The Role of Nucleases and Nucleic Acid Editing Enzymes in the Regulation of Self-Nucleic Acid Sensing

Abstract

Detection of microbial nucleic acids by the innate immune system is mediated by numerous intracellular nucleic acids sensors. Upon the detection of nucleic acids these sensors induce the production of inflammatory cytokines, and thus play a crucial role in the activation of anti-microbial immunity. In addition to microbial genetic material, nucleic acid sensors can also recognize self-nucleic acids exposed extracellularly during turn-over of cells, inefficient efferocytosis, or intracellularly upon mislocalization. Safeguard mechanisms have evolved to dispose of such self-nucleic acids to impede the development of autoinflammatory and autoimmune responses. These safeguard mechanisms involve nucleases that are either specific to DNA (DNases) or RNA (RNases) as well as nucleic acid editing enzymes, whose biochemical properties, expression profiles, functions and mechanisms of action will be detailed in this review. Fully elucidating the role of these enzymes in degrading and/or processing of self-nucleic acids to thwart their immunostimulatory potential is of utmost importance to develop novel therapeutic strategies for patients affected by inflammatory and autoimmune diseases.

Keywords: DNA sensing; DNases; RNA sensing; RNases; aicardi goutieres syndrome; interferonopathies; systemic lupus erythematosus; toll-like receptors.

Figure 1

In red are extracellular source of NAs that originate from dying cells in multiple forms including free, microparticle (MP)-associated, Neutrophil Extracellular Trap (NET)-associated, and protein-associated (Histones, HMGB1, and TFAM). Such NAs can be internalized into endolysosomes where they are recognized by Toll like receptors (TLR), which via MyD88 activate NF-kB and IRF7 transcription factors that upon their translocation to the nucleus induce the production of inflammatory cytokines and type I interferons (IFN-I). The detection of extracellular RNA by NA-sensing PRRs is poorly documented. In blue are represented intracellular sources of NAs. They originate from mitochondria and such mtDNA in the presence of ROS (reactive oxygen species) can be oxidized and acquire the ability to activate NLRP3 inflammasome, which triggers caspase 1-mediated cleavage of pro-IL-1β into active IL-1β. mtDNA can also activate cGAS which upon detection of DNA produces cGAMP that is specifically recognized by STING. STING stimulation triggers IRF3-mediated IFN-I production and NF-kB-mediated inflammatory cytokine production. Upon autophagy mtDNA can gain access to endolysosomal compartments and stimulate TLR9 as well. Furthermore mitochondrial double-stranded RNA (mtdsRNA) if not degraded by mitochondrial RNA-degradosome machinery can activate the RNA sensor MDA5 which via the adaptor molecule MAVS activates IRF3-mediated IFN-I production. Endogenous LTR-retrotransposons are also a source of intracellular NAs, they can lead to the production of dsRNA duplexes that activate IFN-I production after their sensing by MDA5. In purple are common pathways of intracellular and extracellular NA sensing. mtDNA and NET-associated DNA from the extracellular space are internalized in the cytosol and activate cGAS. The same pathway can be activated by ssDNA originating from the reverse transcription of endogenous LTR-retrotransposons and by nuclear DNA released into the cytosol during stress conditions in forms of micronuclei or “speckles”.

Figure 2

DNASE1L3 deficiency leads to the accumulation of numerous forms of DNA including chromatin, MP associated DNA and NET-associated DNA. Accumulation of such DNA contributes to the aberrant activation of TLR7,9 in B cells and plasmacytoid dendritic cells (pDCs). In B cells TLR7,9 activation leads to their differentiation into plasma cells and antibody forming cells (AFC) that produce autoreactive antibodies mostly directed against dsDNA. In pDCs TLR7,9 activation induces the production of type I interferons (IFN-I) which also play an important role in the transition of B cells into AFC. The production of anti-dsDNA antibodies and of IFN-I will ultimately cause the development of Systemic Lupus Erythematosus (SLE).

Figure 3

DNASE2A deficiency causes an accumulation of phagocytosed dsDNA as well as nuclear dsDNA transported by autophagy into endolysosomal compartments. Such dsDNA can gain access to the cytosol and activate the cGAS/STING pathway (orange) that leads to the production of type I interferons (IFN-I), which ultimately causes the development of fatal autoimmunity. In the absence of IFN-I signaling DNASE2A deficiency will induce the development of rheumatoid arthritis which is mediated by TNFα, whose production is triggered by the cGAS/STING pathway, but also by IL-1β and IL-18 which are inflammatory cytokines produced upon the activation of the AIM2 inflammasome by cytosolic self-DNA. Finally, DNASE2A deficiency also induces aberrant activation of endolysosomal TLR (red) which contribute via the activation of the MyD88 to the production of autoantibodies. PLD3/4 are novel endolysosomal nucleases (green) involved in the degradation of ssDNA. Their deficiency induces an accumulation of ssDNA in endolysosomes that ultimately activates TLR9-MyD88-NFκB mediated inflammatory cytokine (IL-6 and IL-12) production, causing fatal autoimmunity.

Figure 4

Intracellular nuclease and NA-editing enzyme deficiency aberrantly activates inflammatory and autoimmune responses. Mutations in TREX1 (yellow) that affect its exonuclease activity or cause its deficiency, lead to the cytosolic accumulation of ssDNA originating from the reverse transcription of endogenous LTR-retrotransposons that activate the cGAS/STING pathway causing the secretion of pathogenic type-I interferons (IFN-I) and the development of familial chilblain lupus (FLC) and Aicardi Goutières Syndrome (AGS). Furthermore, dsDNA and micronuclei may be detected in the cytosol of individuals with dysfunctional TREX1 and contribute the aberrant activation of the cGAS/STING pathway as well. Mutation in SAMHD1 (red) causes the release of ssDNA from stalled replication forks that stimulates IFN-I production upon the activation of the cGAS/STING pathway that may ultimately contribute to AGS and FCL. AGS is also associated with mutations in RNase H2 complex (green) that reduces ribonucleotide excision repair (RER) and thus increases DNA damage and possibly the release of DNA:RNA hybrids, micronuclei and ribonucleotide containing gDNA into the cytosol that may activate cGAS/STING-mediated production of deleterious IFN-I. Finally, dysfunction in ADAR1 (purple) leads to the accumulation of dsRNA duplexes originating from endogenous retrotransposon RNA in the cytosol which upon activation of the MDA5 pathway causes the secretion of pathogenic IFN-I responsible for AGS development.