Multi-omics analysis of arboviral capsid targets in arthropod cells reveals novel pro- and antiviral host factors

Abstract

Arboviral infections constitute a major global health concern due to the constant expansion of arthropod vector habitats driven by rising global urbanization and progressing climate change. Therefore, novel alternative control strategies are urgently needed. While cellular targets of arboviral proteins and their effector functions have been extensively studied in mammalian model systems, their interactions with arthropod host cells are poorly characterized or completely unknown. To close this critical gap, my doctoral thesis aimed to systematically profile arbovirus-arthropod vector interactions in both mosquito and tick cells using multi-omics approaches.

To characterize protein-protein interactions of the highly versatile arboviral capsids with the Aedes aegypti proteome, I generated a proteomics-based pan-arboviral capsid interactome atlas spanning 12 pathogenic arboviral species across three arboviral genera. This approach uncovered novel mosquito host targets with shared and distinct specificities. An RNAi-based phenotypic screen on 110 newly discovered interacting host factors with three prototypic arboviruses (dengue virus, West Nile virus and La Crosse virus) led to the identification of several novel host dependency factors, including the chromatin-remodeling Brahma complex. Functional and biochemical characterization of BAP and PBAP Brahma sub-complex components across a broad range of arboviruses revealed distinct requirements for a subgroup of orthoflaviviruses, and allowed the identification of cellular determinants mediating the interaction with the orthoflaviviral capsid. Using a combination of ATAC- and RNA-sequencing approaches, I further characterized the functional consequences of this interaction on the mosquito transcriptional and chromatin landscape, discovering the ability of orthoflaviviral capsids to selectively remodel chromatin accessibility. Collectively, these findings suggest a novel mechanism evolved by orthoflaviviruses to modulate host cell gene expression via interactions of capsid with the Brahma complex.

The second part of my PhD thesis focuses on the multi-omics characterization of virus-induced changes and virus-host interactions of severe fever with thrombocytopenia syndrome virus (SFTSV) with its tick vector Rhipicephalus microplus. This approach combined proteomics, transcriptomics and protein-protein-interaction analysis experiments to shed light on the completely uncharacterized SFTSV-arthropod host interactions. Here, a proteomics informed by transcriptomics approach combined with extended ortholog mapping was employed to substantially advance the Rhipicephalus microplus genome and proteome annotation. This allowed the characterization of SFTSV-induced cellular pathways and providing insights into tick antiviral responses to arboviral infections. Within this international collaborative study, I leveraged a proteomics-based approach to identify protein-protein interactions, contributing to the first SFTSV nucleocapsid interactome description in tick cells. Subsequent RNAi-based functional assays revealed two novel nucleocapsid-interacting tick host factors restricting viral replication: the nonsense-mediated mRNA decay pathway component UPF1 and the multifunctional RNA helicase DHX9.

Altogether, combining different multi-omics-based approaches led to the identification and characterization of novel arboviral host targets in mosquitoes and ticks as well as improved transcriptomic and proteomic resources for future vector-centric studies. Importantly, these results improved our understanding of arboviral capsids effector functions in arthropod vectors, and revealed a multitude of novel host factors and a new role of orthoflaviviral capsids in host cell transcriptional regulation.