Benoit Chabot

RNA processing plays a key role in gene expression, allowing for increased protein diversity and functional complexity. Consequently, modulating RNA processing can impact gene function. Given HIV-1’s reliance on host RNA processing machinery for viral protein production/replication, modulators of this process could serve as novel anti-virals to complement and/or enhance existing therapies. In this study, screening of several serine-arginine-rich (SR) kinase inhibitors for their impact on HIV-1 gene expression identified harmine as an inhibitor of HIV-1 gene expression in several cell lines and primary CD4 + T cells/macrophages at low micromolar concentrations with limited cell toxicity. Harmine induced a loss of viral structural protein expression associated with reduced HIV-1 unspliced and singly-spliced HIV-1 RNA levels but limited impact on multiply spliced RNAs. Although harmine is a known inhibitor of both DYRK1A and monoaminoxidase A (MAO A), neither DYRK1A depletion nor other MAO A inhibitors had any effect on HIV-1 expression. However, the compound altered the expression of several other SR kinases in primary CD4 + T cells, increasing CLK1 and reducing CLK2 kinase levels, effects known to regulate HIV-1 expression. Harmine was also unique among the SR kinase inhibitors tested for its ability to suppress replication of a seasonal coronavirus, human coronavirus (HCoV)-229E, and multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, reducing viral protein expression and virus release. Harmine acts post-entry, arresting virus replication even after the onset of viral protein production. At doses required to suppress HIV-1 replication, harmine had limited impact on the host transcriptome, alternative splicing, or alterative polyadenylation as assessed by RNA-Seq. Together, our study demonstrates the feasibility of targeting host RNA processing to inhibit a range of viruses with minimal impact on the host cell. IMPORTANCE This study highlights the crucial role RNA processing plays in regulating viral gene expression and replication. By targeting SR kinases, we identified harmine as a potent inhibitor of HIV-1 as well as coronavirus (HCoV-229E and multiple SARS-CoV-2 variants) replication. Harmine inhibits HIV-1 protein expression and reduces accumulation of HIV-1 RNAs in both cell lines and primary CD4 + T cells. Harmine also suppresses coronavirus replication post-viral entry by preferentially reducing coronavirus sub-genomic RNA accumulation. By focusing on host factors rather than viral targets, our study offers a novel approach to combating viral infections that is effective against a range of unrelated viruses. Moreover, at doses required to inhibit virus replication, harmine had limited toxicity and minimal effect on the host transcriptome. These findings support the viability of targeting host cellular processes as a means of developing broad-spectrum anti-virals.

Genotoxic agents, that are used in cancer therapy, elicit the reprogramming of the transcriptome of cancer cells. These changes reflect the cellular response to stress and underlie some of the mechanisms leading to drug resistance. Here, we profiled genome-wide changes in pre-mRNA splicing induced by cisplatin in breast cancer cells. Among the set of cisplatin-induced alternative splicing events we focused on COASY, a gene encoding a mitochondrial enzyme involved in coenzyme A biosynthesis. Treatment with cisplatin induces the production of a short isoform of COASY lacking exons 4 and 5, whose depletion impedes mitochondrial function and decreases sensitivity to cisplatin. We identified RBM39 as a major effector of the cisplatin-induced effect on COASY splicing. RBM39 also controls a genome-wide set of alternative splicing events partially overlapping with the cisplatin-mediated ones. Unexpectedly, inactivation of RBM39 in response to cisplatin involves its interaction with the AP-1 family transcription factor c-Jun that prevents RBM39 binding to pre-mRNA. Our findings therefore uncover a novel cisplatin-induced interaction between a splicing regulator and a transcription factor that has a global impact on alternative splicing and contributes to drug resistance.