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 (1) 237 [2023-10-19; online 2023-10-19]

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.

Category: Genomics & transcriptomics

Funder: VR

Type: Journal article

PubMed 37858234

DOI 10.1186/s13059-023-03080-y

Crossref 10.1186/s13059-023-03080-y

pmc: PMC10588020
pii: 10.1186/s13059-023-03080-y

Publications 9.5.0