Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections

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

Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections

2023

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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