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Tan X, Grice LF, Tran M, Mulay O, Monkman J, Blick T, Vo T, Almeida AC, da Silva Motta J, de Moura KF, Machado-Souza C, Souza-Fonseca-Guimaraes P, Baena CP, de Noronha L, Guimaraes FSF, Luu HN, Drennon T, Williams S, Stern J, Uytingco C, Pan L, Nam A, Cooper C, Short K, Belz GT, Souza-Fonseca-Guimaraes F, Kulasinghe A, Nguyen Q. A robust platform for integrative spatial multi-omics analysis to map immune responses to SARS-CoV-2 infection in lung tissues. Immunology 2023; 170:401-418. [PMID: 37605469 DOI: 10.1111/imm.13679] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/03/2023] [Indexed: 08/23/2023] Open
Abstract
The SARS-CoV-2 (COVID-19) virus has caused a devastating global pandemic of respiratory illness. To understand viral pathogenesis, methods are available for studying dissociated cells in blood, nasal samples, bronchoalveolar lavage fluid and similar, but a robust platform for deep tissue characterization of molecular and cellular responses to virus infection in the lungs is still lacking. We developed an innovative spatial multi-omics platform to investigate COVID-19-infected lung tissues. Five tissue-profiling technologies were combined by a novel computational mapping methodology to comprehensively characterize and compare the transcriptome and targeted proteome of virus infected and uninfected tissues. By integrating spatial transcriptomics data (Visium, GeoMx and RNAScope) and proteomics data (CODEX and PhenoImager HT) at different cellular resolutions across lung tissues, we found strong evidence for macrophage infiltration and defined the broader microenvironment surrounding these cells. By comparing infected and uninfected samples, we found an increase in cytokine signalling and interferon responses at different sites in the lung and showed spatial heterogeneity in the expression level of these pathways. These data demonstrate that integrative spatial multi-omics platforms can be broadly applied to gain a deeper understanding of viral effects on cellular environments at the site of infection and to increase our understanding of the impact of SARS-CoV-2 on the lungs.
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Affiliation(s)
- Xiao Tan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Laura F Grice
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Onkar Mulay
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - James Monkman
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Tony Blick
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Tuan Vo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Ana Clara Almeida
- Pontifícia Universidade Católica do Paraná, PUCPR, Curitiba, Paraná, Brazil
- Laboratório de Patologia Experimental, PPGCS da PUCPR, Curitiba, Brazil
| | | | - Karen Fernandes de Moura
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Cleber Machado-Souza
- Faculdades Pequeno Príncipe-Instituto de Pesquisa Pelé Pequeno príncipe, Curitiba, Paraná, Brazil
| | | | | | - Lucia de Noronha
- Pontifícia Universidade Católica do Paraná, PUCPR, Curitiba, Paraná, Brazil
- Laboratório de Patologia Experimental, PPGCS da PUCPR, Curitiba, Brazil
| | | | - Hung N Luu
- UMPC Hillman Cancer Center & School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | | | | | | | - Liuliu Pan
- NanoString Technologies Inc, Seattle, Washington, USA
| | - Andy Nam
- NanoString Technologies Inc, Seattle, Washington, USA
| | - Caroline Cooper
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Kirsty Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Gabrielle T Belz
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | | | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- QIMR Berghofer Medical Reseach Institute, Queensland, Australia
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George B, Amjesh R, Paul AM, Santhoshkumar TR, Pillai MR, Kumar R. Evidence of a dysregulated vitamin D endocrine system in SARS-CoV-2 infected patient's lung cells. Sci Rep 2021; 11:8570. [PMID: 33883570 PMCID: PMC8060306 DOI: 10.1038/s41598-021-87703-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/30/2021] [Indexed: 12/19/2022] Open
Abstract
Although a defective vitamin D endocrine system has been widely suspected to be associated in SARS-CoV-2 pathobiology, the status of the vitamin D endocrine system and vitamin D-modulated genes in lung cells of patients infected with SARS-CoV-2 remains unknown. To understand the significance of the vitamin D endocrine system in SARS-CoV-2 pathobiology, computational approaches were applied to transcriptomic datasets from bronchoalveolar lavage fluid (BALF) cells of such patients or healthy individuals. Levels of vitamin D receptor, retinoid X receptor, and CYP27A1 in BALF cells of patients infected with SARS-CoV-2 were found to be reduced. Additionally, 107 differentially expressed, predominantly downregulated genes, as potentially modulated by vitamin D endocrine system, were identified in transcriptomic datasets from patient's cells. Further analysis of differentially expressed genes provided eight novel genes with a conserved motif with vitamin D-responsive elements, implying the role of both direct and indirect mechanisms of gene expression by the dysregulated vitamin D endocrine system in SARS-CoV-2-infected cells. Protein-protein interaction network of differentially expressed vitamin D-modulated genes were enriched in the immune system, NF-κB/cytokine signaling, and cell cycle regulation as top predicted pathways that might be affected in the cells of such patients. In brief, the results presented here povide computational evidence to implicate a dysregulated vitamin D endocrine system in the pathobiology of SARS-CoV-2 infection.
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Affiliation(s)
- Bijesh George
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- PhD Program, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Revikumar Amjesh
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Aswathy Mary Paul
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- PhD Program, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - T R Santhoshkumar
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | | | - Rakesh Kumar
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India.
- Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, USA.
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Vega MA, Simón-Fuentes M, González de la Aleja A, Nieto C, Colmenares M, Herrero C, Domínguez-Soto Á, Corbí ÁL. MAFB and MAF Transcription Factors as Macrophage Checkpoints for COVID-19 Severity. Front Immunol 2020; 11:603507. [PMID: 33312178 PMCID: PMC7708330 DOI: 10.3389/fimmu.2020.603507] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/19/2020] [Indexed: 01/10/2023] Open
Abstract
Defective IFN production and exacerbated inflammatory and pro-fibrotic responses are hallmarks of SARS-CoV-2 infection in severe COVID-19. Based on these hallmarks, and considering the pivotal role of macrophages in COVID-19 pathogenesis, we hypothesize that the transcription factors MAFB and MAF critically contribute to COVID-19 progression by shaping the response of macrophages to SARS-CoV-2. Our proposal stems from the recent identification of pathogenic lung macrophage subsets in severe COVID-19, and takes into consideration the previously reported ability of MAFB to dampen IFN type I production, as well as the critical role of MAFB and MAF in the acquisition and maintenance of the transcriptional signature of M-CSF-conditioned human macrophages. Solid evidences are presented that link overexpression of MAFB and silencing of MAF expression with clinical and biological features of severe COVID-19. As a whole, we propose that a high MAFB/MAF expression ratio in lung macrophages could serve as an accurate diagnostic tool for COVID-19 progression. Indeed, reversing the macrophage MAFB/MAF expression ratio might impair the exacerbated inflammatory and profibrotic responses, and restore the defective IFN type I production, thus becoming a potential strategy to limit severity of COVID-19.
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Affiliation(s)
- Miguel A. Vega
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | | | | | | | | | | | | | - Ángel L. Corbí
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
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