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

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.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

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Dataset ID	Description	Technology	Samples
EGAD00001008701	Advamced Visium Spatial Gene Expression assay for FFPE tissues with human and SARS-CoV-2 whole transcriptome (WT) information at a 55 µm resolution. The dataset consists of 13 tissue sections from 5 patient lung tissue samples, 3 from COVID-19 patients and 2 from control patients.	Illumina NovaSeq 6000	13

Publications	Citations
Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections. Sounart H, Lázár E, Masarapu Y, Wu J, Várkonyi T, Glasz T, Kiss A, Borgström E, Hill A, Rezene S, Gupta S, Jurek A, Niesnerová A, Druid H, Bergmann O, Giacomello S. Genome Biol 24: 2023 237	1