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Thrombosis Research May 2022The hypercoagulable state associated with malignancy is well described. However, the mechanisms by which tumors cause this hypercoagulable state are yet to be fully... (Review)
Review
The hypercoagulable state associated with malignancy is well described. However, the mechanisms by which tumors cause this hypercoagulable state are yet to be fully understood. This review summarizes the available literature of human and animal studies examining NETs and cancer-associated thrombosis. The methods for detecting and quantifying NET formation are growing but are not yet standardized in practice. Furthermore, it is important to distinguish between measuring neutrophil activation and NET formation, as the former can be present without the latter. Citrullination of histones by peptidylarginine deiminase 4 (PAD4) is considered one of the key pathways leading to NET formation. Cancer cells can prime neutrophils toward NET formation through the release of soluble mediators, such as interleukin-8, and activation of platelets, and may cause excess NET formation. Dismantling NETs through exogenous deoxyribonuclease has been shown to degrade NETs and reduce thrombus formation in vitro but may simultaneously release prothrombotic NET components, such as DNA and histones. Inhibiting PAD4 is far from clinical trials, but animal models show promising results with a potentially favorable safety profile. Interestingly, results from animal studies suggest that several therapies approved for other indications, such as interleukin-1 receptor blockade and JAK inhibition, may mitigate excessive NET formation or the prothrombotic effects of NETs in cancer. It is yet to be determined if inhibition of NET formation reduces cancer-associated thrombosis also in the clinical setting.
Topics: Animals; DNA; Deoxyribonucleases; Extracellular Traps; Histones; Humans; Interleukin-8; Neoplasms; Neutrophils; Protein-Arginine Deiminases; Receptors, Interleukin-1; Thrombophilia; Thrombosis
PubMed: 36210559
DOI: 10.1016/j.thromres.2021.12.018 -
Nature Jan 2024Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation. Gabija is one of the most prevalent anti-phage...
Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation. Gabija is one of the most prevalent anti-phage defence systems, occurring in more than 15% of all sequenced bacterial and archaeal genomes, but the molecular basis of how Gabija defends cells from viral infection remains poorly understood. Here we use X-ray crystallography and cryo-electron microscopy (cryo-EM) to define how Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA. Gabija protein A (GajA) is a DNA endonuclease that tetramerizes to form the core of the anti-phage defence complex. Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo. We show that a phage-encoded protein, Gabija anti-defence 1 (Gad1), directly binds to the Gabija GajAB complex and inactivates defence. A cryo-EM structure of the virally inhibited state shows that Gad1 forms an octameric web that encases the GajAB complex and inhibits DNA recognition and cleavage. Our results reveal the structural basis of assembly of the Gabija anti-phage defence complex and define a unique mechanism of viral immune evasion.
Topics: Bacteria; Bacterial Proteins; Bacteriophages; Cryoelectron Microscopy; Crystallography, X-Ray; Deoxyribonucleases; DNA, Viral; Immune Evasion; Protein Multimerization
PubMed: 37992757
DOI: 10.1038/s41586-023-06855-2 -
Virulence 2015
Topics: Aeromonas hydrophila; Animals; Deoxyribonucleases; Female; Fishes; Gram-Negative Bacterial Infections; Virulence Factors
PubMed: 26055576
DOI: 10.1080/21505594.2015.1058479 -
Developmental Biology Sep 2017DNA degradation is critical to healthy organism development and survival. Two nuclease families that play key roles in development and in disease are the Dnase1 and... (Review)
Review
DNA degradation is critical to healthy organism development and survival. Two nuclease families that play key roles in development and in disease are the Dnase1 and Dnase2 families. While these two families were initially characterized by biochemical function, it is now clear that multiple enzymes in each family perform similar, non-redundant roles in many different tissues. Most Dnase1 and Dnase2 family members are poorly characterized, yet their elimination can lead to a wide range of diseases, including lethal anemia, parakeratosis, cataracts and systemic lupus erythematosus. Therefore, understanding these enzyme families represents a critical field of emerging research. This review explores what is currently known about Dnase1 and Dnase2 family members, highlighting important questions about the structure and function of family members, and how their absence translates to disease.
Topics: Animals; Deoxyribonucleases; Disease; Health; Humans; Organ Specificity
PubMed: 28666955
DOI: 10.1016/j.ydbio.2017.06.028 -
Cells Oct 2021Neutrophil extracellular traps (NETs) are macromolecular structures programmed to trap circulating bacteria and viruses. The accumulation of NETs in the circulation... (Review)
Review
Neutrophil extracellular traps (NETs) are macromolecular structures programmed to trap circulating bacteria and viruses. The accumulation of NETs in the circulation correlates with the formation of anti-double-stranded (ds) DNA antibodies and is considered a causative factor for systemic lupus erythematosus (SLE). The digestion of DNA by DNase1 and DNases1L3 is the rate- limiting factor for NET accumulation. Mutations occurring in one of these two DNase genes determine anti-DNA formation and are associated with severe Lupus-like syndromes and lupus nephritis (LN). A second mechanism that may lead to DNase functional impairment is the presence of circulating DNase inhibitors in patients with low DNase activity, or the generation of anti-DNase antibodies. This phenomenon has been described in a relevant number of patients with SLE and may represent an important mechanism determining autoimmunity flares. On the basis of the reviewed studies, it is tempting to suppose that the blockade or selective depletion of anti-DNase autoantibodies could represent a potential novel therapeutic approach to prevent or halt SLE and LN. In general, strategies aimed at reducing NET formation might have a similar impact on the progression of SLE and LN.
Topics: Animals; Antibodies; Autoimmunity; DNA; Deoxyribonucleases; Extracellular Traps; Humans; Mutation
PubMed: 34685647
DOI: 10.3390/cells10102667 -
Methods in Molecular Biology (Clifton,... 2021Technology advance during the past decade has greatly expanded our understanding of the higher-order structure of the genome. The various chromosome conformation capture...
Technology advance during the past decade has greatly expanded our understanding of the higher-order structure of the genome. The various chromosome conformation capture (3C)-based techniques such as Hi-C have provided the most widely used tools for interrogating three-dimensional (3D) genome organization. We recently developed a Hi-C variant, DNase Hi-C, for characterizing 3D genome organization. DNase Hi-C employs DNase I for chromatin fragmentation, aiming to overcome restriction enzyme digestion-related limitations associated with traditional Hi-C methods. By combining DNase Hi-C with DNA capture technology, we further implemented a high-throughput approach, called targeted DNase Hi-C, which enables to map fine-scale chromatin architecture at exceptionally high resolution and thereby is an ideal tool for mapping the physical landscapes of cis-regulatory networks and for characterizing phenotype-associated chromatin 3D signatures. Here, I describe a detailed protocol of targeted DNase Hi-C library preparation, which covers experimental steps starting from cell cross-linking to library amplification.
Topics: Chromatin; Chromosomes; Deoxyribonucleases; Genome; Saccharomyces cerevisiae
PubMed: 32820399
DOI: 10.1007/978-1-0716-0664-3_5 -
Nucleic Acids Research Jun 2018Protein engineering is used to generate novel protein folds and assemblages, to impart new properties and functions onto existing proteins, and to enhance our... (Review)
Review
Protein engineering is used to generate novel protein folds and assemblages, to impart new properties and functions onto existing proteins, and to enhance our understanding of principles that govern protein structure. While such approaches can be employed to reprogram protein-protein interactions, modifying protein-DNA interactions is more difficult. This may be related to the structural features of protein-DNA interfaces, which display more charged groups, directional hydrogen bonds, ordered solvent molecules and counterions than comparable protein interfaces. Nevertheless, progress has been made in the redesign of protein-DNA specificity, much of it driven by the development of engineered enzymes for genome modification. Here, we summarize the creation of novel DNA specificities for zinc finger proteins, meganucleases, TAL effectors, recombinases and restriction endonucleases. The ease of re-engineering each system is related both to the modularity of the protein and the extent to which the proteins have evolved to be capable of readily modifying their recognition specificities in response to natural selection. The development of engineered DNA binding proteins that display an ideal combination of activity, specificity, deliverability, and outcomes is not a fully solved problem, however each of the current platforms offers unique advantages, offset by behaviors and properties requiring further study and development.
Topics: Base Pairing; DNA; DNA Cleavage; DNA Restriction Enzymes; DNA-Binding Proteins; Deoxyribonucleases; Gene Editing; Protein Engineering; Recombinant Proteins; Recombinases; Transcription Activator-Like Effectors; Zinc Fingers
PubMed: 29718463
DOI: 10.1093/nar/gky289 -
Current Opinion in Immunology Dec 2018High-affinity antibodies to double-stranded DNA are a hallmark of systemic lupus erythematosus (SLE) and are thought to contribute to disease flares and tissue... (Review)
Review
High-affinity antibodies to double-stranded DNA are a hallmark of systemic lupus erythematosus (SLE) and are thought to contribute to disease flares and tissue inflammation such as nephritis. Notwithstanding their clinical importance, major questions remain about the development and regulation of these pathogenic anti-DNA responses. These include the mechanisms that prevent anti-DNA responses in healthy subjects, despite the constant generation of self-DNA and the abundance of DNA-reactive B cells; the nature and physical form of antigenic DNA in SLE; the regulation of DNA availability as an antigen; and potential therapeutic strategies targeting the pathogenic DNA in SLE. This review summarizes current progress in these directions, focusing on the role of secreted DNases in the regulation of antigenic extracellular DNA.
Topics: Autoantigens; DNA; Deoxyribonucleases; Humans; Lupus Erythematosus, Systemic
PubMed: 30261321
DOI: 10.1016/j.coi.2018.09.009 -
The FEBS Journal Apr 2017Organismal development and function requires multiple and accurate signal transduction pathways to ensure that proper balance between cell proliferation,... (Review)
Review
Organismal development and function requires multiple and accurate signal transduction pathways to ensure that proper balance between cell proliferation, differentiation, inactivation, and death is achieved. Cell death via apoptotic caspase signal transduction is extensively characterized and integral to this balance. Importantly, the view of apoptotic signal transduction has expanded over the previous decades. Subapoptotic caspase signaling has surfaced as mechanism that can promote the adoption of a range of cellular fates. An emerging mechanism of subapoptotic caspase signaling is the activation of the caspase-activated DNase (CAD) through controlled cleavage of the inhibitor of CAD (ICAD). CAD-induced DNA breaks incite a DNA damage response, frequently invoking p53 signaling, that transduces a change in cell fate. Cell differentiation and senescence are fates demonstrated to arise from CAD-induced DNA breaks. Furthermore, an apparent consequence of CAD activity is also emerging, as a potential source of oncogenic mutations. This review will discuss the mechanisms underlying CAD-induced DNA breaks and highlight how CAD activity promotes diverse cell fates.
Topics: Animals; Apoptosis; Caspases; Cell Lineage; DNA Damage; DNA Repair; Deoxyribonucleases; Humans; Neoplasms
PubMed: 27865056
DOI: 10.1111/febs.13970 -
Microbiology (Reading, England) Mar 2018DNases are abundant among the pathogenic streptococci, with most species harbouring genes for at least one. Despite their prevalence, however, the role for these... (Review)
Review
DNases are abundant among the pathogenic streptococci, with most species harbouring genes for at least one. Despite their prevalence, however, the role for these extracellular enzymes is still relatively unclear. The DNases of the Lancefield group A Streptococcus, S. pyogenes are the best characterized, with a total of eight DNase genes identified so far. Six are known to be associated with integrated prophages. Two are chromosomally encoded, and one of these is cell-wall anchored. Homologues of both prophage-associated and chromosomally encoded S. pyogenes DNases have been identified in other streptococcal species, as well as other unique DNases. A major role identified for streptococcal DNases appears to be in the destruction of extracellular traps produced by immune cells, such as neutrophils, to ensnare bacteria and kill them. These traps are composed primarily of DNA which can be degraded by the secreted and cell-wall-anchored streptococcal DNases. DNases can also reduce TLR-9 signalling to dampen the immune response and produce cytotoxic deoxyadenosine to limit phagocytosis. Upper respiratory tract infection models of S. pyogenes have identified a role for DNases in potentiating infection and transmission, possibly by limiting the immune response or through some other unknown mechanism. Streptococcal DNases may also be involved in interacting with other microbial communities through communication, bacterial killing and disruption of competitive biofilms, or control of their own biofilm production. The contribution of DNases to pathogenesis may therefore be wide ranging and extend beyond direct interference with the host immune response.
Topics: Bacterial Proteins; Deoxyribonucleases; Extracellular Traps; Host-Pathogen Interactions; Humans; Immune Evasion; Microbial Interactions; Prophages; Streptococcal Infections; Streptococcus pyogenes
PubMed: 29458565
DOI: 10.1099/mic.0.000612