New Noncoding Base Pair Mutation at the Identical Locus as the Original NCMD/MCDR1 in a Mexican Family, Suggesting a Mutational Hotspot.

Purpose: To clinically and molecularly study a newly found family with North Carolina macular dystrophy (NCMD/MCDR1) from Mexico. Methods: This retrospective study comprised 6 members of a 3-generation Mexican family with NCMD. Clinical ophthalmic examinations, including fundus imaging, spectral-domain optical coherence tomography, electroretinography, and electrooculography, were performed. Genotyping with polymorphic markers in the MCDR1 region was performed to determine haplotypes. Whole-genome sequencing (WGS) was performed followed by variant filtering and copy number variant analysis. Results: Four subjects from 3 generations were found to have macular abnormalities. The proband presented with lifelong bilateral vision impairment with bilaterally symmetric vitelliform Best disease-like appearing macular lesions. Her 2 children had bilateral large macular coloboma-like malformations, consistent with autosomal dominant NCMD. The 80-year-old mother of the proband had drusen-like lesions consistent with grade 1 NCMD. WGS and subsequent Sanger sequencing found a point mutation at chr6:99593030G>C (hg38) in the noncoding region of the DNase I site thought to be a regulatory element of the retinal transcription factor gene PRDM13. This mutation is the identical site/nucleotide as in the original NCMD family (#765) but is a guanine to cytosine change rather than a guanine to thymine mutation, as found in the original NCMD family. Conclusions: We report a new noncoding mutation at the same locus (chr6:99593030G>C) involving the same DNase I site regulating the retinal transcription factor gene PRDM13. This suggests that this site, chr6:99593030, is a mutational hotspot.

Heterologous extracellular DNA facilitates the development of Trichosporon asahii and T. inkin biofilms and enhances their tolerance to antifungals.

Trichosporon asahii and T. inkin are emergent agents of deep-seated and disseminated infections in immunocompromised patients. The present study aimed to investigate the role of extracellular DNA (eDNA) and the enzyme deoxyribonuclease (DNase) on the structure of T. asahii and T. inkin biofilms, as well as to examine their effect on the susceptibility to antifungals. Biofilms reached maturity at 48 h; eDNA concentration in the supernatant increased over time (6 < 24 h < 48h). Exogenous eDNA increased biomass of Trichosporon biofilms at all stages of development, enhanced their tolerance to antifungals and improved their structural complexity. DNase reduced biomass, biovolume and thickness of Trichosporon biofilms, thereby rendering them more susceptibility to voriconazole. The results suggest the relevance of eDNA in the structure and antifungal susceptibility of Trichosporon biofilms and highlight the potential of DNase as adjuvant in biofilm control.

Trichomonas vaginalis triggers neutrophil extracellular traps reducing parasite integrity and growth.

Trichomoniasis-caused by the parasite Trichomonas vaginalis-is associated with a high inflammatory process that may contribute to the risk of suffering from other medical complications. Our study focused on the in vitro interaction of T. vaginalis with human neutrophils because these are the most abundant cells implicated in the characteristic inflammatory process of trichomoniasis. This study showed that T. vaginalis and its surface glycoconjugates (lipophosphoglycan and/or lipoglycan) induced the formation of human neutrophil extracellular traps (NETs). After the trichomonad-neutrophil interaction, parasite integrity was at 32.9%, and the subsequent parasite growth was at 35.2% compared to those of control trophozoites (100%) incubated under the same conditions without neutrophils. In the presence of an antibody against the TLR-4 receptor, DNase I or micrococcal nuclease (MNase), neutrophils reduced the DNA fibres of the NETs and the amount of extracellular DNA, allowing a higher subsequent growth of T. vaginalis, at 52% with the anti-TLR-4 antibody and 62.6% with the enzymes. These results indicated that T. vaginalis induced the formation of extracellular traps by human neutrophils and, because of the interaction with neutrophils and NETs, parasite integrity and growth decreased.

Neutrophil Extracellular Traps Contribute to COVID-19 Hyperinflammation and Humoral Autoimmunity.

The coronavirus disease 2019 (COVID-19) is related to enhanced production of NETs, and autoimmune/autoinflammatory phenomena. We evaluated the proportion of low-density granulocytes (LDG) by flow cytometry, and their capacity to produce NETs was compared with that of conventional neutrophils. NETs and their protein cargo were quantified by confocal microscopy and ELISA. Antinuclear antibodies (ANA), anti-neutrophil cytoplasmic antibodies (ANCA) and the degradation capacity of NETs were addressed in serum. MILLIPLEX assay was used to assess the cytokine levels in macrophages' supernatant and serum. We found a higher proportion of LDG in severe and critical COVID-19 which correlated with severity and inflammatory markers. Severe/critical COVID-19 patients had higher plasmatic NE, LL-37 and HMGB1-DNA complexes, whilst ISG-15-DNA complexes were lower in severe patients. Sera from severe/critical COVID-19 patients had lower degradation capacity of NETs, which was reverted after adding hrDNase. Anti-NET antibodies were found in COVID-19, which correlated with ANA and ANCA positivity. NET stimuli enhanced the secretion of cytokines in macrophages. This study unveils the role of COVID-19 NETs as inducers of pro-inflammatory and autoimmune responses. The deficient degradation capacity of NETs may contribute to the accumulation of these structures and anti-NET antibodies are related to the presence of autoantibodies.

Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks.

Chromatin accessibility is directly linked with transcription in eukaryotes. Accessible regions associated with regulatory proteins are highly sensitive to DNase I digestion and are termed DNase I hypersensitive sites (DHSs). DHSs can be identified by DNase I digestion, followed by high-throughput DNA sequencing (DNase-seq). The single-base-pair resolution digestion patterns from DNase-seq allows identifying transcription factor (TF) footprints of local DNA protection that predict TF-DNA binding. The identification of differential footprinting between two conditions allows mapping relevant TF regulatory interactions. Here, we provide step-by-step instructions to build gene regulatory networks from DNase-seq data. Our pipeline includes steps for DHSs calling, identification of differential TF footprints between treatment and control conditions, and construction of gene regulatory networks. Even though the data we used in this example was obtained from Arabidopsis thaliana, the workflow developed in this guide can be adapted to work with DNase-seq data from any organism with a sequenced genome.

Recombinant human DNase I for the treatment of cancer-associated thrombosis: A pre-clinical study.

Cancer patients are more likely to develop thrombosis, and this co-morbidity is related to the worse prognosis of the disease. The increased formation of neutrophil extracellular traps (NETs) has been proposed as one of the mechanisms to explain cancer-associated thrombosis. In vivo, degradation of NETs with recombinant human DNase I (rhDNase I) prevents thrombus formation in mouse models. In this work, we evaluated the effect of two different chronic treatments with rhDNase I in a murine NET-dependent prothrombotic state in breast cancer model. Medium-term treatment (2.5 mg/kg rhDNase I for eight consecutive days) did not interfere with the primary growth of 4T1 tumors. On the other hand, it effectively prevented thrombus formation in the inferior vena cava stenosis model. Remarkably, medium-term treatment with rhDNase I showed minor impact in the tail-bleeding model. Different from the medium-term, the long-term treatment with rhDNase I (2.5 mg/kg for 18 successive days) drastically reduced the overall survival. Remarkably, the concomitant use of Ertapenem, a carbapenem antibiotic, and rhDNase I significantly attenuated the mortality observed in the long-term treatment. Our results suggest the therapeutic potential of rhDNase I to treat cancer-associated thrombosis, although its chronic use should be carefully evaluated and potentially harmful.

Paracoccidioides brasiliensis Releases a DNase-Like Protein That Degrades NETs and Allows for Fungal Escape.

Paracoccidioidomycosis is a systemic fungal disease, considered endemic in Latin America. Its etiological agents, fungi of the Paracoccidioides complex, have restricted geographic habitat, conidia as infecting form, and thermo-dimorphic characteristics. Polymorphonuclear neutrophils (PMNs) are responsible for an important defense response against fungus, releasing Neutrophil Extracellular Traps (NETs), which can wrap and destroy the yeasts. However, it has been described that some pathogens are able to evade from these DNA structures by releasing DNase as an escape mechanism. As different NETs patterns have been identified in PMNs cultures challenged with different isolates of Paracoccidioides brasiliensis, the general objective of this study was to identify if different patterns of NETs released by human PMNs challenged with Pb18 (virulent) and Pb265 (avirulent) isolates would be correlated with fungal ability to produce a DNase-like protein. To this end, PMNs from healthy subjects were isolated and challenged in vitro with both fungal isolates. The production, release, and conformation of NETs in response to the fungi were evaluated by Confocal Microscopy, Scanning Microscopy, and NETs Quantification. The identification of fungal DNase production was assessed by DNase TEST Agar, and the relative gene expression for hypothetical proteins was investigated by RT-qPCR, whose genes had been identified in the fungal genome in the GenBank (PADG_11161 and PADG_08285). It was possible to verify the NETs release by PMNs, showing different NETs formation when in contact with different isolates of the fungus. The Pb18 isolate induced the release of looser, larger, and more looking like degraded NETs compared to the Pb265 isolate, which induced the release of denser and more compact NETs. DNase TEST Agar identified the production of a DNase-like protein, showing that only Pb18 showed the capacity to degrade DNA in these plates. Besides that, we were able to identify that both PADG_08528 and PADG_11161 genes were more expressed during interaction with neutrophil by the virulent isolate, being PADG_08528 highly expressed in these cultures, demonstrating that this gene could have a greater contribution to the production of the protein. Thus, we identified that the virulent isolate is inducing more scattered and loose NETs, probably by releasing a DNase-like protein. This factor could be an important escape mechanism used by the fungus to escape the NETs action.

Lactoferrin Disaggregates Pneumococcal Biofilms and Inhibits Acquisition of Resistance Through Its DNase Activity.

Streptococcus pneumoniae colonizes the upper airways of children and the elderly. Colonization progresses to persistent carriage when S. pneumoniae forms biofilms, a feature required for the development of pneumococcal disease. Nasopharyngeal biofilms are structured with a matrix that includes extracellular DNA (eDNA), which is sourced from the same pneumococci and other bacteria. This eDNA also allows pneumococci to acquire new traits, including antibiotic resistance genes. In this study, we investigated the efficacy of lactoferrin (LF), at physiological concentrations found in secretions with bactericidal activity [i.e., colostrum (100 µM), tears (25 µM)], in eradicating pneumococcal biofilms from human respiratory cells. The efficacy of synthetic LF-derived peptides was also assessed. We first demonstrated that LF inhibited colonization of S. pneumoniae on human respiratory cells without affecting the viability of planktonic bacteria. LF-derived peptides were, however, bactericidal for planktonic pneumococci but they did not affect viability of pre-formed biofilms. In contrast, LF (40 and 80 µM) eradicated pneumococcal biofilms that had been pre-formed on abiotic surfaces (i.e., polystyrene) and on human pharyngeal cells, as investigated by viable counts and confocal microscopy. LF also eradicated biofilms formed by S. pneumoniae strains with resistance to multiple antibiotics. We investigated whether treatment with LF would affect the biofilm structure by analyzing eDNA. Surprisingly, in pneumococcal biofilms treated with LF, the eDNA was absent in comparison to the untreated control (∼10 µg/ml) or those treated with LF-derived peptides. EMSA assays showed that LF binds S. pneumoniae DNA and a time-course study of DNA decay demonstrated that the DNA is degraded when bound by LF. This LF-associated DNase activity inhibited acquisition of antibiotic resistance genes in both in vitro transformation assays and in a life-like bioreactor system. In conclusion, we demonstrated that LF eradicates pneumococcal-colonizing biofilms at a concentration safe for humans and identified a LF-associated DNAse activity that inhibited the acquisition of resistance.

Alteplase and DNase for the treatment of pleural empyema in rats.

BACKGROUND AND OBJECTIVES: Adjunctive intrapleural fibrinolytic is an option to treat empyema at fibrinopurulent stage, but there is controversy about which should be use. Our objective is to evaluate the action of alteplase and/or desoxyribonuclease at physical and chemical properties in vitro pus derived from an experimental induced empyema in rats. METHODS: Streptococcus pneumoniae was introduced into the pleural cavity by thoracentesis through pleural pressure monitor. Animals were euthanized after 24 h, with macroscopic thoracic evaluation and measurement of amount of intrapleural liquid that was posteriorly stored at -80 °C. Selected samples were randomly distributed into four groups, then thawed at room temperature before exposure to one of the following: G1 = alteplase (n = 12), G2 = DNase (n = 12), G3 = alteplase + DNase (n = 12), or G4 = saline (n = 6). The mean molecular size in the fluid portion of the empyema was evaluated using dynamic light scattering; viscosity of the empyema fluid was measured using the drip method. RESULTS: Macroscopic showed purulent liquid, with fibrin and septation, with mean volume of 4.16 ml (0.5-8 ml). All samples were culture-positive for Streptococcus pneumoniae. Comparing with control, all experimental groups presented reduction of larger than 135 nm molecular size, but there was only significant difference with alteplase (p = 0,02). Viscosity reduced at all experimental groups, but increased at control. DNase group presented negative median (-5 mPa/s) of viscosity, and differed significantly from that observed in the control group (p = 0.04). CONCLUSIONS: Alteplase, DNase and alteplase + DNase changed significantly physical and chemical properties of experimental empyema at fibrinopurulent phase: alteplase reduced molecular size larger than 135 nm and DNase reduced viscosity.

Detection of Potential Infectious Enteric Viruses in Fresh Produce by (RT)-qPCR Preceded by Nuclease Treatment.

Foodborne illnesses associated with contaminated fresh produce are a common public health problem and there is an upward trend of outbreaks caused by enteric viruses, especially human noroviruses (HNoVs) and hepatitis A virus (HAV). This study aimed to assess the use of DNase and RNase coupled to qPCR and RT-qPCR, respectively, to detect intact particles of human adenoviruses (HAdVs), HNoV GI and GII and HAV in fresh produce. Different concentrations of DNase and RNase were tested to optimize the degradation of free DNA and RNA from inactivated HAdV and murine norovirus (MNV), respectively. Results indicated that 10 µg/ml of RNase was able to degrade more than 4 log10 (99.99%) of free RNA, and 1 U of DNase degraded the range of 0.84-2.5 log10 of free DNA depending on the fresh produce analysed. The treatment with nucleases coupled to (RT)-qPCR was applied to detect potential infectious virus in organic lettuce, green onions and strawberries collected in different seasons. As a result, no intact particles of HNoV GI and GII were detected in the 36 samples analysed, HAdV was found in one sample and HAV was present in 33.3% of the samples, without any reasonable distribution pattern among seasons. In conclusion, RT-qPCR preceded by RNase treatment of eluted samples from fresh produce is a good alternative to detect undamaged RNA viruses and therefore, potential infectious viruses. Moreover, this study provides data about the prevalence of enteric viruses in organic fresh produce from Brazil.

Antitumor Effects of Systemic DNAse I and Proteases in an In Vivo Model.

Background Cell-free DNA circulates in cancer patients and induces in vivo cell transformation and cancer progression in susceptible cells. Based on this, we hypothesized that depletion of circulating DNA with DNAse I and a protease mix could have antitumor effects. Study design The study aimed to demonstrate that DNAse I and a protease mix can degrade in vitro DNA and proteins from the serum of healthy individuals and cancer patients, and in vivo in serum of Wistar rats,. Moreover, the antitumor effect of the systemically administered enzyme mix treatmentwas evaluated in nude mice subcutaneously grafted with the human colon cancer cell line SW480. Results The serum DNA of cancer patients or healthy individuals was almost completely degraded in vitro by the enzymatic treatment, but no degradation was found with the enzymes given separately. The intravenous administration of the enzymes led to significant decreases in DNA and proteins from rat serum. No antitumor effect was observed in immunodeficient mice treated with the enzymes given separately. In contrast, the animals that received both enzymes exhibited a marked growth inhibition of tumors, 40% of them having pathological complete response. Conclusion This study demonstrated that systemic treatment with DNAse I and a protease mix in rats decreases DNA and proteins from serum and that this treatment has antitumor effects. Our results support the hypothesis that circulating DNA could have a role in tumor progression, which can be offset by depleting it. Further studies are needed to prove this concept.

Smart lipid nanoparticles containing levofloxacin and DNase for lung delivery. Design and characterization.

Levofloxacin (LV) is a hydrophilic broad-spectrum antibiotic commonly used in pulmonary treatment against recurrent infections of Pseudomonas aeruginosa, and particularly in cystic fibrosis (CF) disease. In order to study feasible carriers for LV, solid lipid nanoparticles (SLN) of myristyl myristate were prepared by the ultrasonication method in the presence of Pluronic(®)F68 under different experimental conditions and characterized by dynamic light scattering, optical, transmission and scanning electron microscopy for size and morphology. Alternatively, nanostructured lipid carriers (NLCs) were developed to improve LV encapsulation and storage. SLN showed 20.1±1.4% LV encapsulation efficiency, while the NLCs encapsulated 55.9±1.6% LV. NLC formulation exhibited a more controlled release profile than SLN formulation, but both showed a biphasic drug release pattern with burst release at the first 5h and prolonged release afterwards, demonstrated by in vitro tests. The hydrodynamic average diameter and zeta potential of NLC were 182.6±3.2nm and -10.2±0.2mV, respectively, and were stable for at least 3 months. Additionally, DNase type I was incorporated into the formulations as a "smart" component, since the enzyme could help to decrease the viscoelasticity found in the lungs of CF patients and improves the antibiotic diffusion. FTIR, XRD, DSC, TGA and nitrogen adsorption isotherms of the nanoparticles indicate the presence of the loads in a noncrystalline state. The developed formulation showed an active antimicrobial activity against P. aeruginosa and even against other opportunistic pathogens such as Staphylococcus aureus. The presence of LV-loaded NLCs reduced the formation of a bacterial biofilm, which highlighted the significance of the nanodevice as a new alternative for CF treatment.

A globally distributed mobile genetic element inhibits natural transformation of Vibrio cholerae.

Natural transformation is one mechanism of horizontal gene transfer (HGT) in Vibrio cholerae, the causative agent of cholera. Recently, it was found that V. cholerae isolates from the Haiti outbreak were poorly transformed by this mechanism. Here, we show that an integrating conjugative element (ICE)-encoded DNase, which we name IdeA, is necessary and sufficient for inhibiting natural transformation of Haiti outbreak strains. We demonstrate that IdeA inhibits this mechanism of HGT in cis via DNA endonuclease activity that is localized to the periplasm. Furthermore, we show that natural transformation between cholera strains in a relevant environmental context is inhibited by IdeA. The ICE encoding IdeA is globally distributed. Therefore, we analyzed the prevalence and role for this ICE in limiting natural transformation of isolates from Bangladesh collected between 2001 and 2011. We found that IdeA(+) ICEs were nearly ubiquitous in isolates from 2001 to 2005; however, their prevalence decreased to ∼40% from 2006 to 2011. Thus, IdeA(+) ICEs may have limited the role of natural transformation in V. cholerae. However, the rise in prevalence of strains lacking IdeA may now increase the role of this conserved mechanism of HGT in the evolution of this pathogen.

Secretion of five extracellular enzymes by strains of chromoblastomycosis agents / Secreção de cinco enzimas extracelulares por amostras de agentes da cromoblastomicose

The gelatinase, urease, lipase, phospholipase and DNase activities of 11 chromoblastomycosis agents constituted by strains of Fonsecaea pedrosoi, F. compacta, Phialophora verrucosa, Cladosporium carrionii, Cladophialophora bantiana and Exophiala jeanselmei were analyzed and compared. All strains presented urease, gelatinase and lipase activity. Phospholipase activity was detected only on five of six strains of F. pedrosoi. DNase activity was not detected on the strains studied. Our results indicate that only phospholipase production, induced by egg yolk substrate, was useful for the differentiation of the taxonomically related species studied, based on their enzymatic profile.

As atividades gelatinase, urease, lipase, fosfolipase e DNase de 11 agentes da cromoblastomicose constituídos por amostras de Fonsecaea pedrosoi, F. compacta, Phialophora verrucosa, Cladosporium carrionii, Cladophialophora bantiana e Exophiala jeanselmei foram analisadas e comparadas. Todas as amostras apresentaram atividade urease, gelatinase e lipase. A atividade fosfolipase foi detectada apenas em cinco das seis amostras de F. pedrosoi. A atividade DNase não foi detectada nas amostras estudadas. Os resultados indicam que para a diferenciação entre espécies taxonomicamente relacionadas estudadas, baseado no seu perfil enzimático, apenas a produção de fosfolipase, induzida pelo substrato com gema de ovo, foi útil.

Desenvolvimento e implementação de métodos laboratoriais aplicados ao diagnóstico fenotípico e genotípico do Corynebacterium diptheriae / Development and implementation of laboratory methods applied to phenotypic and genotypic diagnosis of Corynebacterium diphtheriae

A emergência de cepas de Corynebacterium diphtheriae atoxinogênicas como agentes de endocardite e outras infecções sistêmicas aliada ao aumento do número de adultos susceptíveis à difteria enfatizam a necessidade de métodos alternativos para o diagnóstico laboratorial desta doença, especialmente para laboratórios de rotina clínica. Neste estudo avaliou-se a atividade de DNase de 91 amostras de C. diphtheriae (37 toxinogênicas e 54 atoxinogênicas) e de 564 cepas clínicas de bacilo Gram positivo não diftérico. A atividade de DNase foi detectada em todas as amostras de C. diphtheriae examinadas, previamente identificadas por métodos bioquímicos e pelo sistema API Coryne System. Diferentemente, os resultados do teste de DNase foram negativos em 93.9 porcento das cepas clínicas de bacilo Gram positivo não diftérico. Também foi documentado o valor de uma PCR espécie-específica que tem como alvo o gene dtxR como um método para diferenciação entre C. diphtheriae e colônias similares ao gênero Corynebacterium. Os resultados da PCR-dtxR foram positivos para todas as amostras de C. diphtheriae estudadas e foram concordantes com os obtidos através de metodologia bioquímica padrão. Diferentemente, os resultados da PCR-dtxR foram negativos para 100 porcento das 111 amostras de bacilos Gram positivos não diftéricos estudadas. A partir destes resultados, uma PCR multiplex utilizando três pares de oligonucleotídeos iniciadores foi desenvolvida para a detecção do C. diphtheriae e diferenciação em amostras toxinogênicas ou atoxinogênicas. Dois pares de oligonucleotídeos iniciadores têm como alvo as regiões do gene tox relativas aos domínios A e B da toxina diftérica e um terceiro par direcionado para o gene dtxR. Todas as amostras de C. diphtheriae foram identificadas pela reação de PCR multiplex em concordância com os testes bioquímicos padrão e os ensaios de citotoxicidade celular...

The emergence of non-toxigenic Corynebaterium diphtheriae strains as the causative agent of endocarditis and other systemic infections and the significant rise in the percentage of adults susceptible to diphtheria emphasize the need for new laboratory diagnostic procedures. In this study, we examine techniques as alternative procedures for differentiating C. diphtheriae from Corynebacterium-like colonies for the presumptive identification of this pathogen, especially in the diagnosis laboratory. This study evaluated the DNase activity of 91 C. diphtheriae (37 toxigenic and 54 non-toxigenic) and 564 non-diphtherial Gram-positive rod clinical strains. The DNase activity was detected in all C. diphtheriae strains examined, previously identified by both conventional biochemical methods and API Coryne System. Conversely, DNase test results were negative in 93.9 percent of the 564 non-diphtherial Gram-positive rod clinical strains. We also documented the value of a species-specific PCR assay that targets the dtxR gene as a procedure for differentiating C. diphtheriae from Corynebacterium-like colonies. The results of the PCR-dtxR were all positive for 91 C. diphtheriae strains and completely correlated with the standard biochemical methods and commercial identification system for all strains tested. In other hand, the PCR-dtxR results were negative in 100 percent of the 111 non-diphtherial Gram-positive rod strains. Considering these results, a multiplex PCR using three primers pairs was developed for detection of C. diphtheriae infection and differentiation between toxigenic and non-toxigenic strains. Two primer pairs targeted to domains A and B of tox gene and a third primer pair targeted to a region of dtxR gene. All C. diphtheriae strains were diagnosed by the multiplex PCR in agreement with standard biochemical tests and citotoxicity assay in Vero cells. Thus, these tecniques emerged as viable, cost-effective screening methods for C. diphtheriae laboratory...