Non-coding RNAs as drug targets

Abstract

Most of the human genome encodes RNAs that do not code for proteins. These non-coding RNAs (ncRNAs) may affect normal gene expression and disease progression, making them a new class of targets for drug discovery. Because their mechanisms of action are often novel, developing drugs to target ncRNAs will involve equally novel challenges. However, many potential problems may already have been solved during the development of technologies to target mRNA. Here, we discuss the growing field of ncRNA - including microRNA, intronic RNA, repetitive RNA and long non-coding RNA - and assess the potential and challenges in their therapeutic exploitation.

Figure 1. Regulating RNA levels or splicing with ASOs and duplex RNAs

a) Reduction of cellular RNAs by ASO gapmers. RNase H recognizes the DNA-RNA duplex and cleaves the target. b) Reduction of cellular RNAs by small silencing RNAs (siRNAs). One strand (guide strand) is loaded into argonaute 2 (AGO2) protein and an active RISC complex is formed. The complex binds to the complementary sequences on a target RNA and cleaves it. c) miRNA inhibitors complementary to specific endogenous miRNAs bind to specific miRNAs and inactivate them. d) Gene expression regulation by miRNA mimics. Double-stranded or chemically modified single-stranded miRNA mimics reduce target gene expression by destabilizing target RNAs and/or inhibiting translation. e) Regulation of alternative splicing by ASOs targeting regions close to intron-exon junctions. f) Modulation of transcription and epigenetic status by ASOs or dsRNAs targeting promoter-associated RNAs.

Figure 2. ASOs and duplex RNAs targeting repetitive RNAs

a) Antisense oligonucleotides used for therapy of myotonic dystrophy type 1 (DM1). DM1 is caused by gain-of-function toxicity from CUG-repeat containing DMPK transcripts. ASOs targeting the CUG repeats can be used to prevent binding of muscleblind like splicing regulator 1 (MBNL1) to the repeats. Gapmer ASOs targeting outside the repeat are also used for depleting toxic nuclear DMPK transcripts. b) Activating FXN expression using GAA repeat-targeting oligonucleotides. FXN encoding frataxin is a causative gene for FA and its expression is suppressed at least partly because of the R-loop formation between the expanded GAA repeats within the intron1 of FXN pre-mRNA and the genomic DNA in patients (upper). Double-stranded RNAs or single-stranded locked nucleic acid (LNA) ASOs targeting the GAA repeats can inhibit the R-loop formation in the repeat region and change histone modifications surrounding the repeats, leading to activation of FXN gene expression (lower). Image 2b was modified, with permission, from REF. 77.

Figure 3. Modulating gene expression by targeting cis-acting ncRNAs or promoter RNAs

a) Targeting UBE3a-ATS ncRNAs using ASOs. UBE3a encoding an E3 ubiquitin ligase is the imprinted gene. In the brain, paternal UBE3a is silenced by antisense transcripts UBE3a-ATS and maternal deficiency of UBE3a causes Angelman syndrome. Depletion of nuclear UBE3a-ATS using specific gapmers activates paternal UBE3a expression. b) COX-2 expression regulation mediated by promoter RNAs produced from the upstream of the COX-2 promoter. The transcript could function as a scaffold for interaction of complementary small RNAs in complex with AGO and TNRC6A. Binding of the protein-small RNA complex to the promoter RNAs could further trigger recruitment of some histone modifiers (e.g. WDR5) and transcription factors (e.g. NFκB, CREB1) to the COX-2 promoter, causing transcriptional upregulation of COX-2. These molecular recognitions also affect expression of the adjacent PLA2G4A gene. Image 3b was modified, with permission, from REF. 108.