Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections
2023
Hailey Sounart | Enikő Lázár | Yuvarani Masarapu | Jian Wu | Tibor Várkonyi | Tibor Glasz | András Kiss | Erik Borgström | Andrew Hill | Sefanit Rezene | Soham Gupta | Aleksandra Jurek | Anezka Niesnerová | Henrik Druid | Olaf Bergmann | Stefania Giacomello
Abstract 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.
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