Targeting the Oncogenic Long Non-coding RNA SLNCR1 by Blocking Its Sequence-Specific Binding to the Androgen Receptor

Karyn Schmidt,Chase A Weidmann,Thomas A Hilimire,Elaine Yee,Breanne M Hatfield,John S Schneekloth,Kevin M Weeks,Carl D Novina

doi:10.1016/j.celrep.2019.12.011

Abstract

Long non-coding RNAs (lncRNAs) are critical regulators of numerous physiological processes and diseases, especially cancers. However, development of lncRNA-based therapies is limited because the mechanisms of many lncRNAs are obscure, and interactions with functional partners, including proteins, remain uncharacterized. The lncRNA SLNCR1 binds to and regulates the androgen receptor (AR) to mediate melanoma invasion and proliferation in an androgen-independent manner. Here, we use biochemical analyses coupled with selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) RNA structure probing to show that the N-terminal domain of AR binds a pyrimidine-rich motif in an unstructured region of SLNCR1. This motif is predictive of AR binding, as we identify an AR-binding motif in lncRNA HOXA11-AS-203. Oligonucleotides that bind either the AR N-terminal domain or the AR RNA motif block the SLNCR1-AR interaction and reduce SLNCR1-mediated melanoma invasion. Delivery of oligos that block SLNCR1-AR interaction thus represent a plausible therapeutic strategy.

Highlights

Long non-coding RNAs are capped, usually polyadenylated, and often spliced transcripts of >200 nt
Based on our definition of this binding site, we identify a novel androgen receptor (AR)-binding motif in HOXA11-AS-203 and confirm that this Long non-coding RNAs (lncRNAs) interacts with AR in cells, suggesting that this lncRNA may function in a complex with AR
AR NTD Binds to Unstructured RNA in a SequenceSpecific Manner Previous RNA immunoprecipitation (RIP) assays identified an approximately 100-nt region of SLNCR1 required for interaction with AR in cells (Schmidt et al, 2016)

Summary

Introduction

Long non-coding RNAs (lncRNAs) are capped, usually polyadenylated, and often spliced transcripts of >200 nt. Many lncRNAs play critical roles in tissue physiology, disease processes, immune regulation, and cancer. Despite their established importance, the fundamental mechanism of action of lncRNAs is poorly studied; only a few of the predicted 20,000–90,000 human lncRNAs (GENCODE version 7 [v.7] and NONCODE v.5, respectively) are well characterized (Fang et al, 2018; Harrow et al, 2012). It is believed that many lncRNAs function through direct interactions with protein partners, acting to scaffold the formation of ribonucleoprotein (RNP) complexes required for regulation of critical cellular processes (Ribeiro et al, 2018). There is a critical need for studies of the fundamental biology of lncRNAs and identification of functional lncRNA motifs. Functional characterization of lncRNA motifs and their interactions can begin to reveal the sequence and/or structural ‘‘rules’’ that govern lncRNA biology, advancing our ability to identify and characterize the function of other lncRNAs

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Discussion

Conclusion