Bulk and single-nucleus RNA sequencing highlight immune pathways induced in individuals during an Ixodes scapularis tick bite

Abstract

Ticks are hematophagous arthropods that use a complex mixture of salivary proteins to evade host defenses while taking a blood meal. Little is known about the immunological and physiological consequences of tick feeding on humans. Here, we performed the first bulk and single-nucleus RNA sequencing (snRNA-seq) of skin and blood of four persons presenting with naturally acquired, attached Ixodes scapularis ticks. Pathways and individual genes associated with innate and adaptive immunity were identified based on bulk RNA sequencing, including interleukin-17 signaling and platelet activation pathways at the site of tick attachment or in peripheral blood. snRNA-seq further revealed that the Hippo signaling, cell adhesion, and axon guidance pathways were involved in the response to an I. scapularis bite in humans. Features of the host response in these individuals also overlapped with that of laboratory guinea pigs exposed to I. scapularis and which acquired resistance to ticks. These findings offer novel insights for the development of new biomarkers for I. scapularis exposure and anti-tick vaccines for human use.

Keywords: RNA-seq; acquired resistance; human; immune pathways; tick; tick-borne pathogens.

Fig 1

Sample collection and processing from four individuals. (A) Representative images of tick bite sites from the individuals. (B) Skin biopsies and blood sample processing for bulk and snRNA-seq. The figure was created using BioRender.

Fig 2

Characterization of immune pathways induced in the persons exposed to natural wild I. scapularis tick bites based on bulk RNA-seq. (A) Immune signaling pathways identified by KEGG pathway enrichment analysis. (B) GO enrichment analysis of transcriptome data from individuals’ skin biopsy and blood samples.

Fig 3

Characterization of immune pathways induced in the persons exposed to naturally acquired I. scapularis tick bites based on snRNA-seq. (A) Uniform manifold approximation and projection (UMAP) plot depicting single-nucleus transcriptomes from three tick-bitten human skins. Each dot represents a single cell. (B) Heatmap showing the population clusters with distinct expression patterns. Rows represent the scaled expression of the top five genes that were differentially expressed in each cluster, relative to all other cells. (C) Enriched KEGG pathways in the annotated cells. KEGG pathway analysis was performed with top 100 genes in the annotated cell of tick-bitten human skin.