Antao, N. V. | bioRxiv Science

bioRxiv2026

Single-cell transcriptomics of Encephalitozoon intestinalis infection in Caco-2 and Vero cells

Microsporidia are single-celled, obligate intracellular parasites closely related to fungi. One of the most common human-infecting microsporidian species, Encephalitozoon intestinalis, is an enteric parasite that invades and replicates within the epithelial lining of the small intestine. Two epithelial cell lines, Caco-2 and Vero cells, are routinely used as in vitro models of E. intestinalis infection. Here, we use scRNA-seq to investigate the host response to E. intestinalis infection and the transcriptional dynamics of parasite development in both Caco-2 and Vero cell lines. We observe that most host cells have no direct transcriptional response to parasite invasion or intracellular replication, suggesting that cells fail to detect and/or fail to respond to direct E. intestinalis infection, consistent with previous single-cell transcriptomics of E. intestinalis-infected macrophages. Our data suggest that a small subset of host cells detect intracellular parasites late in the life cycle, and signal to neighboring cells, leading to broad activation of a TNF-[a] response. Analysis of parasite transcripts reveals a developmental program that correlates with the morphological stages of the parasite life cycle. Together our data provide insights into a shared host transcriptional response to E. intestinalis infection and the datasets presented are a valuable resource for future studies.

microbiology↗

bioRxiv2023

3D reconstructions of parasite development and the intracellular niche of the microsporidian pathogen E. intestinalis

Microsporidia are an early-diverging group of fungal pathogens that infect a wide range of hosts. Several microsporidian species infect humans, and infections can lead to fatal disease in immunocompromised individuals. As obligate intracellular parasites with highly reduced genomes, microsporidia are dependent on metabolites from their hosts for successful replication and development. Our knowledge of how microsporidian parasites develop inside the host remains rudimentary, and our understanding of the intracellular niche occupied by microsporidia has thus far relied largely on 2D TEM images and light microscopy. Here, we use serial block face scanning electron microscopy (SBF-SEM) to capture 3D snapshots of the human-infecting microsporidian, Encephalitozoon intestinalis, within host cells. We track the development of E. intestinalis through its life cycle, which allows us to propose a model for how its infection organelle, the polar tube, is assembled de novo in each developing spore. 3D reconstructions of parasite-infected cells provide insights into the physical interactions between host cell organelles and parasitophorous vacuoles, which contain the developing parasites. The host cell mitochondrial network is substantially remodeled during E. intestinalis infection, leading to mitochondrial fragmentation. SBF-SEM analysis shows changes in mitochondrial morphology in infected cells, and live-cell imaging provides insights into mitochondrial dynamics during infection. Together, our data provide insights into parasite development, polar tube assembly, and microsporidia-induced mitochondrial remodeling in the host cell.

microbiology↗