Harnessing ADAR-Mediated Site-Specific RNA Editing in Immune-Related Disease: Prediction and Therapeutic Implications

Abstract

ADAR (Adenosine Deaminases Acting on RNA) proteins are a group of enzymes that play a vital role in RNA editing by converting adenosine to inosine in RNAs. This process is a frequent post-transcriptional event observed in metazoan transcripts. Recent studies indicate widespread dysregulation of ADAR-mediated RNA editing across many immune-related diseases, such as human cancer. We comprehensively review ADARs' function as pattern recognizers and their capability to contribute to mediating immune-related pathways. We also highlight the potential role of site-specific RNA editing in maintaining homeostasis and its relationship to various diseases, such as human cancers. More importantly, we summarize the latest cutting-edge computational approaches and data resources for predicting and analyzing RNA editing sites. Lastly, we cover the recent advancement in site-directed ADAR editing tool development. This review presents an up-to-date overview of ADAR-mediated RNA editing, how site-specific RNA editing could potentially impact disease pathology, and how they could be harnessed for therapeutic applications.

Keywords: ADAR; RNA editing; computational resources; immune-related disease.

Figure 1

Schematic representation of the structure and functions of ADAR1. ADAR1 isoforms, p110 and p150, possess a right-handed A-RNA bindable double-strand RNA binding domain (dsRBD) and a catalysis domain (deaminase). p150 also contains an additional left-hand Z-RNA binding domain (Z-alpha). ADAR1 performs catalysis-independent competitive binding or catalysis-dependent A-I RNA editing through its distinct binding and catalysis domains. ADAR1 has multiple pathways of operation, (A) including binding with endogenous Z-RNA to inhibit RIPK3-induced necroptosis and to block the activation of ZBP1. (B) Additionally, ADAR1 prevents immunogenetic dsRNA from inducing MDA5-mediated Type-I interferon disorder by either binding or editing to impede the recognition of dsRNA. (C) Moreover, ADAR1-mediated RES inhibits the PKR pathway, thus facilitating translation shutdown. (D) Finally, ADAR1 catalyzes the R-loop to promote its degradation and stabilize the telomere.

Figure 2

Multiple contributions can result from A-I RNA editing sites (RESs). (A) RESs located on exons may cause amino acid recoding. (B) RESs located on splicing motifs may change splicing events, and (C) RESs on pre-miRNA may affect the formation of miRNA and consequently impact downstream mRNA regulation induced by miRNA.

Figure 3

Molecular mechanisms of aberrant ADAR-mediated RNA editing lead to the pathogenesis of multiple diseases. Cases of ADAR editing sites contribute to immune-related diseases in various ways. A-I editing sites are shown in red. Arrows in red represent decrease and green arrows represent increase. (A) An A-I editing site affects the splicing of Coiled-Coil Domain Containing 15 (CCDC15) related to tumorigenesis. (B) Multiple A-I editing sites on the 3′ untranslated region (3′UTR) of Mouse Double Minute 2 (MDM2) prevent microRNA binding to promote malignant transformation. (C) A-I editing on the microRNA increases its affinity to the 3′UTR of Parvin Alpha (PARVA) to suppress tumors. (D) ADAR editing creates neoantigen in cyclin I, resulting in an induced immune response. (E) Decreased editing on the immunogenic dsRNA in autoimmune diseases leads to an MDA5-mediated immune response. (F) The RNA editing on the transcript 3′UTR of the catherpsin S protein recruits the HuR protein to make the transcript more stable and encode more catherpsin S, thus increasing the risk of atherosclerosis.

Figure 4

Workflow of ADAR editing site prediction and potential therapeutic application. (A) Data sources can be obtained from publicly available RNA-seq databases or from sequencing in-house samples from human and animal models. (B) Predicting RNA editing sites from RNA-seq data involves multiple steps to increase accuracy. Several databases collect RNA editing sites that can be used for prediction reference and RES annotation. The function of these predicted editing sites can be analyzed using downstream methods, such as differential modification, regulatory impact on gene expression, gain/loss of miRNA binding, or peptide recoding. Some of these analyses can be performed via interactive web servers. (C) ADAR-based in vivo site-direct RNA editing could be classified into two types. Methods based on exogenous ADAR, such as RESCUE, as an example, using modified ADARdd (the adenine deaminase domain of ADAR2 was evolved) fused with catalytically inactivate RNA-targeting CRISPR-Cas13 (dCas13) delivered by designed vehicles to edit target RNA sites. RESCUE has been used to dephosphorylate β-catenin through a C-U conversion, thus leading to T41I substitution and resulting in β-catenin accumulation and increased Wnt/β-catenin signal and cell growth. Endogenous ADAR, such as CLUSTER, was tested on mutated IDUA, which recovers a premature stop codon through A-I editing. A-I RNA editing or C-U RNA editing are shown in red.