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Dual spatially reso...
Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections
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- Sounart, Hailey (author)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Lázár, Enikő (author)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab,Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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- Masarapu, Yuvarani (author)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Wu, Jian (author)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Várkonyi, Tibor (author)
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
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- Glasz, Tibor (author)
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
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- Kiss, András (author)
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
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- Borgström, Erik (author)
- 10X Genomics, Pleasanton, CA, USA
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- Hill, Andrew (author)
- 10X Genomics, Pleasanton, CA, USA
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- Rezene, Sefanit (author)
- Karolinska Institutet
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- Gupta, Soham (author)
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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- Jurek, Aleksandra (author)
- 10X Genomics, Pleasanton, CA, USA
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- Niesnerová, Anezka (author)
- 10X Genomics, Pleasanton, CA, USA
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- Druid, Henrik (author)
- Department of Oncology-Pathology, Karolinska Institutet, 17177, Stockholm, Sweden
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- Bergmann, Olaf (author)
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Center for Regenerative Therapies Dresden (CRTD), TU Dresden, Dresden, Germany, TU Dresden; Universitätsmedizin Göttingen, Institute of Pharmacology and Toxicology, Göttingen, Germany
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- Giacomello, Stefania (author)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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(creator_code:org_t)
- Springer Nature, 2023
- 2023
- English.
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In: Genome Biology. - : Springer Nature. - 1465-6906 .- 1474-760X. ; 24:1
- Related links:
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
Subject headings
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- Technologies to study localized host–pathogen interactions are urgently needed. Here, we present a spatial transcriptomics approach to simultaneously capture host and pathogen transcriptome-wide spatial gene expression information from human formalin-fixed paraffin-embedded (FFPE) tissue sections at a near single-cell resolution. We demonstrate this methodology in lung samples from COVID-19 patients and validate our spatial detection of SARS-CoV-2 against RNAScope and in situ sequencing. Host–pathogen colocalization analysis identified putative modulators of SARS-CoV-2 infection in human lung cells. Our approach provides new insights into host response to pathogen infection through the simultaneous, unbiased detection of two transcriptomes in FFPE samples.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Cell- och molekylärbiologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Cell and Molecular Biology (hsv//eng)
Keyword
- Colocalization analysis
- Formalin-fixed paraffin-embedded (FFPE) tissues
- Host–pathogen interactions
- Spatial transcriptomics
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Sounart, Hailey
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Lázár, Enikő
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Masarapu, Yuvara ...
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Wu, Jian
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Várkonyi, Tibor
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Glasz, Tibor
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show more...
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Kiss, András
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Borgström, Erik
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Hill, Andrew
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Rezene, Sefanit
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Gupta, Soham
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Jurek, Aleksandr ...
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Niesnerová, Anez ...
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Druid, Henrik
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Bergmann, Olaf
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Giacomello, Stef ...
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- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Cancer and Oncol ...
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Cell and Molecul ...
- Articles in the publication
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Genome Biology
- By the university
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Royal Institute of Technology
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Karolinska Institutet