Fig. 1: A spatial transcriptome of F. hepatica cross sections.

a Scheme describing the experimental workflow: Four transversal cryosections of two adult liver flukes were placed on a 10x Visium Spatial Gene Expression slide, stained and imaged. mRNA release, barcoding and sequencing were performed according to the 10x Visium protocol. During the analysis, all transcripts were mapped back to their corresponding spots on the slide and annotated using the reference transcriptome. Clustering was carried out to identify transcriptionally distinct tissues and tissue-specific markers. Selected markers were validated by in situ hybridization (ISH). The dataset was then used to explore spatial expression profiles of drug and vaccine candidates. One promising candidate was finally targeted with a small-molecule compound in vitro. b H&E-stained transversal tissue section and corresponding spatial projection of 412 mRNA-binding spots covered by this tissue section. Clusters are colored and labeled. Sectioning plane and orientation are indicated on the right. The image is representative of the four tissue sections used in the workflow. Please note: There is no Mehlis’ gland in this tissue section. See Supplementary Fig. 2 for H&E stainings and spatial projections of the remaining three tissue sections. g: gut, ov: ovary, par: parenchyma, teg: tegument, tes: testis, ut: uterus, vit: vitellarium. Scale = 100 µm. c Uniform Manifold Approximation and Projection (UMAP) of 2020 spots derived from four different F. hepatica cross sections. Clusters are colored and labeled according to (b). d, e Magnified view of an overlay of the H&E-stained tissue section and the spatial cluster projection shown in (b). mRNA capturing spots have a diameter of 55 µm and therefore span multiple cells and sometimes different tissues. As an example, see Supplementary Fig. 3 for expression patterns of known tegument and muscle markers. Clusters are colored and labeled according to (b). Scale = 100 µm.