Adenosine-to-Inosine Editing of Vasoactive MicroRNAs Alters Their Targetome and Function in Ischemia

Abstract

Adenosine-to-inosine (A-to-I) editing in the seed sequence of microRNAs can shift the microRNAs’ targetomes and thus their function. Using public RNA-sequencing data, we identified 35 vasoactive microRNAs that are A-to-I edited. We quantified A-to-I editing of the primary (pri-)microRNAs in vascular fibroblasts and endothelial cells. Nine pri-microRNAs were indeed edited, and editing consistently increased under ischemia. We determined mature microRNA editing for the highest expressed microRNAs, i.e., miR-376a-3p, miR-376c-3p, miR-381-3p, and miR-411-5p. All four mature microRNAs were edited in their seed sequence. We show that both ADAR1 and ADAR2 (adenosine deaminase acting on RNA 1 and RNA 2) can edit pri-microRNAs in a microRNA-specific manner. MicroRNA editing also increased under ischemia in vivo in a murine hindlimb ischemia model and ex vivo in human veins. For each edited microRNA, we confirmed a shift in targetome. Expression of the edited microRNA targetomes, not the wild-type targetomes, was downregulated under ischemia in vivo . Furthermore, microRNA editing enhanced angiogenesis in vitro and ex vivo . In conclusion, we show that microRNA A-to-I editing is a widespread phenomenon, induced by ischemia. Each editing event results in a novel microRNA with a unique targetome, leading to increased angiogenesis.

Mechanistic Actions of microRNAs in Diabetic Wound Healing

“…Moreover, miRNAs may also undergo adenosine-to-inosine editing by the ADAR1 or ADAR2 enzymes, and since inosine base pairs with cytidine rather than uridine RNA editing can change the target specificity of the miRNA. A large number of miRNAs have been shown to be edited in response to ischemia [ 240 ], but to what extent this occurs in diabetic wound healing has not been investigated.…”

Epitranscriptomics of Ischemic Heart Disease—The IHD-EPITRAN Study Design and Objectives

“…Although the study of RNA modifications, epitranscriptomics remains in its infancy, methodological breakthroughs of the last decade have enabled identification of these modifications with such accuracy that their large-scale screening is rational [ 117 , 118 , 119 , 120 , 121 , 143 ]. Encouragingly, research findings suggest both m 6 A and A-to-I to act as contributors or even potential initiators and drivers for several cardiovascular physiological and pathological processes including cardiogenesis, angiogenesis, hypertension, hypertrophy, atherosclerosis, ischemia, ischemia-reperfusion, fibrosis, HF, congenital heart disease, stroke, aneurysms, as well as cardiac repair and regeneration [ 25 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 51 , 52 , 53 , 54 , 55 , 56 ]. Remarkably, the first indication for coronary atherosclerosis to be reflected in the m 6 A content of mRNAs and long non-coding RNAs of peripheral mononuclear cells with suggested involvement in its pathophysiology has just recently been reported [ 151 ].…”

“…Indeed, ischemic myocardium is known to abundantly secrete EVs encasing cardiac-specific miRNAs with promising biomarker properties [ 76 , 77 ], and such EVs may also hold modified RNAs. This is suggested since m 6 A [ 27 ] and A-to-I [ 22 , 51 , 52 ] have been shown to exist in miRNAs and regulate their biogenesis and targets. Besides, a recent report provides a proof-of-concept for epitranscriptomic signal discovery from EVs, as the m 6 A deposition onto miR-19 during its biogenesis enhances its loading into EVs [ 82 ].…”

“…Like m 6 A, A-to-I editing contributes to RNA stability and innate immunity, but also regulates RNA splicing as well as miRNA biogenesis and function [ 22 , 49 , 50 ]. Changes in the RNA A-to-I modification landscape have been associated with pathologies including cancer, neurological impairment [ 49 ], and cardiovascular disease [ 25 , 51 , 52 , 53 , 54 , 55 , 56 ].…”

Regulatory Mechanisms of the RNA Modification m6A and Significance in Brain Function in Health and Disease

“…This recoding can result in non-synonymous amino acid substitutions, resulting in altered protein-coding sequences and potentially altered protein structure ( Eisenberg and Levanon, 2018 ). Additionally, recoding of the RNA sequence within the 3′-UTR may alter mRNA-translational efficiency as it may affect microRNA-mediated targeting ( Brummer et al, 2017 ; van der Kwast et al, 2020 ). Other modifications are more subtle than overt structural modification of bases, involving covalent modification of RNA such as the addition of methyl groups to specific nucleotides.…”