Sarah Arcos

The battle between viral RNA and host factors begins the instant the viral genome enters a cell. Prior to transcriptional upregulation of interferons, cytokines, and antiviral genes, a cell must rely on mRNAs and proteins that already exist in its cytoplasmic arsenal. In contrast, the virus benefits from any mechanism it can utilize to co-opt host processes before the onslaught of new defenses from transcription alters the internal cellular environment. As the molecular events that comprise these primary interactions between host protein and viral RNA are not well understood, we developed a novel method, VIR-CLASP for Viral Cross-Linking And Solid-phase Purification, to identify proteins that directly bind to pre-replicated, primary, viral RNA genomes. Our approach is applicable to essentially any RNA virus, and captures interactions that occur within minutes of viral entry. We used this approach to identify hundreds of host RBPs that interact with the primary Chikungunya virus (CHIKV) RNA genome, including the YTHDF family of N6-methyladenosine (m6A) binding proteins. We established that m6A modifications are abundant on CHIKV genomic RNA. Furthermore, m6A is involved in regulating many aspects of cellular RNA metabolism and can modulate the pathogenicity of several RNA viruses including Zika, HIV, and Influenza. However, the biological impact of interaction between m6A-binding proteins and primary viral genomes is not known. We discovered that the effect of m6A on CHIKV viral replication is subject to combinatorial regulation by YTHDFs: knockdown and over-expression studies revealed that YTHDF1 strongly restricts viral replication, while YTHDF2 and YTHDF3 have the opposite effect. Our data indicate that the YTHDF proteins have distinct regulatory effects on CHIKV replication and depending on their relative intrinsic cellular levels, can tip the balance of a successful infection. There are currently no direct therapeutic options available to those at risk for CHIKV infection and the debilitating, long-lasting joint pain that follows. VIR-CLASP aims to increase the known repertoire of drug targets for CHIKV, and other RNA viruses, in order to advance current efforts to design vaccines and anti-viral compounds. 

Cohort: 2015
Principal Investigator: Manuel Ascano, Ph.D.
Internship Company: AstraZeneca
Internship Year: 2018
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