A robust platform for integrative spatial multi-omics analysis to map immune responses to SARS-CoV-2 infection in lung tissues.
COVID-19 infection
spatial integration
spatial proteomics
spatial transcriptomics
Journal
Immunology
ISSN: 1365-2567
Titre abrégé: Immunology
Pays: England
ID NLM: 0374672
Informations de publication
Date de publication:
Nov 2023
Nov 2023
Historique:
received:
20
02
2023
accepted:
03
07
2023
pubmed:
22
8
2023
medline:
22
8
2023
entrez:
22
8
2023
Statut:
ppublish
Résumé
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.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
401-418Subventions
Organisme : National Health and Medical Research Council
ID : APP2008542
Organisme : National Health and Medical Research Council
ID : 1135898
Organisme : National Health and Medical Research Council
ID : 1157741
Organisme : National Health and Medical Research Council
ID : 1140406
Organisme : National Health and Medical Research Council
ID : 2001514
Organisme : National Health and Medical Research Council
ID : GNT2008928
Informations de copyright
© 2023 The Authors. Immunology published by John Wiley & Sons Ltd.
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