Fig. 2

Clustering and gene expression analysis of epipharyngeal cells in control and long COVID samples. (a) The left panel shows H&E staining of the epipharyngeal tissue, whereas the right panel displays a clustering map generated via Visium HD on the same region. The upper panels present a low-magnification view, with the dotted box indicating the area that is further magnified in the lower panels. This highlights the high resolution of Visium HD, which enables gene expression analysis at a near single-cell scale. The Visium HD platform achieves a resolution of 8 µm per bin, allowing detailed mapping of gene expression patterns within the complex structure of the epipharyngeal tissue. The black arrow indicates the epithelial region, the white arrowhead indicates the basement membrane, the white double-headed arrow indicates the submucosal region rich in immune cells, and the black arrowhead indicates a blood vessel. This capability facilitates the distinction between epithelial and subepithelial regions and enables comparative analysis of various immune cell populations present in the epipharynx. The cells from the epipharyngeal sample were classified into 16 clusters and mapped onto the tissue. (b) Cells from epipharyngeal samples, including control (n = 2), long COVID pre-EAT (n = 3), and long COVID post-EAT (n = 2) samples, were classified into 16 clusters and mapped onto the tissue. (c) The 16 clusters are visualized via a UMAP plot with dimension reduction. Each cluster was classified into epithelial clusters and nonepithelial clusters on the basis of their distribution within the tissue. (d) Heatmap showing the top 5 DEGs for each of the 16 clusters in the epipharynx.