Individual co-variation between viral RNA load and gene expression reveals novel host factors during early dengue virus infection of the Aedes aegypti midgut

• Published in: PLoS neglected tropical diseases Vol. 11; no. 12; p. e0006152
• Main Authors: Raquin, Vincent, Merkling, Sarah Hélène, Gausson, Valérie, Moltini-Conclois, Isabelle, Frangeul, Lionel, Varet, Hugo, Dillies, Marie-Agnès, Saleh, Maria-Carla, Lambrechts, Louis
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 19.12.2017; Public Library of Science (PLoS)
• Subjects: Aedes; Aedes - virology; Aedes aegypti; Animals; Antiviral agents; Aquatic insects; Biochemistry, Molecular Biology; Biology and Life Sciences; Colonies; Complementarity; Correlation; Correlation analysis; Culicidae; Data analysis; Data processing; Dengue; Dengue - virology; Dengue fever; Dengue Virus; Dengue Virus - genetics; Digestive System; Digestive System - virology; Drosophila; Fatty acids; Female; Funding; Gene expression; Gene Expression Profiling; Gene Expression Regulation; Genes; Genetic aspects; Genomes; Genomics; Host-Pathogen Interactions; Human diseases; Humans; Identification; Immunology; Inbreeding; Infections; Infectivity; Insect Proteins; Insect Proteins - genetics; Insect Vectors; Insect Vectors - virology; Insects; Life Sciences; Lipids; Medicine and Health Sciences; Methods; Microbiology and Parasitology; Midgut; Mosquitoes; Nucleic acids; Proteins; Replication; Research and analysis methods; Ribonucleic acid; Risk factors; RNA; RNA Interference; RNA, Viral; RNA, Viral - analysis; RNA-mediated interference; Screens; Sterol Regulatory Element Binding Proteins; Sterol Regulatory Element Binding Proteins - genetics; Sterol regulatory element-binding protein; Sterols; Survival analysis; Transcriptome; Tropical diseases; Variation; Vector-borne diseases; Viral diseases; Viral infections; Viral Load; Virology; Virus Replication; Viruses
• ISSN: 1935-2735; 1935-2727; 1935-2735
• DOI: 10.1371/journal.pntd.0006152

Dengue virus (DENV) causes more human infections than any other mosquito-borne virus. The current lack of antiviral strategies has prompted genome-wide screens for host genes that are required for DENV infectivity. Earlier transcriptomic studies that identified DENV host factors in the primary vector Aedes aegypti used inbred laboratory colonies and/or pools of mosquitoes that erase individual variation. Here, we performed transcriptome sequencing on individual midguts in a field-derived Ae. aegypti population to identify new candidate host factors modulating DENV replication. We analyzed the transcriptomic data using an approach that accounts for individual co-variation between viral RNA load and gene expression. This approach generates a prediction about the agonist or antagonist effect of candidate genes on DENV replication based on the sign of the correlation between gene expression and viral RNA load. Using this method, we identified 39 candidate genes that went undetected by conventional pairwise comparison of gene expression levels between DENV-infected midguts and uninfected controls. Only four candidate genes were detected by both methods, emphasizing their complementarity. We demonstrated the value of our approach by functional validation of a candidate agonist gene encoding a sterol regulatory element-binding protein (SREBP), which was identified by correlation analysis but not by pairwise comparison. We confirmed that SREBP promotes DENV infection in the midgut by RNAi-mediated gene knockdown in vivo. We suggest that our approach for transcriptomic analysis can empower genome-wide screens for potential agonist or antagonist factors by leveraging inter-individual variation in gene expression. More generally, this method is applicable to a wide range of phenotypic traits displaying inter-individual variation.