DNA damaging and biochemical effects of potassium tetraborate

Potassium tetraborate (PTB) is a product resulting from the controlled reaction of potassium hydroxide, water and boric acid (BA). It is used in many areas of industry such as disinfectant, detergent and treatment of contact lenses. PTB is one of the boron compounds which is most commonly used in many areas of industry although very limited information is available concerning its toxicity. Therefore, in this study, it is aimed to determine genetic and biochemical effects of PTB in human blood cell cultures (n=4). PTB was added into culture tubes at various concentrations (0-1280 μg/ml). Micronucleus (MN) and chromosomal aberration (CA) tests were performed for genotoxic damage influences estimation. In addition, biochemical parameters (total antioxidant capacity (TAC) and total oxidative status (TOS) were examined to determine oxidative effects. The results indicated that all tested concentrations of PTB were found to be non-genotoxic. In addition, low concentrations (1.25, 2.5 and 5 μg/ml) of PTB caused increases of TAC levels. Furthermore, all concentrations of PTB were not changed the TOS levels in cultured human blood cells. Based on these results, in this study it has been reported for the first time that PTB is not genotoxic and it in creases the antioxidant capacity in human peripheral blood lymphocytes

Blagotvorno djelovanje ekstrakta lovorova lista na hepatotoksičnost u štakora uzrokovanu 2,3,7,8-tetraklordibenzo-p-dioksinom in Vitro

2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a very toxic environmental pollutant that raises great public concern about its impact on human health. Recent studies indicate that laurel leaf extract exhibits antioxidant properties that can counter the toxic effects of certain compounds in the liver. The aim of this study was to assess how effective LE is against the toxicity of TCDD in a primary culture of rat hepatocytes. The extract (50 mg L-1, 100 mg L-1, and 200 mg L-1) was added to cultures alone or with TCDD (1.61 mg L-1 and 3.22 mg L-1) for 48 hours. Cell viability was measured using the [3-(4,5-dimethyl-thiazol-2-yl) 2,5-diphenyltetrazolium bromide] (MTT) assay and the lactate dehydrogenase (LDH) cytotoxicity assay, while oxidative damage was assessed by measuring total antioxidant capacity (TAC) and total oxidative stress (TOS). DNA damage was also analysed using the micronucleus (MN) assay of the cultured hepatocytes. TCDD alone lowered, and laurel extract had no effect on cell viability. TCDD also increased TOS and signifi cantly decreased TAC. It signifi cantly increased the frequency of micronucleated hepatocytes in a dose-dependent manner. In cultures exposed to LE alone, TOS did not change and TAC signifi cantly increased in a dose-dependent manner. Added to TCDD, laurel countered its toxic effects and showed protective effects against TCDD-mediated DNA damage. This points to the therapeutic potential of laurel against TCDD toxicity in the liver.2,3,7,8-tetraklordibenzo-p-dioksin (TCDD) vrlo je toksičan onečišćivač okoliša koji izaziva veliku zabrinutost zbog mogućih posljedica za zdravlje ljudi. Nedavna su ispitivanja pokazala da ekstrakt lovorova lista (Laurus nobilis L.) ima antioksidacijska svojstva koja ublažavaju hepatotoksičnost. Cilj je ovog ispitivanja bio istražiti djelotvornost ekstrakta lovorova lista protiv toksičnoga djelovanja TCDD-a na primarnoj kulturi hepatocita. Kulturama je ekstrakt dodan u dozama od 50 mg L-1, 100 mg L-1 odnosno 200 mg L-1 sam ili zajedno s TCDD-om u dozama od 1,61 mg L-1 odnosno 3,22 mg L-1. Izloženost je u oba slučaja trajala 48 h. Zatim je ispitana vijabilnost hepatocita s pomoću MTT-testa i testa na laktat dehidrogenazu (LDH). Oksidativno oštećenje mjerili smo s pomoću ukupnog antioksidativnoga kapaciteta i ukupnoga oksidativnog stresa. Oštećenje DNA hepatocita procijenjeno je s pomoću mikronukleus testa. MTT i LDH pokazali su da TCDD smanjuje vijabilnost hepatocita, ali ne i ekstrakt lovorova lista. TCDD je također povisio razinu ukupnoga oksidativnog stresa te smanjio ukupni antioksidativni kapacitet. Broj mikronukleusa rastao je s dozom TCDD-a. Nasuprot tomu, u hepatocitima izloženim samo ekstraktu lovorova lista nisu izmijenjene razine ukupnoga oksidativnog stresa, dok je ukupni antioksidativni kapacitet značajno rastao s dozom. Ekstrakt lovorova lista usto je ublažio toksično djelovanje TCDD-a na hepatocite u primarnoj kulturi. Stoga lovorov list štiti protiv oštećenja DNA uzrokovanoga TCDD-om. To ukazuje na mogućnost terapijske primjene ekstrakta lovorova lista protiv toksičnoga djelovanja TCDD-a u jetri

Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling

Burkholderia cenocepacia is among the important pathogens isolated from cystic fibrosis (CF) patients. It has attracted considerable attention because of its capacity to evade host immune defenses during chronic infection. Advances in systems biology methodologies have led to the emergence of methods that integrate experimental transcriptomics data and genome-scale metabolic models (GEMs). Here, we integrated transcriptomics data of bacterial cells grown on exponential and biofilm conditions into a manually curated GEM of B. cenocepacia. We observed substantial differences in pathway response to different growth conditions and alternative pathway susceptibility to extracellular nutrient availability. For instance, we found that blockage of the reactions was vital through the lipid biosynthesis pathways in the exponential phase and the absence of microenvironmental lysine and tryptophan are essential for survival. During biofilm development, bacteria mostly had conserved lipid metabolism but altered pathway activities associated with several amino acids and pentose phosphate pathways. Furthermore, conversion of serine to pyruvate and 2,5-dioxopentanoate synthesis are also identified as potential targets for metabolic remodeling during biofilm development. Altogether, our integrative systems biology analysis revealed the interactions between the bacteria and its microenvironment and enabled the discovery of antimicrobial targets for biofilm-related diseases

Informing Pharmacokinetic Models With Physiological Data: Oral Population Modeling of L-Serine in Humans

To determine how to set optimal oral L-serine (serine) dose levels for a clinical trial, existing literature was surveyed. Data sufficient to set the dose was inadequate, and so an (n = 10) phase I-A calibration trial was performed, administering serine with and without other oral agents. We analyzed the trial and the literature data using pharmacokinetic (PK) modeling and statistical analysis. The therapeutic goal is to modulate specific serine-related metabolic pathways in the liver using the lowest possible dose which gives the desired effect since the upper bound was expected to be limited by toxicity. A standard PK approach, in which a common model structure was selected using a fit to data, yielded a model with a single central compartment corresponding to plasma, clearance from that compartment, and an endogenous source of serine. To improve conditioning, a parametric structure was changed to estimate ratios (bioavailability over volume, for example). Model fit quality was improved and the uncertainty in estimated parameters was reduced. Because of the particular interest in the fate of serine, the model was used to estimate whether serine is consumed in the gut, absorbed by the liver, or entered the blood in either a free state, or in a protein- or tissue-bound state that is not measured by our assay. The PK model structure was set up to represent relevant physiology, and this quantitative systems biology approach allowed a broader set of physiological data to be used to narrow parameter and prediction confidence intervals, and to better understand the biological meaning of the data. The model results allowed us to determine the optimal human dose for future trials, including a trial design component including IV and tracer studies. A key contribution is that we were able to use human physiological data from the literature to inform the PK model and to set reasonable bounds on parameters, and to improve model conditioning. Leveraging literature data produced a more predictive, useful model

Discovery of drug targets and therapeutic agents based on drug repositioning to treat lung adenocarcinoma

Background: Lung adenocarcinoma (LUAD) is the one of the most common subtypes in lung cancer. Although various targeted therapies have been used in the clinical practice, the 5-year overall survival rate of patients is still low. Thus, it is urgent to identify new therapeutic targets and develop new drugs for the treatment of the LUAD patients. Methods: Survival analysis was used to identify the prognostic genes. Gene co-expression network analysis was used to identify the hub genes driving the tumor development. A profile-based drug repositioning approach was used to repurpose the potentially useful drugs for targeting the hub genes. MTT and LDH assay were used to measure the cell viability and drug cytotoxicity, respectively. Western blot was used to detect the expression of the proteins. Findings: We identified 341 consistent prognostic genes from two independent LUAD cohorts, whose high expression was associated with poor survival outcomes of patients. Among them, eight genes were identified as hub genes due to their high centrality in the key functional modules in the gene-co-expression network analysis and these genes were associated with the various hallmarks of cancer (e.g., DNA replication and cell cycle). We performed drug repositioning analysis for three of the eight genes (CDCA8, MCM6, and TTK) based on our drug repositioning approach. Finally, we repurposed five drugs for inhibiting the protein expression level of each target gene and validated the drug efficacy by performing in vitro experiments. Interpretation: We found the consensus targetable genes for the treatment of LUAD patients with different races and geographic characteristics. We also proved the feasibility of our drug repositioning approach for the development of new drugs for disease treatment.</p

Addressing the heterogeneity in liver diseases using biological networks

The abnormalities in human metabolism have been implicated in the progression of several complex human diseases, including certain cancers. Hence, deciphering the underlying molecular mechanisms associated with metabolic reprogramming in a disease state can greatly assist in elucidating the disease aetiology. An invaluable tool for establishing connections between global metabolic reprogramming and disease development is the genome-scale metabolic model (GEM). Here, we review recent work on the reconstruction of cell/tissue-type and cancer-specific GEMs and their use in identifying metabolic changes occurring in response to liver disease development, stratification of the heterogeneous disease population and discovery of novel drug targets and biomarkers. We also discuss how GEMs can be integrated with other biological networks for generating more comprehensive cell/tissue models. In addition, we review the various biological network analyses that have been employed for the development of efficient treatment strategies. Finally, we present three case studies in which independent studies converged on conclusions underlying liver disease

Open MoA:revealing the mechanism of action (MoA) based on network topology and hierarchy

MotivationMany approaches in systems biology have been applied in drug repositioning due to the increased availability of the omics data and computational biology tools. Using a multi-omics integrated network, which contains information of various biological interactions, could offer a more comprehensive inspective and interpretation for the drug mechanism of action (MoA).ResultsWe developed a computational pipeline for dissecting the hidden MoAs of drugs (Open MoA). Our pipeline computes confidence scores to edges that represent connections between genes/proteins in the integrated network. The interactions showing the highest confidence score could indicate potential drug targets and infer the underlying molecular MoAs. Open MoA was also validated by testing some well-established targets. Additionally, we applied Open MoA to reveal the MoA of a repositioned drug (JNK-IN-5A) that modulates the PKLR expression in HepG2 cells and found STAT1 is the key transcription factor. Overall, Open MoA represents a first-generation tool that could be utilized for predicting the potential MoA of repurposed drugs and dissecting de novo targets for developing effective treatments.Availability and implementationSource code is available at https://github.com/XinmengLiao/Open_MoA

The Human Pathology Atlas for deciphering the prognostic features of human cancers

Background: Cancer is one of the leading causes of mortality worldwide, highlighting the urgent need for a deeper molecular understanding and the development of personalized treatments. The present study aims to establish a solid association between gene expression and patient survival outcomes to enhance the utility of the Human Pathology Atlas for cancer research. Methods: In this updated analysis, we examined the expression profiles of 6918 patients across 21 cancer types. We integrated data from 10 independent cancer cohorts, creating a cross-validated, reliable collection of prognostic genes. We applied systems biology approach to identify the association between gene expression profiles and patient survival outcomes. We further constructed prognostic regulatory networks for kidney renal clear cell carcinoma (KIRC) and liver hepatocellular carcinoma (LIHC), which elucidate the molecular underpinnings associated with patient survival in these cancers. Findings: We observed that gene expression during the transition from normal to tumorous tissue exhibited diverse shifting patterns in their original tissue locations. Significant correlations between gene expression and patient survival outcomes were identified in KIRC and LIHC among the major cancer types. Additionally, the prognostic regulatory network established for these two cancers showed the indicative capabilities of the Human Pathology Atlas and provides actionable insights for cancer research. Interpretation: The updated Human Pathology Atlas provides a significant foundation for precision oncology and the formulation of personalized treatment strategies. These findings deepen our understanding of cancer biology and have the potential to advance targeted therapeutic approaches in clinical practice. Funding: The Knut and Alice Wallenberg Foundation ( 72110), the China Scholarship Council (Grant No. 202006940003).</p

Longitudinal metabolomics analysis reveals the acute effect of cysteine and NAC included in the combined metabolic activators

Growing evidence suggests that the depletion of plasma NAD+ and glutathione (GSH) may play an important role in the development of metabolic disorders. The administration of Combined Metabolic Activators (CMA), consisting of GSH and NAD+ precursors, has been explored as a promising therapeutic strategy to target multiple altered pathways associated with the pathogenesis of the diseases. Although studies have examined the therapeutic effect of CMA that contains N-acetyl-L-cysteine (NAC) as a metabolic activator, a system-wide comparison of the metabolic response to the administration of CMA with NAC and cysteine remains lacking. In this placebo-controlled study, we studied the acute effect of the CMA administration with different metabolic activators, including NAC or cysteine with/without nicotinamide or flush free niacin, and performed longitudinal untargeted-metabolomics profiling of plasma obtained from 70 well-characterized healthy volunteers. The time-series metabolomics data revealed the metabolic pathways affected after the administration of CMAs showed high similarity between CMA containing nicotinamide and NAC or cysteine as metabolic activators. Our analysis also showed that CMA with cysteine is well-tolerated and safe in healthy individuals throughout the study. Last, our study systematically provided insights into a complex and dynamics landscape involved in amino acid, lipid and nicotinamide metabolism, reflecting the metabolic responses to CMA administration containing different metabolic activators

Klorheksidin diglukonatın insan periferal kan kültürlerinde antioksidan enzim seviyeleri üzerine etkilerinin incelenmesi

Objectives: In the present study, it was aimed to investigate the biochemical effects of chlorhexidine digluconate (CHX) on the antioxidant enzyme levels in human peripheral blood cell cultures. Materials and Methods: The blood cultures were prepared using the blood samples obtained from 10 individuals (5 male and 5 female) who were systemically healthy and were not exposed to any toxic agent before. The cultures were exposed to different concentrations of CHX (0.05, 0.1, 0.2 ve 0.4 mmol/L). Glutation peroxidase (GPx), superoxide dismutase (SOD) and Catalase (CAT) enzyme activities were analyzed in order to evaluate the biochemical effects. Results: A dose-dependent statistically significant reduction was seen in the GPx, SOD and CAT enzyme activities in the blood cultures treated with 0.1, 0.2 ve 0.4 mmol/L concentrations of CHX. Conclusion: This is the first in vitro study investigating the effects of CHX on antioxidant enzyme levels in the human peripheral blood cultures. In conclusion, it was revealed that CHX had dose-depended cytotoxic effects by influencing the antioxidant enzyme activities in blood cells. ÖZET Amaç: Bu çalışmada, klorheksidin diglukonatın (KHG) insan periferal kan kültürlerinde antioksidan enzim seviyeleri üzerine olan biyokimyasal etkilerinin araştırılması amaçlandı. Gereç ve Yöntem: Daha önce herhangi bir toksik ajana maruz kalmamış ve sistemik olarak sağlıklı 10 bireyden (5 erkek, 5 kadın) elde edilen kan örnekleri ile kan kültürleri hazırlandı. Elde edilen kültürler farklı konsantrasyonlarda KHG (0.05, 0.1, 0.2 ve 0.4 mmol/L) ile muamele edildi. Biyokimyasal etkilerin değerlendirilmesi amacıyla glutatyon peroksidaz (GPx), süperoksit dismutaz (SOD) ve katalaz (KAT) enzim aktiviteleri incelendi. Bulgular: KHG'nin 0.1, 0.2 ve 0.4 mmol/L'luk konsantrasyonları ile muamele edilen kan kültürlerinde GPx, SOD ve CAT enzim aktivitelerinde doza bağlı istatistiksel olarak anlamlı derecede azalma izlendi (p&lt;0.05). Sonuç: Bu çalışma, KHG'nin insan periferal kan kültürlerinde antioksidan enzim seviyeleri üzerindeki etkilerini araştıran ilk in vitro çalışmadır. Sonuç olarak, bu bileşiğin kan hücrelerindeki antioksidan enzim aktivitelerini etkilemek suretiyle doza bağlı sitotoksik etkilere sahip olduğu da ortaya konulmuştur