Single-cell transcriptomic characterization of AmE-711, a continuous honey bee (Apis mellifera) derived cell line

Background: AmE-711 was derived from honey bee embryonic tissues and established as a continuous cell line, the only one available to date. Morphologically, the cells display fibroblast-like qualities. AmE-711 is persistently infected with Deformed wing virus (DWV), a prevalent honey bee pathogen. We used single-cell RNA sequencing (scRNA-seq) to characterize its transcriptomic profile. Results: We present a modification to the maintenance protocol for AmE-711 and a transcriptomic analysis. First, by increasing the temperature at which adherent cells are incubated during trypsinization to detach them from their substrate, we evenly split parent flasks to produce daughter flasks consistently seeded at high densities that reached confluence more quickly than previously reported. Using scRNA-seq analysis, we functionally annotated 13 clusters using Drosophila melanogaster protein-coding orthologs. Cluster marker gene set enrichment analysis identified differentially expressed genes typically upregulated in nervous and muscle tissues. Markers were enriched for gene ontology terms including synaptic signaling, cell adhesion and localization, and sarcomere or cytoskeleton organization. Greater than 20% of cells expressed mitotic markers. All cells were infected with DWV, but clusters displayed heterogeneity in viral loads. We used published honey bee scRNA-seq data to determine whether AmE-711 transcriptomes clustered with those of uninfected cells isolated from pupae undergoing metamorphosis or an adult worker brain. Despite clustering with mature Kenyon cells or neurons and muscles undergoing remodeling by plasmatocytes, the transcriptomes of most AmE-711 cells were distinct. Cell-cell communication analysis predicts that the third largest cluster may function as a hub for signaling events coordinating developmental, growth, or transcriptional programs that stabilize cellular identity. Finally, we explored whether host gene expression levels were predictable in a DWV dose-sensitive manner. Our linear regression model identified that antiviral RNAi host defense and ribosomal gene expression is downregulated while cell adhesion and locomotion gene expression is upregulated when cellular DWV abundances increase. Conclusions: As in previous studies, our results demonstrate the utility of scRNA-seq to characterize the heterogeneity of cell lines and indicate that AmE-711 is composed of DWV-infected cells of intermediate identities. We identified host cell gene programs that may help stabilize DWV infection, which could guide future approaches for treatment development.