A comparative analysis of the antiviral response in two bat species reveals conserved and divergent innate immune pathways

Abstract

Bats host a range of viruses that cause severe disease in humans without displaying clinical symptoms to these infections. The mechanisms of bat adaptation to these viruses are a continuous source of interest but remain largely unknown. To understand the landscape of bat antiviral response in a comprehensive and comparative manner, we studied this response in two bat species - the Egyptian fruit bat and the insectivore Kuhl's pipistrelle, representing the two major bat subordinal clades. We profiled the transcriptional response to dsRNA - that triggers a rapid innate immune response - in skin fibroblasts from a large cohort of replicates from each bat species, using RNAsequencing, and compared bat response with responses in primates and rodents. Both bat species upregulate a similar set of genes, many of which are known to be involved in the antiviral response across mammals. However, a subset of these genes is transcriptionally divergent in response between the two bat species. These transcriptionally divergent genes also evolve rapidly in coding sequence across the bat clade and have particular regulatory and functional characteristics, including specific promoter architectures and association with expression programs thought to underlie tolerance and resistance in response to viral infection. In addition, using single-cell transcriptomics, we show that transcriptionally divergent genes display high expression variability between individual cells. A focused analysis of dsRNA-sensing pathways further points to significant differences between bat and human in basal expression of genes important for triggering antiviral responses. Finally, a survey of genes recently lost or duplicated in bats points to a limited set of antiviral genes that have undergone rapid gene loss or gain in bats, with the latter group resulting in paralogs displaying divergence in both coding sequence and expression in bat tissues. Our study reveals a largely conserved regulatory program of genes upregulated in response to viral infection across bats and other mammals, and points to a set of genes that evolved rapidly in bats through multiple evolutionary mechanisms. This divergence can contribute to bat adaptation to viral infection and provides directions to understanding the mechanisms behind it.

Spatial and single-cell transcriptomics illuminate bat immunity and barrier tissue evolution

“…These recent IFN duplicates share the same regulation with more ancient IFN genes, being exclusively expressed in a subset of cells that also upregulates additional cytokines, such as TNF, and genes related to apoptosis, such as DUSP1 and FOS. In summary, our findings and previous work show that IFNB1 is the major IFN upregulated in response to dsRNA in a range of mammals (primates, rodents, ungulates 46 and also bats) and cells 20,46 . Other type-I IFNs, including recently duplicated copies, tend to be co-expressed in the same cells as IFNB1, but in lower levels, suggesting a strong regulatory conservation of upregulation of type-I IFN genes.…”

“…The score is then standardized to be between 0 and 1. We used three scores representing different stages and pathways known to be upregulated during the innate immune response against pathogens: (1) Inflammatory score: A set of inflammatory response-related and inflammatory cytokine and chemokine genes 47 ; (2) Primary antiviral response score: Primary antiviral response genes were taken from a set of genes upregulated following 4h of dsRNA-stimulation in dermal fibroblasts taken from previous studies 20,46 . The set we used here includes 175 genes that were upregulated in all studied species – R. aegyptiacus , mouse and human.…”

“…As such, R. aegyptiacus is considered an important model for studying the mechanisms of immune tolerance to viral infection, and was proposed as one of the key bat species for comprehensive immune characterization 16 . Consequently, R. aegyptiacus was the focus of several works studying different aspects of its immune system and viral infection 13,15,[17][18][19][20][21][22][23] . R. aegyptiacus, like other Old World fruit bats, possess unique adaptations to flight and to a highsugar and low-fat fruit-based diet.…”