MicroRNAs, Long Non-Coding RNAs, and Circular RNAs in the Redox Control of Cell Senescence

Abstract

Cell senescence is critical in diverse aspects of organism life. It is involved in tissue development and homeostasis, as well as in tumor suppression. Consequently, it is tightly integrated with basic physiological processes during life. On the other hand, senescence is gradually being considered as a major contributor of organismal aging and age-related diseases. Increased oxidative stress is one of the main risk factors for cellular damages, and thus a driver of senescence. In fact, there is an intimate link between cell senescence and response to different types of cellular stress. Oxidative stress occurs when the production of reactive oxygen species/reactive nitrogen species (ROS/RNS) is not adequately detoxified by the antioxidant defense systems. Non-coding RNAs are endogenous transcripts that govern gene regulatory networks, thus impacting both physiological and pathological events. Among these molecules, microRNAs, long non-coding RNAs, and more recently circular RNAs are considered crucial mediators of almost all cellular processes, including those implicated in oxidative stress responses. Here, we will describe recent data on the link between ROS/RNS-induced senescence and the current knowledge on the role of non-coding RNAs in the senescence program.

Keywords: aging; cell senescence; circular RNAs; long non-coding RNAs; microRNAs; non-coding RNAs; oxidative stress; redox homeostasis.

Figure 1

Intrinsic and extrinsic causes of cellular senescence. Schematic diagram showing the major inducers of cellular senescence. Damages to telomeres, redox imbalance, mitochondrial dysfunctions, activation of oncogenes, ionizing/ultraviolet radiations, epigenetic and chromatin alterations, chemotherapeutic drugs, and altered translation can promote the senescence program. Redox imbalance can be generated by decreased endogenous antioxidant defenses or increased ROS/RNS production. The main ROS/RNS are reported (the non-radical species are indicated in parenthesis). Most of these senescence inducers act by releasing ROS/RNS or by increasing ROS/RNS production. ROS/RNS can directly affect telomere integrity and cause altered translation process. * indicates senescence inducers that release or increase ROS/RNS.

Figure 2

ROS and RNS biological sources and major scavenging pathways. ROS comprise the superoxide anion (O₂^•−), the hydroxyl (HO^•), and hydroperoxyl (HOO^•) radicals and the non-radical hydrogen peroxide (H₂O₂). Prevalent RNS are the nitric oxide (NO^•), the radical nitrogen dioxide (NO₂^•), and the peroxynitrite anion (ONOO⁻). O₂^•− can originate inside the mitochondrial electron transport chain (ETC) or from enzymatic reactions catalyzed by NAD(P)H oxidases (NOXs), xanthine oxidase (XO) or uncoupling nitric oxide synthase (u-eNOS). H₂O₂ is produced by NOX4, dual oxidase 1 and 2 (DUOX1/2), cytochrome P450s (CYPs), various oxidases (XOs), cyclooxygenases (COXs), as well as transiently by superoxide dismutase (SOD1–3) isoforms. HO^• and HOO^• are directly generated through the Fenton reactions. NO^• is produced by the enzymes nitric oxide synthases (NOSs), while the peroxynitrite anion (ONOO⁻) originates from the radical nitrogen dioxide (NO₂^•) combined with O₂^•−.

Figure 3

Summary of major pathways initiating senescence through ROS/RNS deregulation. (A) Failure of the antioxidant transcription program arising from NRF2 defects can induce senescence. In fact, NRF2 promotes the induction of numerous cytoprotective genes harboring ARE/s cis-element/s in their promoters. NRF2 also engages protective mechanisms to ferroptosis, thus preventing iron accumulation. Under redox imbalance, numerous molecular effectors/factors can mediate senescence-associated growth arrest. This relies on the activation of the p53/p21^CIP1 and p16^INK4a/Rb pathways. Persistent DDR activates the p53/p21^CIP1 pathway, while epigenetic changes due to downregulation of BMI-1 and EZH2 proteins of the PCRs complex, induces p16^INK4a/Rb pathway and establishes the SASP profile. SASP induction is mainly regulated by the redox-sensitive NF-κB pathway, along with C/EBPβ, GATA4, and JNK transcription factors. Dysfunctional mitochondria can also promote SASP (not shown). Mitochondrial dysfunctions increase ROS/RNS levels that also contribute to telomere damage and epigenetic modifications, and thus sustain senescence. Reduced levels of NAD⁺, a mitochondrial metabolite, affects the activities of sirtuins (SIRT1–7), thus provoking senescence by the p53/p21 pathway. Alteration of the NAD⁺/sirtuin pathway also impacts negatively on FOXO and PGC-1α activities, with consequent ROS elevation and mitochondrial dysfunctions. FOXO transcription factors increase catalase and SOD2 expression. FOXO1/3 are primarily inhibited by AKT and activation of AKT gives rise to senescence through increased intracellular ROS levels. FOXO4 activated by JNK induces senescence by engaging the p21 pathway. Low NAD⁺ amounts sustained by dysfunction of PARP1 and NAMPT enzymes also induce senescence. (B) Overview of non-coding RNAs deregulated in senescence that can modulate ROS/RNS signaling pathways. Up and down arrows indicate ncRNA levels that have been found as increased or decreased, respectively in various models of oxidative stress-induced senescence.

Figure 4

Summary of major epigenetic landscape through ROS/RNS. (A) ROS attack cytosines methylated at C5 (5mC), which become 5-hydroxymethylcytosines (5hmCs). These latter can be further oxidized by TET enzymes prompting local DNA demethylation. Increased activity of DNMT3 reduces SOD2 expression that provokes ROS elevation, and consequently, senescence. On the contrary, ROS/RNS reduce the expression of DNMT1 with consequent demethylation of p16^INK4a promoter and increased expression of p16. ROS/RNS can directly generate DNA damages, which are engaged by the kinase ATM/ATR that phosphorylates the serine 139 of the histone H2AX variant. ROS/RNS can reshape histone modifications (such as acetylation and methylation) by altering enzymatic reactions of the histone acetylases/deacetylases, such as EP300 or CREBBP/SIRTs and/or histone methylases/demethylases, such as EZH2, BMI-1 of the PRC complexes. Mitochondrial ROS induce the release of cytoplasmic chromatin fragments involved in SASP stimulation. (B) Overview of non-coding RNAs deregulated in senescence that can impact epigenetic landscape through ROS/RNS signaling pathways. Up and down arrows indicate ncRNA levels that have been found as increased or decreased, respectively in various models of oxidative stress-induced senescence.