Megha Basavappa

“The novel lncRNA ALPHA specifically targets chikungunya virus to control infection”

Megha G. Basavappa, Max Ferretti, Mark Dittmar, Megan Sullivan, Kanupriya Whig, Hui Shen, Julian Stoute, Fange Liu, David Schultz, Daniel Beiting, Kristen Lynch, Jorge Henao-Mejia, Sara Cherry.

Chikungunya virus (CHIKV) is a recently emerged, mosquito-borne alphavirus which causes a severe, symptomatic disease characterized by chronic arthralgia. No vaccines or therapeutics currently exist to combat this virus. Canonical, type I interferon (IFN) signaling is an important line of defense against CHIKV. However, like many viruses, CHIKV has evolved mechanisms to effectively antagonize IFN responses. Despite this, acute infection is typically cleared; thus, alternative, complementary immune strategies must exist to compensate for virus-mediated immune abrogation. The nature of these non-canonical, anti-CHIKV pathways remains unclear. Long noncoding RNAs (lncRNAs) are a recently described class of regulatory RNAs capable of modulating many facets of nucleic acid biology including transcription and translation in a time- and context-specific manner. Recent work has implicated lncRNAs in the maintenance of immune cell homeostasis and the regulation of cytokine expression. However, the role of lncRNAs in antiviral immunity is only beginning to be appreciated. To directly identify antiviral lncRNAs, we performed an unbiased, high-throughput, RNAi screen targeting 2200 lncRNAs in human brain microvascular endothelial cells (HBMEC) infected with CHIKV. Using an automated microscopy platform, we identified 9 lncRNAs that upon depletion, resulted in increased CHIKV infection in the absence of cytotoxicity. Further phenotypic characterization of these antiviral candidates revealed that the human-specific, long intergenic noncoding RNA, ALPHA, is localized in the cytoplasm, is transcriptionally induced upon infection, and displays high antiviral specificity for a subset of alphaviruses. Furthermore, ALPHA does not regulate IFN transcription suggesting a mode of action outside of classical innate immunity. Mechanistically, we found that ALPHA binds to viral genomic RNA and affects viral RNA replication supporting a direct mechanism of antiviral inhibition. Together, our findings reveal that lncRNAs can mediate directed, non-canonical antiviral immune responses against specific viral pathogens.