Differential Effects on the Translation of Immune-Related Alternatively Polyadenylated mRNAs in Melanoma and T Cells by eIF4A Inhibition

SIMPLE SUMMARY: Immune checkpoints blockade has emerged as an effective approach to prevent immune escape of tumor cells, and constitutes a powerful anti-cancer therapeutic strategy. Regulation of the expression of genes encoding immune checkpoint inhibitors has thus become an increasingly important field of study. Beyond transcription, gene expression is regulated at several post-transcriptional levels including pre-mRNA 3′-end processing and mRNA translation. More specifically, the eIF4F translation initiation complex represents an important hub for oncogenic signaling in the etiology of different cancers. The eIF4A RNA helicase component of the eIF4F can be inhibited by the widely characterized small molecule inhibitor silvestrol. Here, we evaluated the effect of eIF4A inhibition with silvestrol on the translation of alternatively polyadenylated mRNAs in melanoma cell lines and activated T cells. We show that silvestrol can selectively inhibit the translation of alternatively polyadenylated isoforms of genes encoding key immune-related proteins. ABSTRACT: Targeting the translation initiation complex eIF4F, which binds the 5′ cap of mRNAs, is a promising anti-cancer approach. Silvestrol, a small molecule inhibitor of eIF4A, the RNA helicase component of eIF4F, inhibits the translation of the mRNA encoding the signal transducer and activator of transcription 1 (STAT1) transcription factor, which, in turn, reduces the transcription of the gene encoding one of the major immune checkpoint proteins, i.e., programmed death ligand-1 (PD-L1) in melanoma cells. A large proportion of human genes produce multiple mRNAs differing in their 3′-ends through the use of alternative polyadenylation (APA) sites, which, when located in alternative last exons, can generate protein isoforms, as in the STAT1 gene. Here, we provide evidence that the STAT1α, but not STAT1β protein isoform generated by APA, is required for silvestrol-dependent inhibition of PD-L1 expression in interferon-γ-treated melanoma cells. Using polysome profiling in activated T cells we find that, beyond STAT1, eIF4A inhibition downregulates the translation of some important immune-related mRNAs, such as the ones encoding TIM-3, LAG-3, IDO1, CD27 or CD137, but with little effect on the ones for BTLA and ADAR-1 and no effect on the ones encoding CTLA-4, PD-1 and CD40-L. We next apply RT-qPCR and 3′-seq (RNA-seq focused on mRNA 3′ ends) on polysomal RNAs to analyze in a high throughput manner the effect of eIF4A inhibition on the translation of APA isoforms. We identify about 150 genes, including TIM-3, LAG-3, AHNAK and SEMA4D, for which silvestrol differentially inhibits the translation of APA isoforms in T cells. It is therefore crucial to consider 3′-end mRNA heterogeneity in the understanding of the anti-tumor activities of eIF4A inhibitors.