Structural characterization of the long noncoding RNA SChLAP1 reveals therapeutically tractable interfaces of RNA:protein recognition

Abstract

Long noncoding RNAs (lncRNAs) are non-proteinogenic RNAs greater than 200 nucleotides in length and can play roles in both housekeeping processes and disease conditions. Prostate cancer is one of the most commonly occurring forms of cancer, and it constitutes the second-leading cause of cancer-related death among American men despite the availability of treatment options. Thus, there is an urgent and unmet need to characterize the molecular drivers of aggressive prostate cancer ultimately to facilitate the development of next-generation prostate cancer therapies. The lncRNA Second Chromosome Locus Associated with Prostate 1 (SChLAP1) has been identified in multiple studies as prognostic of poor patient outcomes and a driver of aggressive prostate cancer in in vivo and cellular models. Despite its association with aggressive prostate cancer, its mechanism of action has remained elusive. We hypothesized that structure-function characterization of SChLAP1 would enable identification of functionally important regions worthy of follow up biological study and therapeutic targeting. Herein, we report our efforts toward this goal. Specifically, we performed SHAPE-MaP on SChLAP1, which allowed us to generate an experimentally informed structure model and identify protein binding regions. Subsequent native gel electrophoresis of a retroviral-derived element within SChLAP1 revealed a heterogenous structure significantly sensitive to metal concentration and RNA preparation. We also provide evidence that SChLAP1 binds chromatin as part of its biochemical mechanism. Lastly, we report our initial efforts to identify SChLAP1- targeted small molecules targeting likely functional substructures based on our data. This work provides a comprehensive analysis of SChLAP1 structure-function relationships, which we hope will inspire future efforts to therapeutically target SChLAP1 and favor better outcomes for prostate cancer patients.