Dual host-pathogen screening of the lung during severe influenza using spatial transcriptomics

ABSTRACT: Here, we assessed whether spatially-resolved capture of polyadenylated mRNA permitted simultaneous screening of host and viral responses in situ. Fresh-frozen lung samples from mice infected with H1N1 influenza A strain, PR8, were processed via genome-wide, spatial transcriptomics (ST) at 10 μm resolution. To determine if specific cell-types were detectable within the ST data, we first performed cellular deconvolution using publicly available, single-cell RNA-seq data of immune and non-immune cells from PR8-infected lungs. This revealed expected structures such as rings of epithelial cells lining airways, and at day 10 post-infection (p.i.) unexpected structures dominated by B cells. We next screened ST data alone for groups of genes displaying similar spatial expression patterns. This again identified at day 10 p.i. cellular aggregates enriched for genes associated with B cell biology. Mapping these gene signatures to a B cell transcriptomic atlas suggested plasmablasts had emerged early in the lung, which was confirmed by flow cytometry. Finally, by mapping ST data to the influenza A genome, we observed widespread expression of all ten viral transcripts across samples at day 4 but not day 10 p.i., consistent with viral clearance. Cellular deconvolution analysis at day 4 p.i. revealed proportions of every detected cell-type harboured viral transcripts, suggesting indiscriminate infection across the specific area of tissue examined. Subsequent whole-section immunohistochemical assessment further supported the phenomenon of localised indiscriminate infection, with these areas found adjacent to minimally-infected zones. Thus, spatial screening of mRNA in tissues can simultaneously inform upon viral pathogenesis and host responses to infection.

ORGANISM(S): Mus musculus

PROVIDER: GSE341918 | GEO | 2026/09/15

REPOSITORIES: GEO