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1.
Nat Commun ; 15(1): 4696, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38824133

ABSTRACT

Age-related microangiopathy, also known as small vessel disease (SVD), causes damage to the brain, retina, liver, and kidney. Based on the DNA damage theory of aging, we reasoned that genomic instability may underlie an SVD caused by dominant C-terminal variants in TREX1, the most abundant 3'-5' DNA exonuclease in mammals. C-terminal TREX1 variants cause an adult-onset SVD known as retinal vasculopathy with cerebral leukoencephalopathy (RVCL or RVCL-S). In RVCL, an aberrant, C-terminally truncated TREX1 mislocalizes to the nucleus due to deletion of its ER-anchoring domain. Since RVCL pathology mimics that of radiation injury, we reasoned that nuclear TREX1 would cause DNA damage. Here, we show that RVCL-associated TREX1 variants trigger DNA damage in humans, mice, and Drosophila, and that cells expressing RVCL mutant TREX1 are more vulnerable to DNA damage induced by chemotherapy and cytokines that up-regulate TREX1, leading to depletion of TREX1-high cells in RVCL mice. RVCL-associated TREX1 mutants inhibit homology-directed repair (HDR), causing DNA deletions and vulnerablility to PARP inhibitors. In women with RVCL, we observe early-onset breast cancer, similar to patients with BRCA1/2 variants. Our results provide a mechanistic basis linking aberrant TREX1 activity to the DNA damage theory of aging, premature senescence, and microvascular disease.


Subject(s)
DNA Damage , Exodeoxyribonucleases , Phosphoproteins , Animals , Exodeoxyribonucleases/genetics , Exodeoxyribonucleases/metabolism , Humans , Phosphoproteins/genetics , Phosphoproteins/metabolism , Mice , Recombinational DNA Repair , Phenotype , Mutation , Drosophila/genetics , Aging/genetics , Aging/metabolism , Female , Drosophila melanogaster/genetics , Male , Retinal Diseases , Vascular Diseases , Hereditary Central Nervous System Demyelinating Diseases
2.
Bioelectrochemistry ; 158: 108727, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38728815

ABSTRACT

Herein, we demonstrate a simple, homogenous and label-free electrochemical biosensing system for sensitive nucleic acid detection based on target-responsive porous materials and nuclease-triggered target recycling amplification. The Fe(CN)63- reporter was firstly sealed into the pores of Fe3O4 nanoparticles by probe DNA. Target DNA recognition triggered the controllable release of Fe(CN)63- for the redox reaction with the electron mediator of methylene blue enriched in the dodecanethiol assembled electrode and thereby generating electrochemical signal. The exonuclease III (Exo III)-assisted target recycling and the catalytic redox recycling between Fe(CN)63- and methylene blue contributed for the enhanced signal response toward target recognition. The low detection limit toward target was obtained as 478 fM and 1.6 pM, respectively, by square wave voltammetry and cyclic voltammetry methods. It also possessed a well-discrimination ability toward mismatched strands and high tolerance to complex sample matrix. The coupling of bio-gated porous nanoparticles, nuclease-assisted target amplification and catalytic redox recycling afforded the sensing system with well-controllable signal responses, sensitive and selective DNA detection, and good stability, reusability and reproducibility. It thus opens a new avenue toward the development of simple but sensitive electrochemical biosensing platform.


Subject(s)
Biosensing Techniques , DNA , Electrochemical Techniques , Limit of Detection , Oxidation-Reduction , Biosensing Techniques/methods , DNA/chemistry , Electrochemical Techniques/methods , Catalysis , Exodeoxyribonucleases/metabolism , Exodeoxyribonucleases/chemistry , Methylene Blue/chemistry
3.
Int J Mol Sci ; 25(10)2024 May 12.
Article in English | MEDLINE | ID: mdl-38791317

ABSTRACT

The myostatin (MSTN) gene also regulates the developmental balance of skeletal muscle after birth, and has long been linked to age-related muscle wasting. Many rodent studies have shown a correlation between MSTN and age-related diseases. It is unclear how MSTN and age-associated muscle loss in other animals are related. In this study, we utilized MSTN gene-edited bovine skeletal muscle cells to investigate the mechanisms relating to MSTN and muscle cell senescence. The expression of MSTN was higher in older individuals than in younger individuals. We obtained consecutively passaged senescent cells and performed senescence index assays and transcriptome sequencing. We found that senescence hallmarks and the senescence-associated secretory phenotype (SASP) were decreased in long-term-cultured myostatin inactivated (MT-KO) bovine skeletal muscle cells (bSMCs). Using cell signaling profiling, MSTN was shown to regulate the SASP, predominantly through the cycle GMP-AMP synthase-stimulator of antiviral genes (cGAS-STING) pathway. An in-depth investigation by chromatin immunoprecipitation (ChIP) analysis revealed that MSTN influenced three prime repair exonuclease 1 (TREX1) expression through the SMAD2/3 complex. The downregulation of MSTN contributed to the activation of the MSTN-SMAD2/3-TREX1 signaling axis, influencing the secretion of SASP, and consequently delaying the senescence of bSMCs. This study provided valuable new insight into the role of MSTN in cell senescence in large animals.


Subject(s)
Cellular Senescence , Myostatin , Animals , Myostatin/genetics , Myostatin/metabolism , Cattle , Cellular Senescence/genetics , Exodeoxyribonucleases/metabolism , Exodeoxyribonucleases/genetics , Signal Transduction , Muscle Fibers, Skeletal/metabolism , Muscle, Skeletal/metabolism , Phosphoproteins/metabolism , Phosphoproteins/genetics , Cells, Cultured
4.
BMC Biol ; 22(1): 119, 2024 May 20.
Article in English | MEDLINE | ID: mdl-38769511

ABSTRACT

BACKGROUND: Many efforts have been made to improve the precision of Cas9-mediated gene editing through increasing knock-in efficiency and decreasing byproducts, which proved to be challenging. RESULTS: Here, we have developed a human exonuclease 1-based genome-editing tool, referred to as exonuclease editor. When compared to Cas9, the exonuclease editor gave rise to increased HDR efficiency, reduced NHEJ repair frequency, and significantly elevated HDR/indel ratio. Robust gene editing precision of exonuclease editor was even superior to the fusion of Cas9 with E1B or DN1S, two previously reported precision-enhancing domains. Notably, exonuclease editor inhibited NHEJ at double strand breaks locally rather than globally, reducing indel frequency without compromising genome integrity. The replacement of Cas9 with single-strand DNA break-creating Cas9 nickase further increased the HDR/indel ratio by 453-fold than the original Cas9. In addition, exonuclease editor resulted in high microhomology-mediated end joining efficiency, allowing accurate and flexible deletion of targeted sequences with extended lengths with the aid of paired sgRNAs. Exonuclease editor was further used for correction of DMD patient-derived induced pluripotent stem cells, where 30.0% of colonies were repaired by HDR versus 11.1% in the control. CONCLUSIONS: Therefore, the exonuclease editor system provides a versatile and safe genome editing tool with high precision and holds promise for therapeutic gene correction.


Subject(s)
Exodeoxyribonucleases , Gene Editing , Gene Editing/methods , Humans , Exodeoxyribonucleases/genetics , Exodeoxyribonucleases/metabolism , CRISPR-Cas Systems , HEK293 Cells , DNA Repair Enzymes
5.
Anal Bioanal Chem ; 416(14): 3295-3303, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38696128

ABSTRACT

Thiabendazole, a widely used broad-spectrum fungicide in agriculture, poses risks to human health. To monitor its presence in water, we propose a fluorescent aptasensor utilizing Escherichia coli exonuclease I (Exo I). The findings demonstrate a linear correlation between thiabendazole concentrations and digestion percentage, with a detection limit (LOD) exceeding 1 µM and a determination coefficient (R2) of 0.959. This aptamer-based fluorescence spectroscopy detection system holds promise for a rapid, specific, and sensitive analysis of thiabendazole in environmental waters and food matrices.


Subject(s)
Aptamers, Nucleotide , Biosensing Techniques , Limit of Detection , Spectrometry, Fluorescence , Thiabendazole , Thiabendazole/analysis , Aptamers, Nucleotide/chemistry , Spectrometry, Fluorescence/methods , Biosensing Techniques/methods , Fungicides, Industrial/analysis , Exodeoxyribonucleases/metabolism , Exodeoxyribonucleases/chemistry , Escherichia coli , Water Pollutants, Chemical/analysis , Fluorescent Dyes/chemistry
6.
Biochem Biophys Res Commun ; 712-713: 149893, 2024 Jun 18.
Article in English | MEDLINE | ID: mdl-38657529

ABSTRACT

RecJ exonucleases are members of the DHH phosphodiesterase family ancestors of eukaryotic Cdc45, the key component of the CMG (Cdc45-MCM-GINS) complex at the replication fork. They are involved in DNA replication and repair, RNA maturation and Okazaki fragment degradation. Bacterial RecJs resect 5'-end ssDNA. Conversely, archaeal RecJs are more versatile being able to hydrolyse in both directions and acting on ssDNA as well as on RNA. In Methanocaldococcus jannaschii two RecJs were previously characterized: RecJ1 is a 5'→3' DNA exonuclease, MjaRecJ2 works only on 3'-end DNA/RNA with a preference for RNA. Here, I present the crystal structure of MjaRecJ2, solved at a resolution of 2.8 Å, compare it with the other RecJ structures, in particular the 5'→3' TkoGAN and the bidirectional PfuRecJ, and discuss its characteristics in light of the more recent knowledge on RecJs. This work adds new structural data that might improve the knowledge of these class of proteins.


Subject(s)
Methanocaldococcus , Models, Molecular , Methanocaldococcus/enzymology , Crystallography, X-Ray , Archaeal Proteins/chemistry , Archaeal Proteins/metabolism , Archaeal Proteins/genetics , Exonucleases/metabolism , Exonucleases/chemistry , Protein Conformation , Amino Acid Sequence , Exodeoxyribonucleases/chemistry , Exodeoxyribonucleases/metabolism , Exodeoxyribonucleases/genetics
7.
Food Chem ; 451: 139399, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-38663240

ABSTRACT

Malachite green (MG) has been illicitly employed in aquaculture as a parasiticide, however, its teratogenic and carcinogenic effects pose a significant human health threat. Herein, a dual-mode colorimetric and electrochemical aptasensor was fabricated for MG detection, capitalizing on the robust catalytic and peroxidase-like activity of P-CeO2NR@Mxene and good capture efficiency of a tetrahedral DNA nanostructure (TDN) designed with multiple aptamers (m-TDN). P-CeO2NR@Mxene-modified complementary DNA (cDNA) served as both colorimetric and electrochemical probe. m-TDN was attached to AuE to capture MG and P-CeO2NR@Mxene/cDNA. The superior aptamer and MG binding to cDNA regulated signals and enabled precise MG quantification. The further introduced Exo I enabled aptamer hydrolysis, releasing MG for further binding rounds, allowing target recycling amplification. Under the optimal conditions, the aptasensor reached an impressively low detection limit 95.4 pM in colorimetric mode and 83.6 fM in electrochemical mode. We believe this dual-mode approach holds promise for veterinary drug residue detection.


Subject(s)
Aptamers, Nucleotide , Biosensing Techniques , Colorimetry , Electrochemical Techniques , Rosaniline Dyes , Aptamers, Nucleotide/chemistry , Rosaniline Dyes/chemistry , Rosaniline Dyes/analysis , Biosensing Techniques/instrumentation , Exodeoxyribonucleases/chemistry , Exodeoxyribonucleases/metabolism , Limit of Detection , Food Contamination/analysis
8.
ACS Appl Mater Interfaces ; 16(19): 24372-24383, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38688864

ABSTRACT

DNA circuits, as a type of biochemical system, have the capability to synchronize the perception of molecular information with a chemical reaction response and directly process the molecular characteristic information in biological activities, making them a crucial area in molecular digital computing and smart bioanalytical applications. Instead of cascading logic gates, the traditional research approach achieves multiple logic operations which limits the scalability of DNA circuits and increases the development costs. Based on the interface reaction mechanism of Lambda exonuclease, the molecular perceptron proposed in this study, with the need for only adjusting weight and bias parameters to alter the corresponding logic expressions, enhances the versatility of the molecular circuits. We also establish a mathematical model and an improved heuristic algorithm for solving weights and bias parameters for arbitrary logic operations. The simulation and FRET experiment results of a series of logic operations demonstrate the universality of molecular perceptron. We hope the proposed molecular perceptron can introduce a new design paradigm for molecular circuits, fostering innovation and development in biomedical research related to biosensing, targeted therapy, and nanomachines.


Subject(s)
Computers, Molecular , DNA , DNA/chemistry , DNA/metabolism , Algorithms , Fluorescence Resonance Energy Transfer , Bacteriophage lambda/genetics , Exonucleases/metabolism , Exodeoxyribonucleases/metabolism , Exodeoxyribonucleases/chemistry , Biosensing Techniques/methods
9.
Viruses ; 16(4)2024 03 25.
Article in English | MEDLINE | ID: mdl-38675842

ABSTRACT

TREX1 acts in the initial prevention of an autoimmune response, but it may contribute to the permissiveness of retrovirus infections. This study investigated the association between the levels of TREX1 gene expression with the polymorphisms TREX1 rs3135941 (T/C) and TREX1 rs3135945 (G/A), and the presence of antinuclear antibodies (ANA) in antiretroviral therapy (ART)-naïve individuals and after 1 year of treatment. Blood samples from 119 individuals with HIV-1 were subjected to genotyping of polymorphisms and quantification of TREX1 gene expression and HIV-1 viral load by qPCR. The concentration of IFN-α and the number of CD4+/CD8+ T lymphocytes were determined by ELISA and flow cytometry, respectively; ANA was investigated by immunofluorescence. A control group of 167 seronegative individuals was used for the comparison of genotypic frequencies. The frequency of the polymorphisms were not associated with HIV infection or with variations in the expression of TREX1 and IFN-α (p > 0.05). ART-naïve individuals exhibited higher TREX1 expression and lower IFN-α expression. After 1 year of ART, TREX1 levels were reduced, while IFN-α and CD4+ T lymphocytes were elevated (p < 0.05). Some individuals on ART presented ANA. These results suggest that ART-mediated restoration of immune competence is associated with a reduction in TREX1 expression, which may induce the development of ANA, regardless of the polymorphism investigated.


Subject(s)
Exodeoxyribonucleases , HIV Infections , HIV-1 , Immune Reconstitution , Phosphoproteins , Adult , Female , Humans , Male , Middle Aged , Antibodies, Antinuclear/blood , CD4-Positive T-Lymphocytes/immunology , Exodeoxyribonucleases/genetics , Exodeoxyribonucleases/metabolism , Genotype , HIV Infections/immunology , HIV Infections/drug therapy , HIV Infections/genetics , HIV Infections/virology , HIV-1/immunology , Immune Reconstitution/genetics , Immune Reconstitution/immunology , Interferon-alpha/blood , Interferon-alpha/metabolism , Phosphoproteins/genetics , Polymorphism, Single Nucleotide , Viral Load , Anti-Retroviral Agents/adverse effects , Anti-Retroviral Agents/therapeutic use
10.
Anal Biochem ; 691: 115547, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38670419

ABSTRACT

MicroRNAs (miRNAs) can serve as biomarkers for early-diagnosis, therapy, and postoperative care of cervical cancer. Sensitive and reliable quantification of miRNA remains a huge challenge due to its low expressing levels and background interference. Herein, we propose a novel exonuclease-III (Exo-III)-propelled DNAzyme cascade for sensitive and high-efficient miRNA analysis. This method involves the engineering of compact DNAzyme hairpin probes, including the H1 probe and H2 probe. The H1 probe is designed with exposed analyte recognition subunits that can specifically recognize target miRNA. This recognition triggers two processes: Exo-iii-assisted target regeneration and successive substrate cleavage catalyzed by DNAzyme. The unique character of Exo-III that catalyzes removal of mononucleotides from the blunt or recessed 3'-OH termini of dsDNA confers the approach with a minimal background signal. The multiple signal cycles provided an abundant signal amplification and consequently, the method exhibited a low limit of detection of 3.12 fM, and a better specificity over several homologous miRNAs. In summary, this powerful Exo-III driven DNAzyme cascaded system offers broader and more adaptable methods for comprehending the activities of miRNA in various biological occurrences.


Subject(s)
DNA, Catalytic , Exodeoxyribonucleases , MicroRNAs , Uterine Cervical Neoplasms , MicroRNAs/analysis , MicroRNAs/genetics , MicroRNAs/metabolism , DNA, Catalytic/metabolism , DNA, Catalytic/chemistry , DNA, Catalytic/genetics , Humans , Exodeoxyribonucleases/metabolism , Uterine Cervical Neoplasms/diagnosis , Uterine Cervical Neoplasms/metabolism , Uterine Cervical Neoplasms/genetics , Female , Limit of Detection , Biosensing Techniques/methods
11.
Talanta ; 275: 126143, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38669960

ABSTRACT

Accurate and sensitive detection of disease-associated proteins in early stage of patients plays an important role in timely treatment and successfully extending patients' lives. To meet this demand, we herein rationally designed a flexible target-induced DNA nanomachine operation (TIDNMO) sensor for the detection of proteins. The TIDNMO system was composed of DNA nanoswitch and DNA walker. Triplex DNA nanoswitch was triggered by specific target, followed by the release of the walking strand, which initiated the DNA walker amplification as signal output. In addition, the Exo III could drive walking strand autonomously move on gold nanoparticle surface to realize 2 orders of magnitude signal amplification. What's more, this sensor could transform its suitable functional recognition element of DNA nanoswitch to recognize other specific molecule and realize different targets sensing based on identical walking tracks. Considering the facile reporter elements and efficient amplification performance, the present DNA nanomachine as a sensor could achieve a detection limit of 68 pM for anti-Dig antibody, 0.95 pM for mucin-1 respectively, along with a superb specificity. Furthermore, the method reported here opened a new chapter in disease-related protein sensing for the development of clinical early diagnosis.


Subject(s)
Biosensing Techniques , DNA , Gold , Metal Nanoparticles , DNA/chemistry , Gold/chemistry , Humans , Metal Nanoparticles/chemistry , Biosensing Techniques/methods , Limit of Detection , Mucin-1/analysis , Exodeoxyribonucleases/chemistry , Exodeoxyribonucleases/metabolism , Nanotechnology , Nucleic Acid Amplification Techniques/methods
12.
Talanta ; 274: 125934, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38574533

ABSTRACT

Nowadays, novel and efficient signal amplification strategy in electrochemiluminescence (ECL) platform is urgently needed to enhance the sensitivity of biosensor. In this work, the dual ECL signal enhancement strategy was constructed by the interactions of Pd nanoparticles attached covalent organic frameworks (Pd NPs@COFs) with tris (bipyridine) ruthenium (RuP) and Exonuclease III (Exo.III) cycle reaction. Within this strategy, the COFs composite was generated from the covalent reaction between 2-nitro-1,4-phenylenediamine (NPD) and trialdehyde phloroglucinol (Tp), and then animated by glutamate (Glu) to attach the Pd NPs. Next, the "signal on" ECL biosensor was constructed by the coordination assembly of thiolation capture DNA (cDNA) onto the Pd NPs@COFs modified electrode. After the aptamer recognition of progesterone (P4) with hairpin DNA 1 (HP1), the Exo. III cycle reaction was initiated with HP2 to generate free DNA, which hybridized with cDNA to form double-stranded DNA (dsDNA). For that, the RuP was embedded into the groove of dsDNA and achieved the ultrasensitive detection of P4 with a lower limit of detection (LOD) down to 0.45 pM, as well as the excellent selectivity and stability. This work expands the COFs-based materials application in ECL signal amplification and valuable DNA cyclic reaction in biochemical testing field.


Subject(s)
Biosensing Techniques , Electrochemical Techniques , Exodeoxyribonucleases , Metal Nanoparticles , Metal-Organic Frameworks , Palladium , Progesterone , Metal Nanoparticles/chemistry , Metal-Organic Frameworks/chemistry , Palladium/chemistry , Progesterone/analysis , Progesterone/chemistry , Biosensing Techniques/methods , Electrochemical Techniques/methods , Exodeoxyribonucleases/chemistry , Exodeoxyribonucleases/metabolism , Limit of Detection , Luminescent Measurements/methods , Humans , DNA/chemistry
13.
Nucleic Acids Res ; 52(7): 4067-4078, 2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38471810

ABSTRACT

Mitochondrial genome maintenance exonuclease 1 (MGME1) helps to ensure mitochondrial DNA (mtDNA) integrity by serving as an ancillary 5'-exonuclease for DNA polymerase γ. Curiously, MGME1 exhibits unique bidirectionality in vitro, being capable of degrading DNA from either the 5' or 3' end. The structural basis of this bidirectionally and, particularly, how it processes DNA from the 5' end to assist in mtDNA maintenance remain unclear. Here, we present a crystal structure of human MGME1 in complex with a 5'-overhang DNA, revealing that MGME1 functions as a rigid DNA clamp equipped with a single-strand (ss)-selective arch, allowing it to slide on single-stranded DNA in either the 5'-to-3' or 3'-to-5' direction. Using a nuclease activity assay, we have dissected the structural basis of MGME1-derived DNA cleavage patterns in which the arch serves as a ruler to determine the cleavage site. We also reveal that MGME1 displays partial DNA-unwinding ability that helps it to better resolve 5'-DNA flaps, providing insights into MGME1-mediated 5'-end processing of nascent mtDNA. Our study builds on previously solved MGME1-DNA complex structures, finally providing the comprehensive functional mechanism of this bidirectional, ss-specific exonuclease.


Subject(s)
DNA, Mitochondrial , Exodeoxyribonucleases , Genome, Mitochondrial , Humans , DNA, Mitochondrial/genetics , DNA, Mitochondrial/metabolism , DNA, Mitochondrial/chemistry , Exodeoxyribonucleases/metabolism , Exodeoxyribonucleases/chemistry , Exodeoxyribonucleases/genetics , Crystallography, X-Ray , Models, Molecular , DNA, Single-Stranded/metabolism , DNA, Single-Stranded/chemistry , Nucleic Acid Conformation , DNA Polymerase gamma/metabolism , DNA Polymerase gamma/genetics , DNA Polymerase gamma/chemistry
14.
Bioorg Med Chem ; 102: 117660, 2024 Mar 15.
Article in English | MEDLINE | ID: mdl-38442524

ABSTRACT

Werner (WRN) syndrome protein is a multifunctional enzyme with helicase, ATPase, and exonuclease activities that are necessary for numerous DNA-related transactions in the human cell. Recent studies identified WRN as a synthetic lethal target in cancers. In this study, a series of new N-arylquinazoline-4-amine analogs were designed and synthesized based on structure optimization of quinazoline. The structures of the thirty-two newly synthesized compounds were confirmed by 1H NMR, 13C NMR and ESI-MS. The anticancer activity in vitro against chronic myeloid leukemia cells (K562), non-small cell lung cancer cells (A549), human prostate cancer cells (PC3), and cervical cancer cells (HeLa) of the target compounds was evaluated. Among them, the inhibition ratio of compounds 17d, 18a, 18b, 11 and 23a against four cancer cells at 5 µM concentration were more than 50 %. The IC50 values of compounds 18a and 18b were 0.3 ± 0.01 µM and 0.05 ± 0.02 µM in K562 cells respectively, compared with HeLa and A549 cells, 18a and 18b were more sensitive to K562 cells. In addition, the PC3 cells with WRN overexpression (PC3-WRN) was constructed, 18a and 18b and 23a were more sensitive to PC3-WRN cells compared with the control group cells (PC3-NC). Then, the cell viability of the novel WRN inhibitors were further assessed by colony formation assay. Compared with PC3-NC cells, 18b and 23a had obvious inhibitory effect on PC3-WRN cell at 1000 nM. In summary, these results indicated that the compounds 18b and 23a could be WRN protein inhibitor with potent anticancer properties in vitro.


Subject(s)
Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , RecQ Helicases , Exodeoxyribonucleases/metabolism , HeLa Cells
15.
Nucleic Acids Res ; 52(9): 5121-5137, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38520409

ABSTRACT

The S-phase checkpoint is involved in coupling DNA unwinding with nascent strand synthesis and is critical to maintain replication fork stability in conditions of replicative stress. However, its role in the specific regulation of leading and lagging strands at stalled forks is unclear. By conditionally depleting RNaseH2 and analyzing polymerase usage genome-wide, we examine the enzymology of DNA replication during a single S-phase in the presence of replicative stress and show that there is a differential regulation of lagging and leading strands. In checkpoint proficient cells, lagging strand replication is down-regulated through an Elg1-dependent mechanism. Nevertheless, when checkpoint function is impaired we observe a defect specifically at the leading strand, which was partially dependent on Exo1 activity. Further, our genome-wide mapping of DNA single-strand breaks reveals that strand discontinuities highly accumulate at the leading strand in HU-treated cells, whose dynamics are affected by checkpoint function and Exo1 activity. Our data reveal an unexpected role of Exo1 at the leading strand and support a model of fork stabilization through prevention of unrestrained Exo1-dependent resection of leading strand-associated nicks after fork stalling.


Subject(s)
DNA Breaks, Single-Stranded , DNA Replication , Exodeoxyribonucleases , S Phase Cell Cycle Checkpoints , Exodeoxyribonucleases/metabolism , Exodeoxyribonucleases/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Ribonuclease H/metabolism , Ribonuclease H/genetics , S Phase/genetics , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/genetics
16.
Cancer Immunol Res ; 12(6): 663-672, 2024 Jun 04.
Article in English | MEDLINE | ID: mdl-38489753

ABSTRACT

The DNA exonuclease three-prime repair exonuclease 1 (TREX1) is critical for preventing autoimmunity in mice and humans by degrading endogenous cytosolic DNA, which otherwise triggers activation of the innate cGAS/STING pathway leading to the production of type I IFNs. As tumor cells are prone to aberrant cytosolic DNA accumulation, we hypothesized that they are critically dependent on TREX1 activity to limit their immunogenicity. Here, we show that in tumor cells, TREX1 restricts spontaneous activation of the cGAS/STING pathway, and the subsequent induction of a type I IFN response. As a result, TREX1 deficiency compromised in vivo tumor growth in mice. This delay in tumor growth depended on a functional immune system, systemic type I IFN signaling, and tumor-intrinsic cGAS expression. Mechanistically, we show that tumor TREX1 loss drove activation of CD8+ T cells and NK cells, prevented CD8+ T-cell exhaustion, and remodeled an immunosuppressive myeloid compartment. Consequently, TREX1 deficiency combined with T-cell-directed immune checkpoint blockade. Collectively, we conclude that TREX1 is essential to limit tumor immunogenicity, and that targeting this innate immune checkpoint remodels the tumor microenvironment and enhances antitumor immunity by itself and in combination with T-cell-targeted therapies. See related article by Toufektchan et al., p. 673.


Subject(s)
Exodeoxyribonucleases , Immunity, Innate , Membrane Proteins , Nucleotidyltransferases , Phosphoproteins , Exodeoxyribonucleases/genetics , Exodeoxyribonucleases/metabolism , Animals , Nucleotidyltransferases/metabolism , Nucleotidyltransferases/genetics , Phosphoproteins/metabolism , Phosphoproteins/genetics , Mice , Membrane Proteins/metabolism , Membrane Proteins/genetics , Humans , Neoplasms/immunology , Neoplasms/metabolism , Neoplasms/genetics , Interferon Type I/metabolism , Mice, Knockout , Mice, Inbred C57BL , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Cell Line, Tumor , Signal Transduction , Immune Checkpoint Inhibitors/pharmacology , Immune Checkpoint Inhibitors/therapeutic use
17.
J Biol Chem ; 300(3): 105708, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38311177

ABSTRACT

A DNA double-strand break (DSB) is one of the most dangerous types of DNA damage that is repaired largely by homologous recombination or nonhomologous end-joining (NHEJ). The interplay of repair factors at the break directs which pathway is used, and a subset of these factors also function in more mutagenic alternative (alt) repair pathways. Resection is a key event in repair pathway choice and extensive resection, which is a hallmark of homologous recombination, and it is mediated by two nucleases, Exo1 and Dna2. We observed differences in resection and repair outcomes in cells harboring nuclease-dead dna2-1 compared with dna2Δ pif1-m2 that could be attributed to the level of Exo1 recovered at DSBs. Cells harboring dna2-1 showed reduced Exo1 localization, increased NHEJ, and a greater resection defect compared with cells where DNA2 was deleted. Both the resection defect and the increased rate of NHEJ in dna2-1 mutants were reversed upon deletion of KU70 or ectopic expression of Exo1. By contrast, when DNA2 was deleted, Exo1 and Ku70 recovery levels did not change; however, Nej1 increased as did the frequency of alt-end joining/microhomology-mediated end-joining repair. Our findings demonstrate that decreased Exo1 at DSBs contributed to the resection defect in cells expressing inactive Dna2 and highlight the complexity of understanding how functionally redundant factors are regulated in vivo to promote genome stability.


Subject(s)
DNA Breaks, Double-Stranded , DNA End-Joining Repair , DNA Helicases , DNA-Binding Proteins , Exodeoxyribonucleases , Saccharomyces cerevisiae Proteins , DNA Helicases/genetics , DNA Helicases/metabolism , DNA-Binding Proteins/metabolism , Exodeoxyribonucleases/genetics , Exodeoxyribonucleases/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism
18.
Nucleic Acids Res ; 52(7): 3722-3739, 2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38321948

ABSTRACT

Telomeres protect chromosome ends and are distinguished from DNA double-strand breaks (DSBs) by means of a specialized chromatin composed of DNA repeats bound by a multiprotein complex called shelterin. We investigated the role of telomere-associated proteins in establishing end-protection by studying viable mutants lacking these proteins. Mutants were studied using a Schizosaccharomyces pombe model system that induces cutting of a 'proto-telomere' bearing telomere repeats to rapidly form a new stable chromosomal end, in contrast to the rapid degradation of a control DSB. Cells lacking the telomere-associated proteins Taz1, Rap1, Poz1 or Rif1 formed a chromosome end that was stable. Surprisingly, cells lacking Ccq1, or impaired for recruiting Ccq1 to the telomere, converted the cleaved proto-telomere to a rapidly degraded DSB. Ccq1 recruits telomerase, establishes heterochromatin and affects DNA damage checkpoint activation; however, these functions were separable from protection of the new telomere by Ccq1. In cells lacking Ccq1, telomere degradation was greatly reduced by eliminating the nuclease activity of Mre11 (part of the Mre11-Rad50-Nbs1/Xrs2 DSB processing complex), and higher amounts of nuclease-deficient Mre11 associated with the new telomere. These results demonstrate a novel function for S. pombe Ccq1 to effect end-protection by restraining Mre11-dependent degradation of the DNA end.


Subject(s)
DNA Breaks, Double-Stranded , Schizosaccharomyces pombe Proteins , Schizosaccharomyces , Telomere-Binding Proteins , Telomere , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Telomere-Binding Proteins/metabolism , Telomere-Binding Proteins/genetics , Telomere/metabolism , Telomere/genetics , Shelterin Complex/metabolism , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Exodeoxyribonucleases/metabolism , Exodeoxyribonucleases/genetics , Telomerase/metabolism , Telomerase/genetics , Mutation , MRE11 Homologue Protein/metabolism , MRE11 Homologue Protein/genetics
19.
Nucleic Acids Res ; 52(8): 4328-4343, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38407383

ABSTRACT

Meiotic recombination is of central importance for the proper segregation of homologous chromosomes, but also for creating genetic diversity. It is initiated by the formation of double-strand breaks (DSBs) in DNA catalysed by evolutionarily conserved Spo11, together with additional protein partners. Difficulties in purifying the Spo11 protein have limited the characterization of its biochemical properties and of its interactions with other DSB proteins. In this study, we have purified fragments of Spo11 and show for the first time that Spo11 can physically interact with Mre11 and modulates its DNA binding, bridging, and nuclease activities. The interaction of Mre11 with Spo11 requires its far C-terminal region, which is in line with the severe meiotic phenotypes of various mre11 mutations located at the C-terminus. Moreover, calibrated ChIP for Mre11 shows that Spo11 promotes Mre11 recruitment to chromatin, independent of DSB formation. A mutant deficient in Spo11 interaction severely reduces the association of Mre11 with meiotic chromatin. Consistent with the reduction of Mre11 foci in this mutant, it strongly impedes DSB formation, leading to spore death. Our data provide evidence that physical interaction between Spo11 and Mre11, together with end-bridging, promote normal recruitment of Mre11 to hotspots and DSB formation.


Subject(s)
Chromatin , DNA Breaks, Double-Stranded , Endodeoxyribonucleases , Meiosis , Saccharomyces cerevisiae Proteins , Chromatin/metabolism , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Endodeoxyribonucleases/metabolism , Endodeoxyribonucleases/genetics , Exodeoxyribonucleases/metabolism , Exodeoxyribonucleases/genetics , Meiosis/genetics , Mutation , Protein Binding , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics
20.
Cancer Immunol Res ; 12(6): 673-686, 2024 Jun 04.
Article in English | MEDLINE | ID: mdl-38408184

ABSTRACT

Chromosomal instability is a hallmark of human cancer that is associated with aggressive disease characteristics. Chromosome mis-segregations help fuel natural selection, but they risk provoking a cGAS-STING immune response through the accumulation of cytosolic DNA. The mechanisms of how tumors benefit from chromosomal instability while mitigating associated risks, such as enhanced immune surveillance, are poorly understood. Here, we identify cGAS-STING-dependent upregulation of the nuclease TREX1 as an adaptive, negative feedback mechanism that promotes immune evasion through digestion of cytosolic DNA. TREX1 loss diminishes tumor growth, prolongs survival of host animals, increases tumor immune infiltration, and potentiates response to immune checkpoint blockade selectively in tumors capable of mounting a type I IFN response downstream of STING. Together, these data demonstrate that TREX1 induction shields chromosomally unstable tumors from immune surveillance by dampening type I IFN production and suggest that TREX1 inhibitors might be used to selectively target tumors that have retained the inherent ability to mount an IFN response downstream of STING. See related article by Lim et al., p. 663.


Subject(s)
Exodeoxyribonucleases , Interferon Type I , Phosphoproteins , Exodeoxyribonucleases/genetics , Exodeoxyribonucleases/metabolism , Interferon Type I/metabolism , Phosphoproteins/metabolism , Phosphoproteins/genetics , Animals , Humans , Mice , Neoplasms/immunology , Neoplasms/genetics , Immune Evasion , Cell Line, Tumor , Nucleotidyltransferases/metabolism , Nucleotidyltransferases/genetics , Membrane Proteins/genetics , Membrane Proteins/metabolism , Mice, Inbred C57BL , Mice, Knockout , Tumor Escape
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