Characterisation of LARP6 interactions with RNA in cancer

Abstract

Hyperactivation of ribosome biogenesis is a hallmark of tumorigenesis and therefore an attractive therapeutic target against a broad spectrum of cancers. The Mardakheh lab recently discovered the RNA-binding protein LARP6 as a key regulator of this process in aggressive mesenchymal-like cancers. Here, I employed an interdisciplinary strategy, combining omics approaches in cells and biophysical methodologies in vitro, to investigate the interaction between LARP6 and RNA, and functionally characterise the role of LARP6 in tumorigenesis. I developed a novel mass spectrometry method to unbiasedly identify RNA-binding regions in RNA-binding proteins and discovered two new RNA-binding regions in LARP6 outside of its canonical RNA-binding domain, the La-module. These new binding regions are localised in intrinsically disordered protein regions, evincing a previously unexplored mode of interaction between LARP6 and RNA. In cells, these disordered regions appear unable to interact with RNA independently, and instead fine-tune the RNA binding of the La-module. LARP6 interacts with the 5’TOP motif in ribosomal protein mRNAs, in cells and in vitro, and the La-module is key for this interaction. LARP6 also localises these transcripts to migratory protrusions of glioblastoma cells, but this localisation is independent of its RNA binding activity. In contrast, ribosomal protein synthesis is upregulated by LARP6, in a process that requires its La-module-dependent RNA binding activity. I propose a model where LARP6 regulates ribosome biogenesis by localising ribosomal protein mRNAs to protrusions, as part of a ribonucleoprotein complex, and by enhancing their translation via direct binding to RNA. Additionally, I discovered that LARP6 strongly interacts with the 3’UTR of cell adhesion mRNAs in cells and possibly negatively regulates their stability, while also modulating the invasion capabilities of glioblastoma cells. Taken together, these results suggest that therapeutically targeting LARP6 could reduce ribosome biogenesis and cell invasion, and therefore ameliorate key features of mesenchymal-like cancer phenotypes.