Unravelling viral epitranscriptomics during SARS-CoV-2 infection

Abstract

The RNA modification N6-methyladenosine (m6A) plays an important role in processes related to gene regulation, such as embryonic development, metabolic diseases, and cancer. Recently, it has been shown that m6A modifications on the RNA transcripts of more than 15 viruses can influence viral replication. Although various aspects of SARS-CoV-2 have been thoroughly studied, little is known about the molecular mechanisms underlying the interaction between the host and viral RNAs. Two studies showed that m6A levels in COVID-19 patients are correlated with disease severity. Previous methods to identify m6A modifications are biased and laborious. Fortunately, direct RNA sequencing (DRS) can be used to recognise m6A modifications more precisely and more efficiently. We propose to study the role of m6A RNA modifications in the host-virus interaction during SARS-CoV-2 infection. First, the DRS method will be improved and validated for the measurement of m6A modifications in context of SARS-CoV-2. Second, we will identify m6A modifications with DRS on RNA transcripts in samples of a) human cell lines, b) human organoids, and c) patient-derived samples to find associations between m6A modifications and cell types, time after infection, the viral replication rate, and COVID-19 severity. Third, we will look closely at the influence of m6A modification levels on the SARS-CoV-2 replication rate, by administrating drugs that alter m6A levels. Additionally, antiviral drugs will be tested to determine whether they influence m6A levels. Taken together, this research will provide insights in the role of epitranscriptomics during viral infection and could provide targets for antiviral therapeutics.