Cytosolic Nuclease Research Articles

MRE11 and TREX1 control senescence by coordinating replication stress and interferon signaling

Oncogene-induced senescence (OIS) arrests cell proliferation in response to replication stress (RS) induced by oncogenes. OIS depends on the DNA damage response (DDR), but also on the cGAS-STING pathway, which detects cytosolic DNA and induces type I interferons (IFNs). Whether and how RS and IFN responses cooperate to promote OIS remains unknown. Here, we show that the induction of OIS by the H-RASV12 oncogene in immortalized human fibroblasts depends on the MRE11 nuclease. Indeed, treatment with the MRE11 inhibitor Mirin prevented RS, micronuclei formation and IFN response induced by RASV12. Overexpression of the cytosolic nuclease TREX1 also prevented OIS. Conversely, overexpression of a dominant negative mutant of TREX1 or treatment with IFN-β was sufficient to induce RS and DNA damage, independent of RASV12 induction. These data suggest that the IFN response acts as a positive feedback loop to amplify DDR in OIS through a process regulated by MRE11 and TREX1.

Functionalizing Dendrimers for Targeted Delivery of Bioactive Molecules to Macrophages: A Potential Treatment for Mycobacterium tuberculosis Infection-A Review.

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that replicates inside human alveolar macrophages. This disease causes significant morbidity and mortality throughout the world. According to the World Health Organization 1.4 million people died of this disease in 2021. This indicates that despite the progress of modern medicine, improvements in diagnostics, and the development of drug susceptibility tests, TB remains a global threat to public health. In this sense, host-directed therapy may provide a new approach to the cure of TB, and the expression of miRNAs has been correlated with a change in the concentration of various inflammatory mediators whose concentrations are responsible for the pathophysiology of M. tuberculosis infection. Thus, the administration of miRNAs may help to modulate the immune response of organisms. However, direct administration of miRNAs, without adequate encapsulation, exposes nucleic acids to the activity of cytosolic nucleases, limiting their application. Dendrimers are a family of highly branched molecules with a well-defined architecture and a branched conformation which gives rise to cavities that facilitate physical immobilization, and functional groups that allow chemical interaction with molecules of interest. Additionally, dendrimers can be easily functionalized to target different cells, macrophages among them. In this sense, various studies have proposed the use of different cell receptors as target molecules to aim dendrimers at macrophages and thus release drugs or nucleic acids in the cell of interest. Based on the considerations, the primary objective of this review is to comprehensively explore the potential of functionalized dendrimers as delivery vectors for miRNAs and other therapeutic agents into macrophages. This work aims to provide insights into the use of functionalized dendrimers as an innovative approach for TB treatment, focusing on their ability to target and deliver therapeutic cargo to macrophages.

Structural basis of human TREX1 DNA degradation and autoimmune disease

TREX1 is a cytosolic DNA nuclease essential for regulation of cGAS-STING immune signaling. Existing structures of mouse TREX1 establish a mechanism of DNA degradation and provide a key model to explain autoimmune disease, but these structures incompletely explain human disease-associated mutations and have limited ability to guide development of small-molecule therapeutics. Here we determine crystal structures of human TREX1 in apo and DNA-bound conformations that provide high-resolution detail of all human-specific features. A 1.25 Å structure of human TREX1 establishes a complete model of solvation of the exonuclease active site and a 2.2 Å structure of the human TREX1–DNA complex enables identification of specific substitutions involved in DNA recognition. We map each TREX1 mutation associated with autoimmune disease and establish distinct categories of substitutions predicted to impact enzymatic function, protein stability, and interaction with cGAS-DNA liquid droplets. Our results explain how human-specific substitutions regulate TREX1 function and provide a foundation for structure-guided design of TREX1 therapeutics.

TREX1-induced chromosome fragmentation at the interface of innate immunity and genomic instability

Abstract The cGAS-STING pathway, a crucial component of innate immunity, recognizes viral DNA in the cytosol. cGAS binds dsDNA and catalyzes the production of the second messenger cGAMP, resulting in the expression of Type I interferons and other pro-inflammatory genes. To prevent autoimmunity, activation of cGAS by cytosolic self-DNA is normally counteracted by the cytosolic nuclease TREX1. In many chromosomally instable cancers, cytosolic self-DNA accumulates as DNA bridges or micronuclei (MN), whose nuclear envelopes are prone to rupture, exposing contained DNA to the cytosol. cGAS activation at ruptured MN is implicated in anti-tumor immunity. However, mechanisms regulating cGAS activation at ruptured MN are yet unknown. Here, we show that TREX1 partially degrades chromosomal DNA in the cytosol to suppress cGAS activation. We observed localization of cGAS and TREX1 to ruptured MN and DNA bridges, strongly suggesting an unknown role for TREX1 in regulating cGAS activation in cancer. After induction of MN or DNA bridge formation, TREX1 KO causes dramatic increases in cGAMP production and cGAS-STING pathway signaling. Furthermore, ruptured MN exhibit TREX1-dependent DNA damage and ssDNA foci. TREX1 is bound to the ER, which is known to invade ruptured MN. We found that an ER binding mutant of TREX1 does not localize to MN anymore and was not able to rescue the TREX1 KO phenotype, suggesting a role for the ER to recruit TREX1 to MN. In summary, we propose that TREX1 enters MN as a consequence of nuclear envelope rupture to partially degrade DNA, thereby suppressing cGAS activation. By eliminating the immunogenic potential of these DNA species, TREX1 may dampen anti-tumor immunity and thereby help cancer cells escape the immune system.

HIV-1 uses dynamic capsid pores to import nucleotides and fuel encapsidated DNA synthesis.

During the early stages of infection, the HIV-1 capsid protects viral components from cytosolic sensors, such as cGAS, and nucleases, such as TREX, while allowing access to nucleotides for efficient reverse transcription1. Here we show that each capsid hexamer has a size-selective pore bounded by a ring of six arginine residues and a ‘molecular iris’ formed by the N-terminal β-hairpin. The arginine ring creates a strongly positively charged channel that recruits the four nucleotides with on-rates that near diffusion limits. Progressive removal of pore arginines results in a dose-dependent and concomitant decrease in nucleotide affinity, reverse transcription and infectivity. This positively charged channel is universally conserved in lentiviral capsids despite the fact that it is strongly destabilising without nucleotides to counteract charge repulsion. We also describe a channel inhibitor, hexacarboxybenzene, which competes for nucleotide binding and efficiently blocks encapsidated reverse transcription demonstrating the tractability of the pore as a novel drug target.

SiRNA Delivery: Current Trends and Future Perspectives

2016 Delivery of therapeutic nucleic acids in general and small interfering RNAs (siRNAs) in particular although a relatively nascent area of research, has already overcome several technical and regulatory hurdles over past few years. Some lead formulations undergoing clinical evaluation against wide range of diseases from age-related macular degeneration (AMD) to hypercholesteremia, amyloidosis and cancer. Roughly 4000 diseases are associated with malfunctioning genes in a particular cell type [1]. Gene therapy provides opportunity to modify (inhibit or enhance) the expression of disease-causing genes at the cellular level. Gene correction at the DNA level poses risks of inciting mutations or teratogenicity in comparison with RNA interference (RNAi) approach, which works at the transcription level leading to desired outcomes at the protein production stage such as therapeutic gene silencing of a cancer-causing gene. Currently, the key molecules employed in executing RNAi strategies are short hairpin RNA (shRNA), small interfering RNA (siRNA) or endogenous microRNA, of which siRNA forms the major mode presently under clinical evaluation [2]. siRNA molecules are easy to synthesize and do not need to be delivered into the nucleus as they do not require genome integration or the usage of DNA promoters [3]. They act in a sequence-specific manner against a target messenger RNA (mRNA), which avoids unintended off-target effects. The RNA-induced silencing complex (RISC), which drives RNAi, protects siRNA from degradation by cytosolic nucleases thereby recycling the molecule for many rounds of cleavage activity against the target mRNA. This implies that even few siRNA molecules if delivered stably into the cell cytosol are sufficient to trigger long-lasting gene silencing. In order to reach the desired organ/tissue and subsequently cross the cell membrane, these therapeutic siRNAs need to overcome several physiological barriers such as renal clearance, serum degradation and cellspecific uptake. Following crossing the cell membrane, intracellular barriers in the form of saturation of endogenous RNAi machinery or endosomal escape postendocytosis can reduce the efficiency of the delivered siRNA molecules [4]. Small negatively charged siRNAs can also lead to immunotoxicity and over the past years efforts have been dedicated to develop an efficient carrier modalities to overcome these systemic barriers and toxicity issues, which broadly falls into viral and nonviral strategies. Due to safety concerns on usage of viral vectors, nonviral techniques have taken the center-stage in siRNAs delivery. Delivery vehicles such as liposomes, lipidbased nanoparticles (LNPs) or polymeric nanoparticles are biodegradable, have relatively low toxicity, are stable in storage, easyto scale up and have low production costs – traits favored from an industrial perspective. Moreover, most components used in the development of nanostructures in the form of lipids or polymers are approved by the siRNA delivery: current trends and future perspectives

Cytosolic Nuclease TREX1 Regulates Oligosaccharyltransferase Activity Independent of Nuclease Activity to Suppress Immune Activation

TREX1 is an endoplasmic reticulum (ER)-associated negative regulator of innate immunity. TREX1 mutations are associated with autoimmune and autoinflammatory diseases. Biallelic mutations abrogating DNase activity cause autoimmunity by allowing immunogenic self-DNA to accumulate, but it is unknown how dominant frameshift (fs) mutations that encode DNase-active but mislocalized proteins cause disease. We found that the TREX1 C terminus suppressed immune activation by interacting with the ER oligosaccharyltransferase (OST) complex and stabilizing its catalytic integrity. C-terminal truncation of TREX1 by fs mutations dysregulated the OST complex, leading to free glycan release from dolichol carriers, as well as immune activation andautoantibody production. A connection between OST dysregulation and immune disorders was demonstrated in Trex1(-/-) mice, TREX1-V235fs patient lymphoblasts, and TREX1-V235fs knock-in mice. Inhibiting OST with aclacinomycin corrects the glycan and immune defects associated with Trex1 deficiency or fs mutation. This function of the TREX1 C terminus suggests a potential therapeutic option for TREX1-fs mutant-associated diseases.

Quantification of cytosolic plasmid DNA degradation using high-throughput sequencing: implications for gene delivery

Although cytosolic DNA degradation plays an important role in decreasing transgene expression, the plasmid degradation pattern remains largely unexplored. Illumina dye sequencing was employed to provide degradation site information for S1 and cytosolic nucleases. S1 nuclease provided a positive control for a comparison between the agarose gel method and sequencing approaches. The poly(A) region between the β-lactamase gene and the cytomegalovirus (CMV) promoter was identified as the most likely cut site for polyplex-treated cytosol. The second most likely site, at the 5' end of the β-lactamase gene, was identified by gel electrophoresis and sequencing. Additional sites were detected in the OriC region, the SV40/poly(A) region, the luciferase gene and the CMV promoter. Sequence analysis of plasmid treated with cytosol from control cells showed the greatest cut activity in the OriC region, the β-lactamase gene and the poly(A) region following the luciferase gene. Additional regions of cut activity include the SV40 promoter and the β-lactamase poly(A) termination sequence. Both cytosolic nucleases and the S1 nuclease showed substantial activity at the bacterial origin of replication (OriC). High-throughput plasmid sequencing revealed regions of the luciferase plasmid DNA sequence that are sensitive to cytosolic nuclease degradation. This provides new targets for improving plasmid and/or polymer design to optimize the likelihood of protein expression.

Oxidative Damage of DNA Confers Resistance to Cytosolic Nuclease TREX1 Degradation and Potentiates STING-Dependent Immune Sensing

Immune sensing of DNA is critical for antiviral immunity but can also trigger autoimmune diseases such as lupus erythematosus (LE). Here we have providedevidence for the involvement of a damage-associated DNA modification in the detection of cytosolicDNA. The oxidized base 8-hydroxyguanosine (8-OHG), a marker of oxidative damage in DNA,potentiated cytosolic immune recognition by decreasing its susceptibility to 3' repair exonuclease 1 (TREX1)-mediated degradation. Oxidizative modifications arose physiologically in pathogen DNA during lysosomal reactive oxygen species (ROS) exposure, as well as in neutrophil extracellular trap (NET) DNA during the oxidative burst. 8-OHG was also abundantin UV-exposed skin lesions of LE patients and colocalized with type I interferon (IFN). Injection of oxidized DNA in the skin of lupus-prone mice induced lesions that closely matched respective lesions in patients. Thus, oxidized DNA represents a prototypic damage-associated molecular pattern (DAMP) with important implications for infection, sterile inflammation, and autoimmunity.

Polyplex-Induced Cytosolic Nuclease Activation Leads to Differential Transgene Expression

Cytosolic nucleases have been proposed to play an important role in limiting the effectiveness of polyplex-based gene delivery agents. In order to explore the effect of cell membrane disruption on nuclease activation, nuclease activity upon polyplex uptake and localization, and nuclease activity upon gene expression, we employed an oligonucleotide molecular beacon (MB). The MB was incorporated as an integral part of the polymer/DNA polyplex, and two-color flow cytometry experiments were performed to explore the relationship of MB cleavage with propidium iodide (PI) uptake, protein expression, and polyplex uptake. In addition, confocal fluorescence microcopy was performed to examine both polyplex and cleaved MB localization. The impact of cell membrane disruption was also probed using whole-cell patch clamp measurement of the plasma membrane's electrical conductance. Differential activation of cytosolic nuclease was observed with substantial activity for B-PEI and G5 PAMAM dendrimer (G5), less cleavage for jetPEI, and little activity for L-PEI. jetPEI and L-PEI exhibited substantially greater transgene expression, consistent with the lower amounts of MB oligonucleotide cleavage observed. Cytosolic nuclease activity, although dependent on the choice of polymer employed, was not related to the degree of cell plasma membrane disruption that occurred as measured by PI uptake or whole-cell patch clamp.

Optimizing the generation of stable neuronal cell lines via pre-transfection restriction enzyme digestion of plasmid DNA

Transfection of mammalian cell lines is a widely used technique that requires significant optimization, including transfection method or product used, DNA vector, cell density, media composition and incubation time. Generation and isolation of stable transfectants from the large pool of untransfected or only transiently transfected cells can be laborious and time-consuming. Transfection of DNA is usually performed with a non-linearized plasmid, since it is assumed that cutting the plasmid beforehand leads to a lower efficiency of transfection or the degradation of linearized DNA by cytosolic nucleases. However, the transfected circular plasmid will be linearized by a random cut within the cell and it might be possible that sensitive parts of the plasmid such as the resistance gene or the gene of interest are destroyed upon linearization. On the other hand, linearizing a plasmid before transfection by a single, defined cut with a selected restriction enzyme in a non-coding area of the gene has the advantage of ensuring the integrity of all necessary gene elements of the plasmid. In this study, we have compared these different methods in order to increase both transient and stable transfection efficiency in mammalian cells. We report that linearization of plasmid DNA prior to transfection can increase both the efficiency of stable clone generation and target gene expression, but is dependant on the site of linearization within the vector.

Investigation of factors responsible for cell line cytoplasmic expression differences

BackgroundPrevious work has described a novel cytoplasmic expression system that results in a 20-fold increase in the levels of gene expression over a standard CMV-based nuclear expression system, as compared with a 2–3 fold increase seen with previous similar systems. While this increase was seen with BHK and Neuro-2a cells, further studies revealed that some cell lines, such as COS-7, demonstrated relatively poor levels of cytoplasmic expression. The objective of this study was to determine what factors were responsible for the different expression levels between BHK (a high expressing cell line) and COS-7 (a low expressing cell line).ResultsThe main findings of this work are that the individual elements of the cytoplasmic expression system (such as the T7 RNAP gene and Internal Ribosome Entry Sequence) are functioning similarly in both cell types. Both cell types were found to have the same amount of cytosolic nuclease activity, and that the cells appeared to have differences in the intra-cellular processing of DNA -cationic lipid complexes.ConclusionAfter exploring many factors, it was found that differences in the intra-cellular processing of the DNA-cationic lipid complex was the most probable factor responsible for the difference in cytoplasmic gene expression.

Ca2+-sensitive cytosolic nucleases prevent efficient delivery to the nucleus of injected plasmids.

Efficient gene delivery by synthetic vectors is a major challenge in gene therapy. However, inefficient nuclear delivery of cDNA is thought to be a major limiting step in gene transfer using non-viral vectors. It is commonly thought that, in the cytosol, cDNA has to be released from its vector before importation to the nucleus. The stability of naked cDNA in the cytoplasm is not well established. cDNA plasmids, either free or complexed with poly(ethyleneimine) (PEI), were microinjected into the cytoplasm of mammalian cells and their turnover was assessed by fluorescence in situ hybridization (FISH). Incubations of cDNA plasmids in cytosolic extracts were also performed. FISH experiments showed that naked cDNA rapidly fade with time when injected into the cytosol. Fading was not observed when naked cDNA plasmids were injected into the nucleus. Incubation of naked cDNA in a cytosolic fraction isolated from mammalian cells reproduced cDNA degradation as observed in microinjection experiments. Nuclease inhibitors, including aurin tricarboxylic acid or Zn2+, prevented in vitro cDNA degradation. The cytosolic nuclease activity was optimal at physiological pH and physiological Ca2+ concentration. By contrast, it was insensitive to Mg2+ or Na+ concentrations. Finally, cDNA complexation with PEI or addition of oligonucleotides prevented in vitro cDNA degradation. Altogether, these experiments suggest that cDNA digestion by cytosolic nucleases occur when the decomplexed transgene is present in the cytosol. We propose that the inefficient transfer of cDNA into the nucleus during transfection with synthetic vectors may result from rapid digestion of naked cDNA by a Ca2+-sensitive cytosolic nuclease.

Metabolic instability of plasmid DNA in the cytosol: a potential barrier to gene transfer.

Inefficient nuclear delivery of plasmid DNA is thought to be one of the daunting hurdles to gene transfer, utilizing a nonviral delivery system such as polycation-DNA complex. Following its internalization by endocytosis, plasmid DNA has to be released into the cytosol before its nuclear entry can occur. However, the stability of plasmid DNA in the cytoplasm, that may play a determinant role in the transfection efficiency, is not known. The turnover of plasmid DNA, delivered by microinjection into the cytosol, was determined by fluorescence in situ hybridization (FISH) and quantitative single-cell fluorescence video-image analysis. Both single- and double-stranded circular plasmid DNA disappeared with an apparent half-life of 50-90 min from the cytoplasm of HeLa and COS cells, while the amount of co-injected dextran (MW 70,000) remained unaltered. We propose that cytosolic nuclease(s) are responsible for the rapid-degradation of plasmid DNA, since (1) elimination of plasmid DNA cannot be attributed to cell division or to the activity of apoptotic and lysosomal nucleases; (2) disposal of microinjected plasmid DNA was inhibited in cytosol-depleted cells or following the encapsulation of DNA in phospholipid vesicles; (3) generation and subsequent elimination of free 3'-OH ends could be detected by the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling assay (TUNEL), reflecting the fragmentation of the injected DNA; and finally (4) isolated cytosol, obtained by selective permeabilization of the plasma membrane, exhibits divalent cation-dependent, thermolabile nuclease activity, determined by Southern blotting and 32P-release from end-labeled DNA. Collectively, these findings suggest that the metabolic instability of plasmid DNA, caused by cytosolic nuclease, may constitute a previously unrecognized impediment for DNA translocation into the nucleus and a possible target to enhance the efficiency of gene delivery.

Cytosolic Nuclease Activated by Caspase-3 and Inhibited by DFF-45

To study the intracellular apoptotic signaling pathways, we have established a cell-free system, in which DNA fragmentation of the isolated mouse liver nuclei was induced with lysates from the Fas-activated cells. We have found that the inactive nuclease present in the intact cell cytosol is activated by a caspase-3-like protease and the activated nuclease induces the nucleosomal DNA fragmentation. We attempted the purification of the inactive nuclease from bovine liver cytosol. The partially purified nuclease was activated by recombinant caspase-3, and to a lesser extent by caspase-6. The activated nuclease was able to digest plasmid DNA in addition to induce the DNA fragmentation of nuclei. DFF-45, which is a subunit of heterodimeric protein leading to DNA fragmentation upon its digestion by caspase-3, is found to inhibit the activity of the activated nuclease. These results suggest that the inactive nuclease in cytoplasm is converted to the active form by caspases, and the activated nuclease enters into nucleus to induce the DNA fragmentation. It is suggested that DFF-45 may function as an inhibitory factor of the caspase-sensitive nucleasein vivo.