Knowledge on the cell types and cell-specific gene expression of multicellular pathogens facilitates drug discovery and allows gaining a deeper understanding of pathogen biology. By utilizing single-cell RNA sequencing (scRNA-seq), we analyzed 19,581 cells of a globally prevalent parasitic flatworm, the liver fluke Fasciola hepatica, which causes a neglected tropical disease and zoonosis known as fascioliasis. We identified 15 distinct clusters, including cells of the reproductive tract and gastrodermis, and report the identification and transcriptional characterization of potential differentiation lineages of stem cells within this parasite. Furthermore, a previously unrecognized ELF5- and TRPMPZQ-expressing muscle cell type was discovered, characterized by high expression of protein kinases. Among these, the p21-activated kinase PAK4 was essential for parasite survival. These data provide novel insight into the cellular composition of a complex multicellular parasite and demonstrate how gene expression at single-cell resolution can serve as a resource for the identification of new drug targets.

Single-cell transcriptomics identifies a p21-activated kinase important for survival of the zoonotic parasiteFasciola hepatica