Deoxyribonucleic Acid Replication Research Articles

A Comprehensive Review of Analytical Techniques for Quantifying Cyclin‐dependent Kinase 4 and 6 Inhibitors in Biological Samples, Bulk, and Pharmaceutical Samples

ABSTRACTCyclin‐dependent kinase 4 and 6 (CDK4/6) inhibitors are utilized as a remedy for advanced hormone receptor‐positive, HER2‐negative breast cancer (BC). By targeting CDK4/6, these drugs inhibit the phosphorylation of the retinoblastoma protein during the early G1 phase, leading to cell cycle arrest, disruption of deoxyribonucleic acid replication, and effective suppression of cancer cell proliferation. Recently, there has been an increasing focus on the advancement of analytical techniques for the determination of CDK4/6 inhibitors. These analytical methods are essential in the enhancement and refinement of CDK4/6 inhibitors for the management of advanced BC. This review provides a comprehensive overview of the various analytical techniques used for the analysis of palbociclib, ribociclib, and abemaciclib, along with their metabolites in biological fluids (such as blood and urine samples), commercial products, Ringer's solution, and simultaneous estimation. High‐performance liquid chromatography and liquid chromatography‐mass spectrometry are the primary analytical techniques commonly employed for the analysis of CDK4/6 inhibitors. This analytical review also provides insights into pharmacokinetics and stability studies, as well as the use of analytical techniques in detecting impurities and determining the structure of degraded products.

Machine learning-based prediction of DNA G-quadruplex folding topology with G4ShapePredictor

Deoxyribonucleic acid (DNA) is able to form non-canonical four-stranded helical structures with diverse folding patterns known as G-quadruplexes (G4s). G4 topologies are classified based on their relative strand orientation following the 5’ to 3’ phosphate backbone polarity. Broadly, G4 topologies are either parallel (4+0), antiparallel (2+2), or hybrid (3+1). G4s play crucial roles in biological processes such as DNA repair, DNA replication, transcription and have thus emerged as biological targets in drug design. While computational models have been developed to predict G4 formation, there is currently no existing model capable of predicting G4 folding topology based on its nucleic acid sequence. Therefore, we introduce G4ShapePredictor (G4SP), an application featuring a collection of multi-classification machine learning models that are trained on a custom G4 dataset combining entries from existing literature and in-house circular dichroism experiments. G4ShapePredictor is designed to accurately predict G4 folding topologies in potassium (K+\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\hbox {K}^+$$\\end{document}) buffer based on its primary sequence and is able to incorporate a threshold optimization strategy allowing users to maximise precision. Furthermore, we have identified three topological sequence motifs that suggest specific G4 folding topologies of (4+0), (2+2) or (3+1) when utilising the decision-making mechanisms of G4ShapePredictor.

In silico functional analysis of DNA repair proteins (OGG1, MYH) in Arabidopsis thaliana

Deoxyribonucleic acid (DNA) is a hereditary material found in every living organism. However, every organism is exposed to endogenous and exogenous an agent which causes damage to DNA molecules. Even though genetic variation is important for evolution, every organism requires genetic stability for survival. Not only it is needed for DNA to replicate accurately but also several DNA repair mechanisms are used to fix the damage which occurred in DNA. A detailed structure analysis along with docking site and metabolic pathway prediction were used to confirm that these proteins are involved in DNA repair mechanisms. This study investigated OGG1 and MYH proteins from Arabidopsis thaliana, and showed their interaction with predicted partners, focusing on their detailed interactome and 3D structure predictions. This study concluded that OGG1 and MYH are not only found in DNA repair mechanisms but also show strong functions in DNA replication and the development of plant and cell cycle.

Identification of Population-Specific Novel Protein Biomarkers and Possible Therapeutic Targets in Gliomas by Proteomics Approach

Abstract Objective To analyze the differential proteomic profile of gliomas in patients from South India and to identify novel protein glioma biomarkers and possible therapeutic targets to tailor the treatment to individual patients. Material and Methods We have prospectively analyzed the differential proteomic profile of 34 patients with glioma imaging characteristics and compared them with that of normal brain tissue. This research was conducted at the Institute of Neurosurgery, Madras Medical College, in technical collaboration with the Indian Institute of Technology, Madras, over 1 year. Statistical Analysis Biological variate analysis (I-ANALYSIS OF VARIANCE (ANOVA)) was used, with p-value less than 0.05 being significant. Results Twenty proteins (10 upregulated and 10 downregulated) were differentially expressed in tumor tissue. The expression of three pro-apoptotic proteins was downregulated and the expression of three anti-apoptotic proteins was upregulated with statistical significance. The cellular functions of the 20 differentially regulated proteins were subjected to pathway analysis revealing significant alterations in heme biosynthesis, deoxyribonucleic acid (DNA) replication, fibroblast growth factor (FGF) signaling, and epidermal growth factor (EGF0 receptor signaling in glioma. Conclusion KRT18, PRS4, and EF1A2 are anti-apoptotic proteins and are significantly upregulated in gliomas. EARS2, COX5A, and LSM3 are pro-apoptotic proteins, and are significantly downregulated in gliomas. This subverts the apoptotic pathways resulting in prolonged cell survival. This study's statistically significant dysregulation of these six proteins was unique, suggesting that they might be considered population-specific biomarkers and possible therapeutic targets for patients from South India. Abnormalities of heme biosynthesis at the proteomic level were identified in this study, which has not been very well studied previously.

Proofreading exonuclease activity of replicative polymerase epsilon promotes cellular tolerance to arabinosides in CTF18-dependent and -independent manner

Ara-A, Ara-C, Ara-G, and Ara-T are arabinose sugars combined with adenine, cytosine, guanine, and thymine bases, respectively. These drugs are clinically important as these drugs are commonly used as anti-viral and anti-cancer drugs. Ara-C, an arabinoside, serves as a chain terminator of deoxyribonucleic acid (DNA) replication by interfering with replication after it is incorporated at the 3′ end of nascent DNA, thereby restricting the proliferation of viruses and cancer cells. The incorporated Ara-CMP is efficiently removed by the proofreading exonuclease activity of polymerase epsilon (Polε), in which the alternative clamp loader CTF18 plays a pivotal role. However, the requirement of CTF18 for the removal of the other arabinosides from the 3′ end of nascent DNA remains unclear. Here, we explored DNA repair pathways responsible for the cellular tolerance to Ara-A and found that cells deficient in the proofreading exonuclease activity of Polε (POLE1exo−/−) showed the highest sensitivity to Ara-A. This activity was also required for cellular tolerance to Ara-G and Ara-T. CTF18−/− cells showed higher Ara-A sensitivity than wild-type cells, though it was critically lower than that of POLE1exo−/− cells. Similar trends were observed for the sensitivity to Ara-G and Ara-T. These results indicate that these arabinosides are removed by Polε proofreading exonuclease activity, and CTF18 is pivotal for Polε-mediated Ara-C removal but does not play critical roles for Polε-mediated removal of Ara-A, Ara-G, and Ara-T. In this study, we unveiled a difference between Ara-C and the other arabinosides (Ara-A, Ara-G, and Ara-T) in the removal from the 3′ end of nascent DNA.

Computational exploration of allosteric inhibitors targeting CDK4/CDK6 proteins: a promising approach for multi-target drug development

Cyclin-dependent kinases (CDKs) play a pivotal role in orchestrating the intricate regulation of the cell cycle, a fundamental process governing cell growth and division. In particular, CDK4 and CDK6 are critical for the transition from the G1 phase to the S phase, where Deoxyribonucleic acid (DNA) replication occurs, and their dysregulation is linked to various diseases, notably cancer. While ATP-binding site inhibitors for CDKs are well-documented, this study focuses on uncovering allosteric inhibitors, providing a fresh perspective on CDK inhibition. Computational techniques were employed in this investigation, utilizing Molecular Operating Environment (MOE) for virtual screening of a drug-like compound library. Moreover, the stability of the most promising binding inhibitors was assessed through Molecular Dynamics (MD) simulations and MMPBSA/MMGBSA analyses. The outcome reveals that three inhibitors (C1, C2, and C3) exhibited the strongest binding affinity for CDK4/CDK6, as corroborated by docking and simulation analyses. The computed binding energies ranged from −6.1 to −7.6 kcal/mol, underscoring the potency of these allosteric inhibitors. Notably, this study identifies key residues (PHE31, HIS95, HIS100, VAL101, ASP102, ASP104, and THR107) that play pivotal roles in mediating inhibitor binding within the allosteric sites. Among the findings, the C1–CDK4 complex and C2–CDK6 complex emerge as particularly promising inhibitors, exhibiting high binding energies, favorable interaction patterns, and sustained presence within the active site. This study contributes significantly to the pursuit of multi-target drugs against CDK4/CDK6 proteins, with potential implications for the development of innovative therapies across various disorders, including cancer and other cell cycle-related conditions. Communicated by Ramaswamy H. Sarma

Perilipin2 inhibits the replication of hepatitis B virus deoxyribonucleic acid by regulating autophagy under high-fat conditions.

Chronic hepatitis B virus (HBV) infection is often associated with increased lipid deposition in hepatocytes. However, when combined with non-alcoholic fatty liver disease or hyperlipidemia, it tends to have a lower HBV deoxyribonucleic acid (DNA) load. The relationship between lipid metabolism and HBV DNA replication and its underlying mechanisms are not well understood. To investigate the relationship between lipid metabolism and HBV DNA replication and its underlying mechanisms. 1603 HBsAg-seropositive patients were included in the study. We first explored the relationship between patients' lipid levels, hepatic steatosis, and HBV DNA load. Also, we constructed an HBV infection combined with a hepatic steatosis cell model in vitro by fatty acid stimulation of HepG2.2.15 cells to validate the effect of lipid metabolism on HBV DNA replication in vitro. By knocking down and overexpressing Plin2, we observed whether Plin2 regulates autophagy and HBV replication. By inhibiting both Plin2 and cellular autophagy under high lipid stimulation, we examined whether the Plin2-autophagy pathway regulates HBV replication. The results revealed that serum triglyceride levels, high-density lipoprotein levels, and hepatic steatosis ratio were significantly lower in the HBV-DNA high load group. Logistic regression analysis indicated that hepatic steatosis and serum triglyceride levels were negatively correlated with HBV-DNA load. Stratified analysis by HBeAg showed significant negative correlations between HBV-DNA load and hepatic steatosis ratio in both HBeAg-positive and HBeAg-negative groups. An in vitro cell model was developed by stimulating HepG2.2.15 cells with palmitic acid and oleic acid to study the relationship between HBV-DNA load and lipid metabolism. The results of the in vitro experiments suggested that fatty acid treatment increased lipid droplet deposition and decreased the expression of cell supernatant HBsAg, HBeAg, and HBV DNA load. Western blot and polymerase chain reaction analysis showed that fatty acid stimulation significantly induced Plin2 protein expression and inhibited the expression of hepatocyte autophagy proteins. Inhibition of Plin2 protein expression under fatty acid stimulation reversed the reduction in HBsAg and HBeAg expression and HBV DNA load induced by fatty acid stimulation and the inhibition of cellular autophagy. Knocking down Plin2 and blocking autophagy with 3-methyladenine (3-MA) inhibited HBV DNA replication. In conclusion, lipid metabolism is a significant factor affecting HBV load in patients with HBV infection. The in vitro experiments established that fatty acid stimulation inhibits HBV replication via the Plin2-autophagy pathway.

Nanoparticles and Their Antibacterial Application in Endodontics.

Root canal treatment represents a significant challenge as current cleaning and disinfection methodologies fail to remove persistent bacterial biofilms within the intricate anatomical structures. Recently, the field of nanotechnology has emerged as a promising frontier with numerous biomedical applications. Among the most notable contributions of nanotechnology are nanoparticles, which possess antimicrobial, antifungal, and antiviral properties. Nanoparticles cause the destructuring of bacterial walls, increasing the permeability of the cell membrane, stimulating the generation of reactive oxygen species, and interrupting the replication of deoxyribonucleic acid through the controlled release of ions. Thus, they could revolutionize endodontics, obtaining superior results and guaranteeing a promising short- and long-term prognosis. Therefore, chitosan, silver, graphene, poly(lactic) co-glycolic acid, bioactive glass, mesoporous calcium silicate, hydroxyapatite, zirconia, glucose oxidase magnetic, copper, and zinc oxide nanoparticles in endodontic therapy have been investigated in the present review. The diversified antimicrobial mechanisms of action, the numerous applications, and the high degree of clinical safety could encourage the scientific community to adopt nanoparticles as potential drugs for the treatment of endodontic diseases, overcoming the limitations related to antibiotic resistance and eradication of the biofilm.

ПЕРСПЕКТИВЫ РАЗРАБОТКИ НОВЫХ ОРИГИНАЛЬНЫХ АНТИСЕПТИЧЕСКИХ СРЕДСТВ НА ОСНОВЕ УСНИНОВОЙ КИСЛОТЫ

Introduction. Environment changing not least because of human activities determines the appearance of modified microorganisms. Many pathogens have enhanced their pathogenic properties. Their increasing drug resistance represents quite a serious problem. Among potentially efficient antiseptic substances, usnic acid and its derivatives are greatly emphasized on. Aim of our study was to conduct a narrative review of the prospects for the practical (pharmaceutical) use of usnic acid as an antiseptic. Research Materials. To perform the literature analysis, we used sources from international databases, such as Web of Science, Scopus, and PubMed, as well as from the domestic library system, eLibrary. Results. Usnic acid is found in large amounts in various lichen species. It has quite a broad spectrum of antimicrobial action. Its anti-inflammatory effects and enhancement of tissue regeneration wasproven both experimentally and clinically. The operation of usnic acid and its derivatives is determined by inhibiting the synthesis of ribonucleic acid and breaking the deoxyribonucleic acid replication. Moreover, it has a cytotoxic effect and destroys the membranes of microorganisms. In pharmaceutical industry, usnic acid is produced in many forms, such as powders, capsules, antiseptic gels, creams, and protective tapes. They are used in combined treatment of infectious diseases, in general therapy, in post-burn wound healing procedures, and in dentistry. We have concluded that lichens are very promising as raw materials for isolating usnic acid. It is necessary to search for new highly efficient methods to manufacture and use it in various farmaceutical forms.

The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.

The three-dimensional organization of chromatin plays a crucial role in gene regulation and cellular processes like deoxyribonucleic acid (DNA) transcription, replication and repair. Hi-C and related techniques provide detailed views of spatial proximities within the nucleus. However, data analysis is challenging partially due to a lack of well-defined, underpinning mathematical frameworks. Recently, recognizing and analyzing geometric patterns in Hi-C data has emerged as a powerful approach. This review provides a summary of algorithms for automatic recognition and analysis of geometric patterns in Hi-C data and their correspondence with chromatin structure. We classify existing algorithms on the basis of the data representation and pattern recognition paradigm they make use of. Finally, we outline some of the challenges ahead and promising future directions.

Identification of discriminant features from stationary pattern of nucleotide bases and their application to essential gene classification.

Introduction: Essential genes are essential for the survival of various species. These genes are a family linked to critical cellular activities for species survival. These genes are coded for proteins that regulate central metabolism, gene translation, deoxyribonucleic acid replication, and fundamental cellular structure and facilitate intracellular and extracellular transport. Essential genes preserve crucial genomics information that may hold the key to a detailed knowledge of life and evolution. Essential gene studies have long been regarded as a vital topic in computational biology due to their relevance. An essential gene is composed of adenine, guanine, cytosine, and thymine and its various combinations. Methods: This paper presents a novel method of extracting information on the stationary patterns of nucleotides such as adenine, guanine, cytosine, and thymine in each gene. For this purpose, some co-occurrence matrices are derived that provide the statistical distribution of stationary patterns of nucleotides in the genes, which is helpful in establishing the relationship between the nucleotides. For extracting discriminant features from each co-occurrence matrix, energy, entropy, homogeneity, contrast, and dissimilarity features are computed, which are extracted from all co-occurrence matrices and then concatenated to form a feature vector representing each essential gene. Finally, supervised machine learning algorithms are applied for essential gene classification based on the extracted fixed-dimensional feature vectors. Results: For comparison, some existing state-of-the-art feature representation techniques such as Shannon entropy (SE), Hurst exponent (HE), fractal dimension (FD), and their combinations have been utilized. Discussion: An extensive experiment has been performed for classifying the essential genes of five species that show the robustness and effectiveness of the proposed methodology.

Molecular genetic clusters of triple-negative breast cancer and their prognostic significance

Background. Triple-negative breast cancer is a group of tumors with different clinical and morphological features, prognosis, and response to therapy. There are from 4 to 6 molecular genetic varieties of this type of malignant neoplasm.
 Aim. Identification of individual clusters of triple-negative breast cancer that differed in terms of overall and disease-free survival.
 Material and methods. On the basis of the Regional Clinical Oncological Dispensary (Ulyanovsk) and National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov of the Ministry of Health of Russia (Moscow) in the period from 2017 to 2021, a molecular genetic analysis using a 45-gene signature in 246 patients with triple-negative breast cancer, confirmed by immunohistochemical method, was performed. Using the K-means clustering method, it was possible to form 4 molecular genetic clusters. When comparing clusters according to clinical and morphological features, the Student's t-test, MannWhitney U-test, Fisher's exact test, Pearson's 2 test were used. Survival analysis was performed using the construction of KaplanMeier curves (the observation period was 3 years and 8 months). Comparison of clusters in terms of survival was carried out using a long-rank test. Multivariate analysis was used to determine the significance of variables affecting overall and disease-free survival. Differences between groups were considered statistically significant at p 0.05.
 Results. Cluster 1 included patients with clinical stage IIA, invasive nonspecific subtype, G3, N0, Ki67 31%, with hypoexpression of most genes, unstable prognostic outcome: high survival rate at stage IV (62%) and zero survival rate at stage IIIB. Patients of the 2nd cluster were associated with stage IIA, medullary histological subtype, G3, N0, Ki67 31%, overexpression of genes for hormone receptors, growth factor receptors and transcription factors and a favorable prognosis: the best indicators of overall (100% in stage I, 66% in stage IV) and relapse-free (75% in stage I, 33% in stage IV) survival. Patients of the 3rd cluster more often had stage IA, invasive lobular and special histological tumor subtypes, N+, Ki67 14%, high expression of genes responsible for the regulation of proliferation, mitosis, spindle formation and regulation of the cell cycle, genes that regulate cell transport, the processes of replication and repair of deoxyribonucleic acid, tumor cell differentiation markers, and genes that regulate immune processes, had a regular prognosis with an increase in the clinical stage, a decrease in survival occurred. Cluster 4 patients correlated with stage IV, invasive non-specific subtype, G1G2, N0, Ki67=1530%, mean values of most genes, and worse overall and recurrence-free survival (64% in stage I, 0% in stage IV).
 Conclusion. Based on the data of molecular genetic profiling of triple-negative breast cancer, it is possible to identify individual clusters that are statistically significantly different from each other in terms of survival rates.

Case report: a rare presentation of typhoid fever due to eating over-ripened pineapple.

A 26-year-old black African male health care worker was admitted to the clinic on 21 July 2022, with a significant chief complaint of headache, loss of appetite, and watery diarrhea. The admitted patient presented with a 2-day history of hyperthermia, headache, loss of appetite, and watery diarrhea, as well as back pain, joint weakness, and insomnia. The H antigen titer was positive, which was 1:189 greater than the normal range and showed the past history of S. typhi infection. The O antigen titer value detected was a false negative result because it was done before the 7-day onset of fever. On admission, ciprofloxacillin 500mg was given orally twice a day for 7 days to treat typhoid by inhibiting the deoxyribonucleic acid replication of S. typhi by preventing S. typhi deoxyribonucleic acid topoisomerase and deoxyribonucleic acid gyrase. Typhoid fever pathogenesis is based on pathogenic factors, infecting species, and host immunity. By using the agglutination biochemical test, the Widal test was able to identify the patient's bloodstream as carrying the S. typhi bacteria that causes typhoid fever. Due to contaminated food or unsafe drinking water sources, typhoid fever is associated with travel to developing nations.

Recent approaches in the drug research and development of novel antimalarial drugs with new targets.

Malaria is a serious worldwide medical issue that results in substantial annual death and morbidity. The availability of treatment alternatives is limited, and the rise of resistant parasite types has posed a significant challenge to malaria treatment. To prevent a public health disaster, novel antimalarial agents with single-dosage therapies, extensive curative capability, and new mechanisms are urgently needed. There are several approaches to developing antimalarial drugs, ranging from alterations of current drugs to the creation of new compounds with specific targeting abilities. The availability of multiple genomic techniques, as well as recent advancements in parasite biology, provides a varied collection of possible targets for the development of novel treatments. A number of promising pharmacological interference targets have been uncovered in modern times. As a result, our review concentrates on the most current scientific and technical progress in the innovation of new antimalarial medications. The protein kinases, choline transport inhibitors, dihydroorotate dehydrogenase inhibitors, isoprenoid biosynthesis inhibitors, and enzymes involved in the metabolism of lipids and replication of deoxyribonucleic acid, are among the most fascinating antimalarial target proteins presently being investigated. The new cellular targets and drugs which can inhibit malaria and their development techniques are summarised in this study.

LncRNA-ATB inhibits the proliferation and invasion of NSCLC cells by regulating MiR-200s expression

Purpose: To investigate the effect of lncRNA-ATB on the proliferation and invasion of non-small cell lung cancer (NSCLC) cells, and its mechanism of action. 
 Methods: LncRNA-ATB mRNA levels in carcinoma tissues and normal adjacent tissues of 38 NSCLC patients in Peking University Shougang Hospital were determined by reverse transcription-polymerase chain reaction (RT-PCR). Human NSCLC A549 cell line was divided into control and lncRNA-ATB inhibition (si-ATB) groups, respectively. The proliferation and invasion of cells in each group were assessed. Subsequently, the effect of lncRNA-ATB inhibition on the growth of NSCLC cells was evaluated by subcutaneous tumor formation assay. 
 Results: The expression of lncRNA-ATB was significantly higher in carcinoma tissues than in normal adjacent tissues in NSCLC patients. Cell counting kit-8 (CCK-8) assay results showed that si-ATB group displayed a weakened ability of the cells to proliferate (p < 0.05). Furthermore, deoxyribonucleic acid (DNA) replication ability was weaker in si-ATB group than in the control group. Wound healing assay results showed that the migration ability of cells in the si-ATB group was lower than that in the control group. Also, lncRNA-ATB knockdown inhibited the invasion ability of human NSCLC cells (p < 0.05). Tumor formation assay data indicate that lncRNA-ATB knockdown significantly repressed the subcutaneous tumor formation ability of NSCLC cells. Furthermore, lncRNA-ATB knockdown in NSCLC cells up-regulated miR-200a, miR-200b and miR-200c. 
 Conclusion: The expression level of LncRNA-ATB is elevated in carcinoma tissues of NSCLC patients, and its knockdown suppresses the proliferation and invasion of NSCLC cells by up-regulating miR-200s. This finding suggests that it is a potential strategy for the management of NSCLC patients.

Peripheral blood mononuclear cell mitochondrial copy number and adenosine triphosphate inhibition test in NAFLD.

Non-alcoholic fatty liver disease (NAFLD) is associated with mitochondrial dysfunction. This study aims to develop biomarkers for assessing mitochondrial dysfunction in patients with NAFLD. Mitochondrion-associated transcriptome analysis was performed. Peripheral blood mononuclear cells obtained from patients with NAFLD (69) and healthy controls (19) were used to determine the mitochondrial DNA (mtDNA) copy number. A mitochondrial inhibition substrate test (ATP assay) was performed in HepG2 cells using the patient serum. Hepatic mRNA transcriptome analysis showed that the gene expression related to mitochondrial functions (mitochondrial fusion, apoptotic signal, and mitochondrial envelope) increased in patients with steatohepatitis, but not in those with NAFL. Gene set enrichment analysis revealed that the upregulated expression of genes is related to the pathways of the tricarboxylic (TCA) cycle and deoxyribonucleic acid (DNA) replication in patients with steatohepatitis, but not in healthy controls. The mtDNA copy number in the peripheral blood mononuclear cells was 1.28-fold lower in patients with NAFLD than that in healthy controls (P <.0001). The mitochondrial inhibition substrate test showed that the cellular adenosine triphosphate (ATP) concentration was 1.2-fold times less in NAFLD patients than that in healthy controls (P <.0001). The mtDNA copy number and mitochondrial ATP inhibition substrate test demonstrated negative correlations with the degree of hepatic steatosis, whereas the ATP concentration showed a positive correlation with the mtDNA copy number. The mitochondrial copy number of peripheral blood mononuclear cells and mitochondrial ATP inhibition substrate can be used as biomarkers for assessing the mitochondrial dysfunction in patients with NAFLD.

Design of Two Phase III, Randomized, Multicenter Studies Comparing Gepotidacin with Nitrofurantoin for the Treatment of Uncomplicated Urinary Tract Infection in Female Participants.

BackgroundUncomplicated urinary tract infections (uUTIs) are among the most common community-acquired infections for women worldwide. Treatment options are increasingly limited by antibiotic resistance; novel oral antibiotics are urgently needed. Gepotidacin is a novel, bactericidal, first-in-class triazaacenaphthylene antibiotic that inhibits bacterial deoxyribonucleic acid (DNA) replication by a distinct mechanism of action, which confers activity against most strains of target pathogens, such as Escherichia coli and Staphylococcus saprophyticus, including those resistant to current antibiotics. Here, we describe the designs of two near-identical phase III clinical trials (EAGLE-2 and EAGLE-3) evaluating gepotidacin for the treatment of uUTI.MethodsThese are phase III, randomized, multicenter, parallel-group, double-blind, double-dummy, comparator-controlled, noninferiority studies, comparing the efficacy and safety of gepotidacin to nitrofurantoin in the treatment of uUTI. Eligible participants are women aged ≥ 12 years with ≥ 2 uUTI symptoms, randomized (1:1) to receive oral gepotidacin (1500 mg) plus placebo or nitrofurantoin (100 mg) plus placebo, twice daily for 5 days. The primary therapeutic endpoint is composite clinical and microbiological efficacy, with noninferiority comparisons made in individuals with a qualifying (≥ 105 colony-forming units/mL urine) nitrofurantoin-susceptible uropathogen.ResultsThese trials were designed in accordance with US Food and Drug Administration (2019) and European Medicines Agency (2018) guidance, particularly the composite endpoint and microbiological evaluability requirements. Across the trials ~ 5000 participants are planned to be enrolled from > 200 centers globally.ConclusionsGepotidacin represents an important potential treatment option being evaluated to address the need for novel oral antibiotics to treat uUTI.These trials are registered at ClinicalTrials.gov (https://clinicaltrials.gov/) where the full protocols can be accessed under trial IDs: NCT04020341 (EAGLE-2) and NCT04187144 (EAGLE-3).Supplementary InformationThe online version contains supplementary material available at 10.1007/s40121-022-00706-9.

Regulator of telomere elongation helicase 1 gene and its association with malignancy.

With the progression of next-generation sequencing technologies, researchers have identified numerous variants of the regulator of telomere elongation helicase 1 (RTEL1) gene that are associated with a broad spectrum of phenotypic manifestations, including malignancies. At the molecular level, RTEL1 is involved in the regulation of the repair, replication, and transcription of deoxyribonucleic acid (DNA) and the maintenance of telomere length. RTEL1 can act both as a promotor and inhibitor of tumorigenesis. Here, we review the potential mechanisms implicated in the malignant transformation of tissues under conditions of RTEL1 deficiency or its aberrant overexpression. A major hemostatic challenge during RTEL1 dysfunction could arise from its unbalanced activity for unwinding guanine-rich quadruplex DNA (G4-DNA) structures. In contrast, RTEL1 deficiency leads to alterations in telomeric and genome-wide DNA maintenance mechanisms, ribonucleoprotein metabolism, and the creation of an inflammatory and immune-deficient microenvironment, all promoting malignancy. Additionally, we hypothesize that functionally similar molecules could act to compensate for the deteriorated functions of RTEL1, thereby facilitating the survival of malignant cells. On the contrary, RTEL1 over-expression was directed toward G4-unwinding, by promoting replication fork progression and maintaining intact telomeres, may facilitate malignant transformation and proliferation of various pre-malignant cellular compartments. Therefore, restoring the equilibrium of RTEL1 functions could serve as a therapeutic approach for preventing and treating malignancies.

Fast-forwarding evolution-Accelerated adaptation in a proofreading-deficient hypermutator herpesvirus.

Evolution relies on the availability of genetic diversity for fitness-based selection. However, most deoxyribonucleic acid (DNA) viruses employ DNA polymerases (Pol) capable of exonucleolytic proofreading to limit mutation rates during DNA replication. The relative genetic stability produced by high-fidelity genome replication can make studying DNA virus adaptation and evolution an intensive endeavor, especially in slowly replicating viruses. Here, we present a proofreading-impaired Pol mutant (Y547S) of Marek's disease virus that exhibits a hypermutator phenotype while maintaining unimpaired growth in vitro and wild-type (WT)-like pathogenicity in vivo. At the same time, mutation frequencies observed in Y547S virus populations are 2-5-fold higher compared to the parental WT virus. We find that Y547S adapts faster to growth in originally non-permissive cells, evades pressure conferred by antiviral inhibitors more efficiently, and is more easily attenuated by serial passage in cultured cells compared to WT. Our results suggest that hypermutator viruses can serve as a tool to accelerate evolutionary processes and help identify key genetic changes required for adaptation to novel host cells and resistance to antiviral therapy. Similarly, the rapid attenuation achieved through adaptation of hypermutators to growth in cell culture enables identification of genetic changes underlying attenuation and virulence, knowledge that could practically exploited, e.g.in the rational design of vaccines.

Clinical impact of amrubicin monotherapy in patients with relapsed small cell lung cancer: a multicenter retrospective study.

BackgroundTopoisomerase is an essential enzyme for deoxyribonucleic acid replication, and its inhibitors suppress tumor progression. Amrubicin, a topoisomerase II inhibitor, is mainly used in the second-line treatment of patients with extensive-stage small cell lung cancer (ES-SCLC). However, the impact of different types of topoisomerase inhibitors for first-line chemotherapy on the efficacy of amrubicin remains unclear. In the present study, we aimed to evaluate the efficacy of second-line amrubicin in patients with relapsed SCLC who were previously treated with platinum-based chemotherapy, including topoisomerase I and II inhibitors.MethodsThis study retrospectively analyzed patients with ES-SCLC who experienced recurrence and were treated with amrubicin at 22 institutions in Japan between April 2015 and November 2020. The progression-free survival of amrubicin monotherapy was investigated using the Kaplan-Meier method.ResultsA total of 320 patients were enrolled in this study, with 59 (18%) receiving platinum plus topoisomerase I inhibitor irinotecan and 261 (82%) receiving platinum plus topoisomerase II inhibitor etoposide as first-line treatment. The progression-free survival of amrubicin was significantly longer in the irinotecan group than in the etoposide group (3.2 vs. 2.5 months; P=0.034).ConclusionsThese results showed that different types of topoisomerase inhibitors could affect the efficacy of amrubicin monotherapy in the second-line treatment of patients with relapsed ES-SCLC.