A robust platform for integrative spatial multi‐omics analysis to map immune responses to SARS‐CoV ‐2 infection in lung tissues
Article Swipe
Xiao Tan
,
Laura F. Grice
,
Minh Tran
,
Onkar Mulay
,
James Monkman
,
Tony Blick
,
Tuan Vo
,
Ana Clara Almeida
,
Jarbas da Silva Motta
,
Karen Fernandes de Moura
,
Cleber Machado‐Souza
,
Paulo Souza‐Fonseca‐Guimaraes
,
Cristina Pellegrino Baena
,
Lúcia de Noronha
,
Fernanda Simoes Fortes Guimaraes
,
Hung N. Luu
,
Tingsheng Yu
,
Stephen R. Williams
,
Jacob Stern
,
Cedric R. Uytingco
,
Liuliu Pan
,
Andy Nam
,
Caroline Cooper
,
Kirsty R. Short
,
Gabrielle T. Belz
,
Fernando Souza-Fonseca-Guimarães
,
Arutha Kulasinghe
,
Quan Nguyen
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1111/imm.13679
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1111/imm.13679
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.
Related Topics
Concepts
Biology
Transcriptome
Lung
Bronchoalveolar lavage
Proteome
Proteomics
Immune system
Omics
Computational biology
Coronavirus disease 2019 (COVID-19)
Virus
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Immunology
Bioinformatics
Pathology
Medicine
Gene expression
Gene
Genetics
Infectious disease (medical specialty)
Disease
Internal medicine
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1111/imm.13679
- https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/imm.13679
- OA Status
- hybrid
- Cited By
- 11
- References
- 58
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4386045822
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4386045822Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1111/imm.13679Digital Object Identifier
- Title
-
A robust platform for integrative spatial multi‐omics analysis to map immune responses to
SARS‐CoV ‐2 infection in lung tissuesWork title - Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-08-21Full publication date if available
- Authors
-
Xiao Tan, Laura F. Grice, Minh Tran, Onkar Mulay, James Monkman, Tony Blick, Tuan Vo, Ana Clara Almeida, Jarbas da Silva Motta, Karen Fernandes de Moura, Cleber Machado‐Souza, Paulo Souza‐Fonseca‐Guimaraes, Cristina Pellegrino Baena, Lúcia de Noronha, Fernanda Simoes Fortes Guimaraes, Hung N. Luu, Tingsheng Yu, Stephen R. Williams, Jacob Stern, Cedric R. Uytingco, Liuliu Pan, Andy Nam, Caroline Cooper, Kirsty R. Short, Gabrielle T. Belz, Fernando Souza-Fonseca-Guimarães, Arutha Kulasinghe, Quan NguyenList of authors in order
- Landing page
-
https://doi.org/10.1111/imm.13679Publisher landing page
- PDF URL
-
https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/imm.13679Direct link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
- OA URL
-
https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/imm.13679Direct OA link when available
- Concepts
-
Biology, Transcriptome, Lung, Bronchoalveolar lavage, Proteome, Proteomics, Immune system, Omics, Computational biology, Coronavirus disease 2019 (COVID-19), Virus, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Immunology, Bioinformatics, Pathology, Medicine, Gene expression, Gene, Genetics, Infectious disease (medical specialty), Disease, Internal medicineTop concepts (fields/topics) attached by OpenAlex
- Cited by
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11Total citation count in OpenAlex
- Citations by year (recent)
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2025: 5, 2024: 4, 2023: 2Per-year citation counts (last 5 years)
- References (count)
-
58Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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