Adenosine-to-inosine Alu RNA editing controls the stability of the pro-inflammatory long noncoding RNA NEAT1 in atherosclerotic cardiovascular disease

Abstract

Long non-coding RNAs (lncRNAs) have emerged as critical regulators in human disease including atherosclerosis. However, the mechanisms involved in the post-transcriptional regulation of the expression of disease-associated lncRNAs are not fully understood. Gene expression studies revealed that Nuclear Paraspeckle Assembly Transcript 1 (NEAT1) lncRNA expression was increased by >2-fold in peripheral blood mononuclear cells (PBMCs) derived from patients with coronary artery disease (CAD) or in carotid artery atherosclerotic plaques. We observed a linear association between NEAT1 lncRNA expression and prevalence of CAD which was independent of age, sex, cardiovascular traditional risk factors and renal function. NEAT1 expression was induced by TNF-α, while silencing of NEAT1 profoundly attenuated the TNF-α-induced vascular endothelial cell pro-inflammatory response as defined by the expression of CXCL8, CCL2, VCAM1 and ICAM1. Overexpression of the RNA editing enzyme adenosine deaminase acting on RNA-1 (ADAR1), but not of its editing-deficient mutant, upregulated NEAT1 levels. Conversely, silencing of ADAR1 suppressed the basal levels and the TNF-α-induced increase of NEAT1. NEAT1 lncRNA expression was strongly associated with ADAR1 in CAD and peripheral arterial vascular disease. RNA editing mapping studies revealed the presence of several inosines in close proximity to AU-rich elements within the AluSx3 + /AluJodouble-stranded RNA complex. Silencing of the stabilizing RNA-binding protein AUF1 reduced NEAT1 levels while silencing of ADAR1 profoundly affected the binding capacity of AUF1 to NEAT1. Together, our findings propose a mechanism by which ADAR1-catalyzed A-to-I RNA editing controls NEAT1 lncRNA stability in ASCVD.

A high-throughput approach to predict A-to-I effects on RNA structure indicates a change of double-stranded content in non-coding RNAs

“…nucleotides 7400-7600; Figure 5 ) is predicted to associate with TIA1 in a A-to-I dependent manner and, specifically, to interact tightly when the number of inosines increases ( Figure 7 ). As the A-to-I editing is observed in adenosines that are in close proximity to the AU-rich of NEAT and TIA1 is a AU-rich binding protein (74), it is tempting to speculate that TIA1 propensity to phase separation might influence NEAT1 ability to form paraspeckles depending on ADAR editing.…”

“…It has been recently demonstrated that ADAR1 controls NEAT1 stability by editing Alu sequences located in proximity of the AUF1 binding region. The modification decreases the ability of AUF1 to interact with its target (74).…”

Adenosine-to-inosine RNA editing contributes to type I interferon responses in systemic sclerosis

“…A-to-I RNA editing of individual adenosines was examined, as we have previously described [ 21 , 23 , 30 ], in AluJo - and AluSx + elements of CTSS 3 ′ untranslated region (UTR). Primer sequences are available in Supplementary Table 2 .…”

“…Using the UCSC browser for the human genome 38, we identified the 3 ′ UTR of CTSS including the 3 Alu elements ( AluSz6 - , AluJo - , AluSx + ) . Subsequently, we used the RNAfold webtool from the Vienna RNA Websuite [ 40 ] to predict the RNA folding structure, as we have previously described [ 30 ]. Folding analysis was performed using the default parameters and the algorithm ‘minimum free energy (MFE) and partition function’.…”

Roles of Major RNA Adenosine Modifications in Head and Neck Squamous Cell Carcinoma

“…ADAR1p150 expression is driven by an interferon inducible promoter and is upregulated in situations of cellular stress or viral infection ( Patterson and Samuel, 1995 ). ADAR1 plays an important role in A-to-I RNA editing and influences cancer development ( Qin et al, 2014 ; Heraud-Farlow et al, 2019 ; Vlachogiannis et al, 2021 ). ADAR2 is present in the nucleus of cells and ADAR2 along with ADAR1 may both influence the function of neurons ( Behm et al, 2017 ; Hosaka et al, 2019 ).…”