorphism rs71327024 located in the human 3p21.31 locus has been associated with an elevated risk of hospitalization upon SARS-CoV-2 infection. The 3p21.31 locus contains several genes encoding chemokine receptors potentially relevant to severe COVID-19. In particular, CXCR6, which is prominently expressed in T lymphocytes, NK, and NKT cells, has been shown to be involved in the recruitment of immune cells to non-lymphoid organs in chronic inflammatory and respiratory diseases. In COVID-19, CXCR6 expression is reduced in lung resident memory T cells from patients with severe disease as compared to the control cohort with moderate symptoms. We demonstrate here that rs71327024 is located within an active enhancer that augments the activity of the CXCR6 promoter in human CD4+ T lymphocytes. The common rs71327024(G) variant makes a functional binding site for the c-Myb transcription factor, while the risk rs71327024(T) variant disrupts c-Myb binding and reduces the enhancer activity. Concordantly, c-Myb knockdown in PMA-treated Jurkat cells negates rs71327024's allele-specific effect on CXCR6 promoter activity. We conclude that a disrupted c-Myb binding site may decrease CXCR6 expression in T helper cells of individuals carrying the minor rs71327024(T) allele and thus may promote the progression of severe COVID-19 and other inflammatory pathologies.
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Affiliation(s)
- Aksinya N. Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (S.A.S.); (K.V.Z.); (M.A.R.)
| | - Ekaterina M. Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
| | - Alina S. Ustiugova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
| | - Nikita A. Mitkin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
| | - Elina A. Zheremyan
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (S.A.S.); (K.V.Z.); (M.A.R.)
| | - Savely A. Sheetikov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (S.A.S.); (K.V.Z.); (M.A.R.)
- National Research Center for Hematology, 125167 Moscow, Russia;
| | - Ksenia V. Zornikova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (S.A.S.); (K.V.Z.); (M.A.R.)
- National Research Center for Hematology, 125167 Moscow, Russia;
| | | | - Mikhail A. Rubtsov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (S.A.S.); (K.V.Z.); (M.A.R.)
| | | | - Dmitry V. Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (S.A.S.); (K.V.Z.); (M.A.R.)
| | - Kirill V. Korneev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.M.S.); (A.S.U.); (N.A.M.); (E.A.Z.); (D.V.K.)
- National Research Center for Hematology, 125167 Moscow, Russia;
| | - Anton M. Schwartz
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, 199 Abba Khoushy Avenue, Mount Carmel, Haifa 3498838, Israel;
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191
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Potere N, Garrad E, Kanthi Y, Di Nisio M, Kaplanski G, Bonaventura A, Connors JM, De Caterina R, Abbate A. NLRP3 inflammasome and interleukin-1 contributions to COVID-19-associated coagulopathy and immunothrombosis. Cardiovasc Res 2023; 119:2046-2060. [PMID: 37253117 PMCID: PMC10893977 DOI: 10.1093/cvr/cvad084] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 01/30/2023] [Accepted: 02/21/2023] [Indexed: 06/01/2023] Open
Abstract
Immunothrombosis-immune-mediated activation of coagulation-is protective against pathogens, but excessive immunothrombosis can result in pathological thrombosis and multiorgan damage, as in severe coronavirus disease 2019 (COVID-19). The NACHT-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome produces major proinflammatory cytokines of the interleukin (IL)-1 family, IL-1β and IL-18, and induces pyroptotic cell death. Activation of the NLRP3 inflammasome pathway also promotes immunothrombotic programs including release of neutrophil extracellular traps and tissue factor by leukocytes, and prothrombotic responses by platelets and the vascular endothelium. NLRP3 inflammasome activation occurs in patients with COVID-19 pneumonia. In preclinical models, NLRP3 inflammasome pathway blockade restrains COVID-19-like hyperinflammation and pathology. Anakinra, recombinant human IL-1 receptor antagonist, showed safety and efficacy and is approved for the treatment of hypoxaemic COVID-19 patients with early signs of hyperinflammation. The non-selective NLRP3 inhibitor colchicine reduced hospitalization and death in a subgroup of COVID-19 outpatients but is not approved for the treatment of COVID-19. Additional COVID-19 trials testing NLRP3 inflammasome pathway blockers are inconclusive or ongoing. We herein outline the contribution of immunothrombosis to COVID-19-associated coagulopathy, and review preclinical and clinical evidence suggesting an engagement of the NLRP3 inflammasome pathway in the immunothrombotic pathogenesis of COVID-19. We also summarize current efforts to target the NLRP3 inflammasome pathway in COVID-19, and discuss challenges, unmet gaps, and the therapeutic potential that inflammasome-targeted strategies may provide for inflammation-driven thrombotic disorders including COVID-19.
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Affiliation(s)
- Nicola Potere
- Department of Medicine and Ageing Sciences, ‘G. d’Annunzio’ University, Via Luigi Polacchi 11, Chieti 66100, Italy
| | - Evan Garrad
- Laboratory of Vascular Thrombosis and Inflammation, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- University of Missouri School of Medicine, Columbia, MO, USA
| | - Yogendra Kanthi
- Laboratory of Vascular Thrombosis and Inflammation, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marcello Di Nisio
- Department of Medicine and Ageing Sciences, ‘G. d’Annunzio’ University, Via Luigi Polacchi 11, Chieti 66100, Italy
| | - Gilles Kaplanski
- Aix-Marseille Université, INSERM, INRAE, Marseille, France
- Division of Internal Medicine and Clinical Immunology, Assistance Publique - Hôpitaux de Marseille, Hôpital Conception, Aix-Marseille Université, Marseille, France
| | - Aldo Bonaventura
- Department of Internal Medicine, Medicina Generale 1, Medical Center, Ospedale di Circolo e Fondazione Macchi, ASST Sette Laghi, Varese, Italy
| | - Jean Marie Connors
- Division of Hematology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Raffaele De Caterina
- University Cardiology Division, Pisa University Hospital, Pisa, Italy
- Chair and Postgraduate School of Cardiology, University of Pisa, Pisa, Italy
- Fondazione Villa Serena per la Ricerca, Città Sant’Angelo, Pescara, Italy
| | - Antonio Abbate
- Robert M. Berne Cardiovascular Research Center, Department of Medicine, Division of Cardiovascular Medicine, University of Virginia, 415 Lane Rd (MR5), PO Box 801394, Charlottesville, VA 22903, USA
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192
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Forlenza EM, Serino J, Weintraub MT, Burnett RA, Karas V, Della Valle CJ. Elective Joint Arthroplasty Should be Delayed by One Month After COVID-19 Infection to Prevent Postoperative Complications. J Arthroplasty 2023; 38:1676-1681. [PMID: 36813216 PMCID: PMC9941067 DOI: 10.1016/j.arth.2023.02.032] [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: 07/04/2022] [Revised: 02/05/2023] [Accepted: 02/11/2023] [Indexed: 02/23/2023] Open
Abstract
BACKGROUND It remains unclear whether a history of recent COVID-19 infection affects the outcomes and risks of complications of total joint arthroplasty (TJA). The purpose of this study was to compare the outcomes of TJA in patients who have and have not had a recent COVID-19 infection. METHODS A large national database was queried for patients undergoing total hip and total knee arthroplasty. Patients who had a diagnosis of COVID-19 within 90-days preoperatively were matched to patients who did not have a history of COVID-19 based on age, sex, Charlson Comorbidity Index, and procedure. A total of 31,453 patients undergoing TJA were identified, of which 616 (2.0%) had a preoperative diagnosis of COVID-19. Of these, 281 COVID-19 positive patients were matched with 281 patients who did not have COVID-19. The 90-day complications were compared between patients who did and did not have a diagnosis of COVID-19 at 1, 2, and 3 months preoperatively. Multivariate analyses were used to further control for potential confounders. RESULTS Multivariate analysis of the matched cohorts showed that COVID-19 infection within 1 month prior to TJA was associated with an increased rate of postoperative deep vein thrombosis (odds ratio [OR]: 6.50, 95% confidence interval: 1.48-28.45, P = .010) and venous thromboembolic events (odds ratio: 8.32, confidence interval: 2.12-34.84, P = .002). COVID-19 infection within 2 and 3 months prior to TJA did not significantly affect outcomes. CONCLUSION COVID-19 infection within 1 month prior to TJA significantly increases the risk of postoperative thromboembolic events; however, complication rates returned to baseline after that time point. Surgeons should consider delaying elective total hip arthroplasty and total knee arthroplasty until 1 month after a COVID-19 infection.
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Affiliation(s)
| | | | | | | | - Vasili Karas
- Rush University Medical Center, Chicago, Illinois
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193
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Zhou Z, Li D, Zhao Z, Shi S, Wu J, Li J, Zhang J, Gui K, Zhang Y, Ouyang Q, Mei H, Hu Y, Li F. Dynamical modelling of viral infection and cooperative immune protection in COVID-19 patients. PLoS Comput Biol 2023; 19:e1011383. [PMID: 37656752 PMCID: PMC10501599 DOI: 10.1371/journal.pcbi.1011383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/14/2023] [Accepted: 07/24/2023] [Indexed: 09/03/2023] Open
Abstract
Once challenged by the SARS-CoV-2 virus, the human host immune system triggers a dynamic process against infection. We constructed a mathematical model to describe host innate and adaptive immune response to viral challenge. Based on the dynamic properties of viral load and immune response, we classified the resulting dynamics into four modes, reflecting increasing severity of COVID-19 disease. We found the numerical product of immune system's ability to clear the virus and to kill the infected cells, namely immune efficacy, to be predictive of disease severity. We also investigated vaccine-induced protection against SARS-CoV-2 infection. Results suggested that immune efficacy based on memory T cells and neutralizing antibody titers could be used to predict population vaccine protection rates. Finally, we analyzed infection dynamics of SARS-CoV-2 variants within the construct of our mathematical model. Overall, our results provide a systematic framework for understanding the dynamics of host response upon challenge by SARS-CoV-2 infection, and this framework can be used to predict vaccine protection and perform clinical diagnosis.
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Affiliation(s)
- Zhengqing Zhou
- School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Dianjie Li
- School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Ziheng Zhao
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Shuyu Shi
- Peking University Third Hospital, Peking University, Beijing, China
| | - Jianghua Wu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianwei Li
- School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Jingpeng Zhang
- School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Ke Gui
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Yu Zhang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Qi Ouyang
- School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Heng Mei
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fangting Li
- School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
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194
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Kurioka A, Klenerman P. Aging unconventionally: γδ T cells, iNKT cells, and MAIT cells in aging. Semin Immunol 2023; 69:101816. [PMID: 37536148 PMCID: PMC10804939 DOI: 10.1016/j.smim.2023.101816] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023]
Abstract
Unconventional T cells include γδ T cells, invariant Natural Killer T cells (iNKT) cells and Mucosal Associated Invariant T (MAIT) cells, which are distinguished from conventional T cells by their recognition of non-peptide ligands presented by non-polymorphic antigen presenting molecules and rapid effector functions that are pre-programmed during their development. Here we review current knowledge of the effect of age on unconventional T cells, from early life to old age, in both mice and humans. We then discuss the role of unconventional T cells in age-associated diseases and infections, highlighting the similarities between members of the unconventional T cell family in the context of aging.
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Affiliation(s)
- Ayako Kurioka
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
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195
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Ghaddar B, Blaser MJ, De S. Denoising sparse microbial signals from single-cell sequencing of mammalian host tissues. NATURE COMPUTATIONAL SCIENCE 2023; 3:741-747. [PMID: 37946872 PMCID: PMC10634611 DOI: 10.1038/s43588-023-00507-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 08/07/2023] [Indexed: 11/12/2023]
Abstract
Existing genomic sequencing data can be used to study host-microbiome ecosystems, however distinguishing signals originating from truly present microbes versus contaminating species and artifacts is a substantial and often prohibitive challenge. Here we show that emerging sequencing technologies definitely capture reads from present microbes. We developed SAHMI, a computational resource to identify truly present microbial nucleic acids and filter contaminants and spurious false-positive taxonomic assignments from standard transcriptomic sequencing of mammalian tissues. In benchmark studies, SAHMI correctly identifies known microbial infections present in diverse tissues, and we validate SAHMI's enrichment for correctly classified, truly present species using multiple orthogonal computational experiments. The application of SAHMI to single-cell and spatial genomic data thus enables co-detection of somatic cells and microorganisms and joint analysis of host-microbiome ecosystems.
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Affiliation(s)
- Bassel Ghaddar
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University; 195 Albany St., New Brunswick, New Jersey 08901
| | - Martin J. Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University; 679 Hoes Lane West, Piscataway, New Jersey 08854
| | - Subhajyoti De
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University; 195 Albany St., New Brunswick, New Jersey 08901
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196
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Aiello A, Najafi-Fard S, Goletti D. Initial immune response after exposure to Mycobacterium tuberculosis or to SARS-COV-2: similarities and differences. Front Immunol 2023; 14:1244556. [PMID: 37662901 PMCID: PMC10470049 DOI: 10.3389/fimmu.2023.1244556] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) and Coronavirus disease-2019 (COVID-19), whose etiologic agent is severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), are currently the two deadliest infectious diseases in humans, which together have caused about more than 11 million deaths worldwide in the past 3 years. TB and COVID-19 share several aspects including the droplet- and aerosol-borne transmissibility, the lungs as primary target, some symptoms, and diagnostic tools. However, these two infectious diseases differ in other aspects as their incubation period, immune cells involved, persistence and the immunopathological response. In this review, we highlight the similarities and differences between TB and COVID-19 focusing on the innate and adaptive immune response induced after the exposure to Mtb and SARS-CoV-2 and the pathological pathways linking the two infections. Moreover, we provide a brief overview of the immune response in case of TB-COVID-19 co-infection highlighting the similarities and differences of each individual infection. A comprehensive understanding of the immune response involved in TB and COVID-19 is of utmost importance for the design of effective therapeutic strategies and vaccines for both diseases.
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Affiliation(s)
| | | | - Delia Goletti
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
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197
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Zeng Z, Geng X, Wen X, Chen Y, Zhu Y, Dong Z, Hao L, Wang T, Yang J, Zhang R, Zheng K, Sun Z, Zhang Y. Novel receptor, mutation, vaccine, and establishment of coping mode for SARS-CoV-2: current status and future. Front Microbiol 2023; 14:1232453. [PMID: 37645223 PMCID: PMC10461067 DOI: 10.3389/fmicb.2023.1232453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023] Open
Abstract
Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its resultant pneumonia in December 2019, the cumulative number of infected people worldwide has exceeded 670 million, with over 6.8 million deaths. Despite the marketing of multiple series of vaccines and the implementation of strict prevention and control measures in many countries, the spread and prevalence of SARS-CoV-2 have not been completely and effectively controlled. The latest research shows that in addition to angiotensin converting enzyme II (ACE2), dozens of protein molecules, including AXL, can act as host receptors for SARS-CoV-2 infecting human cells, and virus mutation and immune evasion never seem to stop. To sum up, this review summarizes and organizes the latest relevant literature, comprehensively reviews the genome characteristics of SARS-CoV-2 as well as receptor-based pathogenesis (including ACE2 and other new receptors), mutation and immune evasion, vaccine development and other aspects, and proposes a series of prevention and treatment opinions. It is expected to provide a theoretical basis for an in-depth understanding of the pathogenic mechanism of SARS-CoV-2 along with a research basis and new ideas for the diagnosis and classification, of COVID-19-related disease and for drug and vaccine research and development.
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Affiliation(s)
- Zhaomu Zeng
- Department of Neurosurgery, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
- Department of Neurosurgery, Xiangya Hospital Jiangxi Hospital of Central South University, National Regional Medical Center for Nervous System Diseases, Nanchang, China
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Xiuchao Geng
- Department of Nursing, School of Medicine, Taizhou University, Taizhou, China
| | - Xichao Wen
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Yueyue Chen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yixi Zhu
- Department of Pharmacy, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zishu Dong
- Department of Zoology, Advanced Research Institute, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Liangchao Hao
- Department of Plastic Surgery, Shaoxing People’s Hospital, Shaoxing, China
| | - Tingting Wang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Jifeng Yang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Ruobing Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Kebin Zheng
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yuhao Zhang
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, China
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198
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Wang Y, Yang C, Wang Z, Wang Y, Yan Q, Feng Y, Liu Y, Huang J, Zhou J. Epithelial Galectin-3 Induced the Mitochondrial Complex Inhibition and Cell Cycle Arrest of CD8 + T Cells in Severe/Critical COVID-19. Int J Mol Sci 2023; 24:12780. [PMID: 37628961 PMCID: PMC10454470 DOI: 10.3390/ijms241612780] [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: 06/29/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Previous research suggested that the dramatical decrease in CD8+ T cells is a contributing factor in the poor prognosis and disease progression of COVID-19 patients. However, the underlying mechanisms are not fully understood. In this study, we conducted Single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) analysis, which revealed a proliferative-exhausted MCM+FASLGlow CD8+ T cell phenotype in severe/critical COVID-19 patients. These CD8+ T cells were characterized by G2/M cell cycle arrest, downregulation of respiratory chain complex genes, and inhibition of mitochondrial biogenesis. CellChat analysis of infected lung epithelial cells and CD8+ T cells found that the galectin signaling pathway played a crucial role in CD8+ T cell reduction and dysfunction. To further elucidate the mechanisms, we established SARS-CoV-2 ORF3a-transfected A549 cells, and co-cultured them with CD8+ T cells for ex vivo experiments. Our results showed that epithelial galectin-3 inhibited the transcription of the mitochondrial respiratory chain complex III/IV genes of CD8+ T cells by suppressing the nuclear translocation of nuclear respiratory factor 1 (NRF1). Further findings showed that the suppression of NRF1 translocation was associated with ERK-related and Akt-related signaling pathways. Importantly, the galectin-3 inhibitor, TD-139, promoted nuclear translocation of NRF1, thus enhancing the expression of the mitochondrial respiratory chain complex III/IV genes and the mitochondrial biogenesis of CD8+ T cells. Our study provided new insights into the immunopathogenesis of COVID-19 and identified potential therapeutic targets for the prevention and treatment of severe/critical COVID-19 patients.
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Affiliation(s)
- Yudie Wang
- Department of Biology and Genetics, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Cheng Yang
- Department of Biology and Genetics, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Zhongyi Wang
- Department of Biology and Genetics, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Yi Wang
- Department of Biology and Genetics, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Qing Yan
- Department of Biology and Genetics, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Ying Feng
- Department of Biology and Genetics, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Yanping Liu
- Department of Biology and Genetics, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Juan Huang
- Department of Hematology, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430070, China
| | - Jingjiao Zhou
- Department of Biology and Genetics, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan 430065, China
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199
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Kleeman SO, Thakir TM, Demestichas B, Mourikis N, Loiero D, Ferrer M, Bankier S, Riazat-Kesh YJ, Lee H, Chantzichristos D, Regan C, Preall J, Sinha S, Rosin N, Yipp B, de Almeida LG, Biernaskie J, Dufour A, Tober-Lau P, Ruusalepp A, Bjorkegren JL, Ralser M, Kurth F, Demichev V, Heywood T, Gao Q, Johannsson G, Koelzer VH, Walker BR, Meyer HV, Janowitz T. Cystatin C is glucocorticoid responsive, directs recruitment of Trem2+ macrophages, and predicts failure of cancer immunotherapy. CELL GENOMICS 2023; 3:100347. [PMID: 37601967 PMCID: PMC10435381 DOI: 10.1016/j.xgen.2023.100347] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 03/23/2023] [Accepted: 05/30/2023] [Indexed: 08/22/2023]
Abstract
Cystatin C (CyC), a secreted cysteine protease inhibitor, has unclear biological functions. Many patients exhibit elevated plasma CyC levels, particularly during glucocorticoid (GC) treatment. This study links GCs with CyC's systemic regulation by utilizing genome-wide association and structural equation modeling to determine CyC production genetics in the UK Biobank. Both CyC production and a polygenic score (PGS) capturing predisposition to CyC production were associated with increased all-cause and cancer-specific mortality. We found that the GC receptor directly targets CyC, leading to GC-responsive CyC secretion in macrophages and cancer cells. CyC-knockout tumors displayed significantly reduced growth and diminished recruitment of TREM2+ macrophages, which have been connected to cancer immunotherapy failure. Furthermore, the CyC-production PGS predicted checkpoint immunotherapy failure in 685 patients with metastatic cancer from combined clinical trial cohorts. In conclusion, CyC may act as a GC effector pathway via TREM2+ macrophage recruitment and may be a potential target for combination cancer immunotherapy.
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Affiliation(s)
- Sam O. Kleeman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | - Dominik Loiero
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Miriam Ferrer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Sean Bankier
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | | | - Hassal Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Dimitrios Chantzichristos
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Endocrinology Diabetes and Metabolism, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Claire Regan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Sarthak Sinha
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Nicole Rosin
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Bryan Yipp
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Luiz G.N. de Almeida
- Department of Biochemistry and Molecular Biology and Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
| | - Jeff Biernaskie
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Antoine Dufour
- Department of Biochemistry and Molecular Biology and Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
| | | | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia
| | - Johan L.M. Bjorkegren
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Markus Ralser
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Florian Kurth
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Todd Heywood
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Qing Gao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gudmundur Johannsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Endocrinology Diabetes and Metabolism, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Viktor H. Koelzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oncology and Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Brian R. Walker
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Tobias Janowitz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Cancer Institute, Northwell Health, New Hyde Park, NY, USA
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200
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Castanheira FVS, Nguyen R, Willson M, Davoli-Ferreira M, David BA, Kelly MM, Lee WY, Kratofil RM, Zhang WX, Bui-Marinos M, Corcoran JA, Kubes P. Intravital imaging of three different microvascular beds in SARS-CoV-2-infected mice. Blood Adv 2023; 7:4170-4181. [PMID: 37307197 PMCID: PMC10284260 DOI: 10.1182/bloodadvances.2022009430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/08/2023] [Accepted: 05/29/2023] [Indexed: 06/14/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) enters the respiratory tract, where it infects the alveoli epithelial lining. However, patients have sequelae that extend well beyond the alveoli into the pulmonary vasculature and, perhaps, beyond to the brain and other organs. Because of the dynamic events within blood vessels, histology does not report platelet and neutrophil behavior. Because of the rapid nontranscriptional response of these cells, neither single-cell RNA sequencing nor proteomics report robustly on their critical behaviors. We used intravital microscopy in level-3 containment to examine the pathogenesis of SARS-CoV-2 within 3 organs in mice expressing human angiotensin converting enzyme 2 (ACE-2) ubiquitously (CAG-AC-70) or on epithelium (K18-promoter). Using a neon-green SARS-CoV-2, we observed both the epithelium and endothelium infected in AC70 mice but only the epithelium in K18 mice. There were increased neutrophils in the microcirculation but not in the alveoli of the lungs of AC70 mice. Platelets formed large aggregates in the pulmonary capillaries. Despite only neurons being infected within the brain, profound neutrophil adhesion forming the nidus of large platelet aggregates were observed in the cerebral microcirculation, with many nonperfused microvessels. Neutrophils breached the brain endothelial layer associated with a significant disruption of the blood-brain-barrier. Despite ubiquitous ACE-2 expression, CAG-AC-70 mice had very small increases in blood cytokine, no increase in thrombin, no infected circulating cells, and no liver involvement suggesting limited systemic effects. In summary, our imaging of SARS-CoV-2-infected mice gave direct evidence that there is a significant perturbation locally in the lung and brain microcirculation induced by local viral infection leading to increased local inflammation and thrombosis in these organs.
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Affiliation(s)
- Fernanda V. S. Castanheira
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB
| | - Rita Nguyen
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB
| | - Michelle Willson
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB
| | - Marcela Davoli-Ferreira
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB
| | - Bruna A. David
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB
| | - Margaret M. Kelly
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB
- Pathology and Laboratory Medicine, University of Calgary, Calgary, AB
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB
| | - Woo-Yong Lee
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB
| | - Rachel M. Kratofil
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB
| | - Wen X. Zhang
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB
| | - Maxwell Bui-Marinos
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, AB
| | - Jennifer A. Corcoran
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, AB
| | - Paul Kubes
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB
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