Functional significance of U2AF1 S34F mutations in lung adenocarcinomas

Mohammad S Esfahani,Eric Kildebeck,Maximilian Diehn,Aaron M Newman,Luke J Lee,Young-Jun Jeon,Matthew H Porteus,Angela B Hui,Noriko Ishisoko,Scott V Bratman,Ryan A Flynn,Henning Stehr,Ash A Alizadeh,Howard Y Chang

doi:10.1038/s41467-019-13392-y

Abstract

The functional role of U2AF1 mutations in lung adenocarcinomas (LUADs) remains incompletely understood. Here, we report a significant co-occurrence of U2AF1 S34F mutations with ROS1 translocations in LUADs. To characterize this interaction, we profiled effects of S34F on the transcriptome-wide distribution of RNA binding and alternative splicing in cells harboring the ROS1 translocation. Compared to its wild-type counterpart, U2AF1 S34F preferentially binds and modulates splicing of introns containing CAG trinucleotides at their 3′ splice junctions. The presence of S34F caused a shift in cross-linking at 3′ splice sites, which was significantly associated with alternative splicing of skipped exons. U2AF1 S34F induced expression of genes involved in the epithelial-mesenchymal transition (EMT) and increased tumor cell invasion. Finally, S34F increased splicing of the long over the short SLC34A2-ROS1 isoform, which was also associated with enhanced invasiveness. Taken together, our results suggest a mechanistic interaction between mutant U2AF1 and ROS1 in LUAD.

Highlights

The functional role of U2AF1 mutations in lung adenocarcinomas (LUADs) remains incompletely understood
To characterize the role of U2AF1 mutations, we collated sequencing data from a diverse set of 2112 LUADs, including cases from the original study identifying U2AF1 in LUAD20, The Cancer Genome Atlas[33], metastatic tumors profiled with MSKIMPACT42, tumors profiled as part of the TRACERx study[43], and cases profiled using Stanford’s Solid Tumor Actionable Mutation Panel (STAMP)[44]
We explored whether U2AF1 mutations were truncal events in LUADs analyzed by multi-region sequencing

Summary

Introduction

The functional role of U2AF1 mutations in lung adenocarcinomas (LUADs) remains incompletely understood. Mutant U2AF1 results in significant changes in hematopoiesis in mouse models, including expansion of hematopoietic stem cells and associated cytopenias, as well as alternative splicing of genes recurrently mutated in MDS/AML18. Unlike in MDS/AML, U2AF1 S34Y variants are exceedingly rare in lung cancers, as are mutations in other components of the spliceosome While this distinct pattern of somatic mutation and histological specificity in lung cancers suggests a functional interaction within these tumors, the role of S34F in LUADs remains incompletely understood. We show that overexpression of U2AF1 S34F leads to elevated expression of genes associated with the epithelialmesenchymal transition (EMT) Consistent with this observation, U2AF1 S34F induces cell invasiveness and that this appears to be in part mediated via preferential splicing of the SLC34A2-ROS1 long isoform, whose expression increases tumor cell invasion. Our results suggest a mechanistic interaction between mutant U2AF1 and ROS1 in LUADs that may be of clinical and therapeutic relevance

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Conclusion