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A robust platform for integrative spatial multi-omics analysis to map immune responses to SARS-CoV-2 infection in lung tissues |
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| Authors: | Xiao Tan Laura F. Grice Minh Tran Onkar Mulay James Monkman Tony Blick Tuan Vo Ana Clara Almeida Jarbas da Silva Motta Junior Karen Fernandes de Moura Cleber Machado-Souza Paulo Souza-Fonseca-Guimaraes Cristina Pellegrino Baena Lucia de Noronha Fernanda Simoes Fortes Guimaraes Hung N. Luu Tingsheng Drennon Stephen Williams Jacob Stern Cedric Uytingco Liuliu Pan Andy Nam Caroline Cooper Kirsty Short Gabrielle T. Belz Fernando Souza-Fonseca-Guimaraes Arutha Kulasinghe Quan Nguyen |
| Affiliation: | 1. Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia;2. Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia;3. Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia;4. Pontifícia Universidade Católica do Paraná, PUCPR, Curitiba, Paraná, Brazil;5. Faculdades Pequeno Príncipe—Instituto de Pesquisa Pelé Pequeno príncipe, Curitiba, Paraná, Brazil;6. Pontifícia Universidade Católica do Paraná, PUCPR, Curitiba, Paraná, Brazil Laboratório de Patologia Experimental, PPGCS da PUCPR, Curitiba, Brazil;7. Positive University—School of Medicine, Curitiba, Brazil;8. UMPC Hillman Cancer Center & School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA;9. 10x Genomics, Pleasanton, California, USA;10. NanoString Technologies Inc, Seattle, Washington, USA;11. School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia |
| 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. |
| Keywords: | COVID-19 infection spatial integration spatial proteomics spatial transcriptomics |