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. 2023 Nov;170(3):401-418.
doi: 10.1111/imm.13679. Epub 2023 Aug 21.

A robust platform for integrative spatial multi-omics analysis to map immune responses to SARS-CoV-2 infection in lung tissues

Xiao Tan  1 , Laura F Grice  1   2 , Minh Tran  1 , Onkar Mulay  1 , James Monkman  3 , Tony Blick  3 , Tuan Vo  1 , Ana Clara Almeida  4   5 , Jarbas da Silva Motta Junior  4 , Karen Fernandes de Moura  3 , Cleber Machado-Souza  6 , Paulo Souza-Fonseca-Guimaraes  4 , Cristina Pellegrino Baena  4 , Lucia de Noronha  4   5 , Fernanda Simoes Fortes Guimaraes  7 , Hung N Luu  8 , Tingsheng Drennon  9 , Stephen Williams  9 , Jacob Stern  9 , Cedric Uytingco  9 , Liuliu Pan  10 , Andy Nam  10 , Caroline Cooper  3 , Kirsty Short  11 , Gabrielle T Belz  3 , Fernando Souza-Fonseca-Guimaraes  3 , Arutha Kulasinghe  3 , Quan Nguyen  1   12
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Free article

A robust platform for integrative spatial multi-omics analysis to map immune responses to SARS-CoV-2 infection in lung tissues

Xiao Tan et al. Immunology. 2023 Nov.
Free article

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.

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