sendigR: an R package to leverage the value of CDISC SEND datasets for cross-study analysis.

The CDISC Standard for Exchange of Nonclinical Data (SEND) data standard has created new opportunities for collaborative development of open-source software solutions to facilitate cross-study analyses of toxicology study data. A public-private partnership between BioCelerate and the FDA/Center for Drug Evaluation and Research (CDER) was established in part to develop and publicize novel methods to facilitate cross-study analysis of SEND datasets. As part of this work in collaboration with the Pharmaceutical Users Software Exchange (PHUSE), an R package sendigR has been developed to enable users to construct a relational database from a collection of SEND datasets and then query that database to perform cross-study analyses. The sendigR package also includes an integrated Python package, xptcleaner, which can be used to harmonize the terminology used in SEND datasets by mapping to CDISC controlled terminologies. The sendigR R package is freely available on the comprehensive R Archive Network (CRAN) and at https://github.com/phuse-org/sendigR. An R Shiny web application was included in the R package to enable toxicologists with no coding experience to perform historical control analyses. Experienced R programmers will be able to integrate the package functions into their own custom scripts/packages and potentially contribute improvements to the functionality of sendigR. sendigR reference manual: https://phuse-org.github.io/sendigR/. sendigR R Shiny demo app: https://phuse-org.shinyapps.io/sendigR/.

Altered long non-coding RNAs expression in normal and diseased primary human airway epithelial cells exposed to diesel exhaust particles.

BACKGROUND: Exposure to diesel exhaust particles (DEP) has been linked to a variety of adverse health effects, including increased morbidity and mortality from cardiovascular diseases, chronic obstructive pulmonary disease (COPD), metabolic syndrome, and lung cancer. The epigenetic changes caused by air pollution have been associated with increased health risks. However, the exact molecular mechanisms underlying the lncRNA-mediated pathogenesis induced by DEP exposure have not been revealed. METHODS: Through RNA-sequencing and integrative analysis of both mRNA and lncRNA profiles, this study investigated the role of lncRNAs in altered gene expression in healthy and diseased human primary epithelial cells (NHBE and DHBE-COPD) exposed to DEP at a dose of 30 µg/cm2. RESULTS: We identified 503 and 563 differentially expressed (DE) mRNAs and a total of 10 and 14 DE lncRNAs in NHBE and DHBE-COPD cells exposed to DEP, respectively. In both NHBE and DHBE-COPD cells, enriched cancer-related pathways were identified at mRNA level, and 3 common lncRNAs OLMALINC, AC069234.2, and LINC00665 were found to be associated with cancer initiation and progression. In addition, we identified two cis-acting (TMEM51-AS1 and TTN-AS1) and several trans-acting lncRNAs (e.g. LINC01278, SNHG29, AC006064.4, TMEM51-AS1) only differentially expressed in COPD cells, which could potentially play a role in carcinogenesis and determine their susceptibility to DEP exposure. CONCLUSIONS: Overall, our work highlights the potential importance of lncRNAs in regulating DEP-induced gene expression changes associated with carcinogenesis, and individuals suffering from COPD are likely to be more vulnerable to these environmental triggers.

Formation of Redox-Active Duroquinone from Vaping of Vitamin E Acetate Contributes to Oxidative Lung Injury.

In late 2019, the outbreak of e-cigarette or vaping-associated lung injuries (EVALIs) in the United States demonstrated to the public the potential health risks of vaping. While studies since the outbreak have identified vitamin E acetate (VEA), a diluent of tetrahydrocannabinol (THC) in vape cartridges, as a potential contributor to lung injuries, the molecular mechanisms through which VEA may cause damage are still unclear. Recent studies have found that the thermal degradation of e-liquids during vaping can result in the formation of products that are more toxic than the parent compounds. In this study, we assessed the role of duroquinone (DQ) in VEA vaping emissions that may act as a mechanism through which VEA vaping causes lung damage. VEA vaping emissions were collected and analyzed for their potential to generate reactive oxygen species (ROS) and induce oxidative stress-associated gene expression in human bronchial epithelial cells (BEAS-2B). Significant ROS generation by VEA vaping emissions was observed in both acellular and cellular systems. Furthermore, exposure to vaping emissions resulted in significant upregulation of NQO1 and HMOX-1 genes in BEAS-2B cells, indicating a strong potential for vaped VEA to cause oxidative damage and acute lung injury; the effects are more profound than exposure to equivalent concentrations of DQ alone. Our findings suggest that there may be synergistic interactions between thermal decomposition products of VEA, highlighting the multifaceted nature of vaping toxicity.

Chemical and Toxicological Characterization of Vaping Emission Products from Commonly Used Vape Juice Diluents.

Recent reports have linked severe lung injuries and deaths to the use of e-cigarettes and vaping products. Nevertheless, the causal relationship between exposure to vaping emissions and the observed health outcomes remains to be elucidated. Through chemical and toxicological characterization of vaping emission products, this study demonstrates that during vaping processes, changes in chemical composition of several commonly used vape juice diluents (also known as cutting agents) lead to the formation of toxic byproducts, including quinones, carbonyls, esters, and alkyl alcohols. The resulting vaping emission condensates cause inhibited cell proliferation and enhanced cytotoxicity in human airway epithelial cells. Notably, substantial formation of the duroquinone and durohydroquinone redox couple was observed in the vaping emissions from vitamin E acetate, which may be linked to acute oxidative stress and lung injuries reported by previous studies. These findings provide an improved molecular understanding and highlight the significant role of toxic byproducts in vaping-associated health effects.

Role of functional groups in reaction kinetics of dithiothreitol with secondary organic aerosols.

The toxicity of organic aerosols has been largely ascribed to the generation of reactive oxygen species, which could subsequently induce oxidative stress in biological systems. The reaction of DTT with redox-active species in PM has been generally assumed to be pseudo-first order, with the oxidative potential of PM being represented by the DTT consumption per minute of reaction time per µg of PM. Although catalytic reactive species such as transition metals and quinones are long believed to be the main contributors of DTT responses, the role of non-catalytic DTT reactive species such as organic hydroperoxides (ROOH) and electron-deficient alkenes (e.g., conjugated carbonyls) in DTT consumption has been recently highlighted. Thus, understanding the reaction kinetics and mechanisms of DTT consumption by various PM components is required to interpret the oxidative potential measured by DTT assays more accurately. In this study, we measured the DTT consumptions over time and characterized the reaction products using model compounds and secondary organic aerosols (SOA) with varying initial concentrations. We observed that the DTT consumption rates linearly increased with both initial DTT and sample concentrations. The overall reaction order of DTT with non-catalytic reactive species and SOA in this study is second order. The reactions of DTT with different functional groups have significantly different rate constants. The reaction rate constant of isoprene SOA with DTT is mainly determined by the concentration of ROOH. For toluene SOA, both ROOH and electron-deficient alkenes may dominate its DTT reaction rates. These results provide some insights into the interpretation of DTT-based aerosol oxidative potential and highlight the need to study the toxicity mechanism of ROOH and electron-deficient alkenes in PM for future work.

Toxicological responses in human airway epithelial cells (BEAS-2B) exposed to particulate matter emissions from gasoline fuels with varying aromatic and ethanol levels.

In this study, we assessed the toxicological potencies of particulate matter (PM) emissions from a modern vehicle equipped with a gasoline direct injection (GDI) engine when operated on eight different fuels with varying aromatic hydrocarbon and ethanol contents. Testing was conducted over the LA92 driving cycle using a chassis dynamometer with a constant volume sampling system, where particles were collected onto Teflon filters. The extracted PM constituents were analyzed for their oxidative potential using the dithiothreitol (DTT) chemical assay and exposure-induced gene expression in human airway epithelial cells (BEAS-2B). Different trends of DTT activities were seen when testing PM samples in 100% aqueous buffer solutions versus elevated fraction of methanol in aqueous buffers (50:50), indicating the effect of solubility of organic PM constituents on the measured oxidative potential. Higher aromatics content in fuels corresponded to higher DTT activities in PM. Exposure to PM exhaust upregulated the expression of HMOX-1, but downregulated the expression of IL-6, TNF-α, CCL5 and NOS2 in BEAS-2B cells. The principal component regression analysis revealed different patterns of correlations. Aromatics content contributed to more significant PAH-mediated IL-6 downregulation, whereas ethanol content was associated with decreased downregulation of IL-6. Our findings highlighted the key role of fuel composition in modulating the toxicological responses to GDI PM emissions.

Exposure to Dimethyl Selenide (DMSe)-Derived Secondary Organic Aerosol Alters Transcriptomic Profiles in Human Airway Epithelial Cells.

Dimethyl selenide (DMSe) is one of the major volatile organoselenium compounds released from aquatic and terrestrial environments through microbial transformation and plant metabolism. The detailed processes of DMSe leading to secondary organic aerosol (SOA) formation and the pulmonary health effects induced by inhalation of DMSe-derived SOA remain largely unknown. In this study, we characterized the chemical composition and formation yields of SOA produced from the oxidation of DMSe with OH radicals and O3 in controlled chamber experiments. Further, we profiled the transcriptome-wide gene expression changes in human airway epithelial cells (BEAS-2B) after exposure to DMSe-derived SOA. Our analyses indicated a significantly higher SOA yield resulting from the OH-initiated oxidation of DMSe. The oxidative potential of DMSe-derived SOA, as measured by the dithiothreitol (DTT) assay, suggested the presence of oxidizing moieties in DMSe-derived SOA at levels higher than typical ambient aerosols. Utilizing RNA sequencing (RNA-Seq) techniques, gene expression profiling followed by pathway enrichment analysis revealed several major biological pathways perturbed by DMSe-derived SOA, including elevated genotoxicity, DNA damage, and p53-mediated stress responses, as well as downregulated cholesterol biosynthesis, glycolysis, and interleukin IL-4/IL-13 signaling. This study highlights the significance of DMSe-derived SOA as a stressor in human airway epithelial cells.

Characterization of electrophilicity and oxidative potential of atmospheric carbonyls.

Carbonyls are reactive and electrophilic compounds found ubiquitously in the atmosphere. The interactions between atmospheric carbonyls and biological nucleophiles (e.g., thiol-containing compounds) have important implications on their toxicity, but the underlying mechanisms have not been fully understood. In this study, we used combined computational and experimental approaches to assess the reactivities of atmospheric carbonyls in respect to their electrophilic properties. Global electrophilicity indexes (ω) were calculated based on density functional theory. The reactivities of carbonyls with thiols were assessed using the dithiothreitol (DTT) assay as a surrogate of biological nucleophilic antioxidants. The computational results indicated that the ω of a given carbonyl compound is largely influenced by its molecular structure and adjacent functional groups. The calculated ω values showed a strong linear correlation with the logarithm of measured carbonyl mass-normalized DTT consumption rates (r2 = 0.8378 and 0.9899 for simple and α,ß-unsaturated carbonyls, respectively). The removal of DTT through the nucleophilic addition pathway was confirmed by the detection of carbonyl-DTT adducts using the gas chromatography/electron ionization-mass spectrometry (GC/EI-MS) technique. Our results demonstrated that electrophilicity index can be potentially used as a molecular descriptor to predict toxicity of atmospheric carbonyls towards thiol-containing biomolecules. This work also highlights the significance of carbonyls in interpreting DTT-based aerosol oxidative potential.

Development and Phenotypic Screening of an Ethyl Methane Sulfonate Mutant Population in Soybean.

Soybean is an important oil-producing crop in the Fabaceae family and there are increasing demands for soybean oil and other soybean products. Genetic improvement of soybean is needed to increase its production. In order to provide genetic diversity and resources for identifying important genes, a new ethyl methane sulfonate (EMS) mutagenized soybean population was generated using the newly released germplasm, JTN-5203 (maturity group V). Treatment of soybean seeds with 60 mM EMS concentration was found to be suitable for inducing mutation. A total of 1,820 M1 individuals were produced from 15,000 treated seeds. The resulting M2 population was planted in the field for phenotyping. After harvest, seed traits including total oil, protein, starch, moisture content, fatty acid and amino acid compositions were measured by NIR. Phenotypic variations observed in this population include changes in leaf morphology, plant architecture, seed compositions, and yield. Of most interest, we identified plants with increased amounts of total protein (50% vs. 41% for control) and plants with higher amounts of total oil (25% vs. 21.2% control). Similarly, we identified plants with increases in oleic acid content and decreases in linoleic acid and linolenic acid. This EMS mutant population will be used for further studies including screening for various traits such as amino acid pathways, allergens, phytic acids, and other important soybean agronomic traits. In addition, these mutant individuals will be evaluated in the next generation to assess the heritability. Beneficial traits from these mutants can be exploited for future soybean breeding programs. This germplasm can also be used for discovering novel mutant alleles and for functional gene expression analysis using reverse genetics tools such as TILLING.

Identification and analysis of potential targets in Streptococcus sanguinis using computer aided protein data analysis.

PURPOSE: Streptococcus sanguinis is a Gram-positive, facultative aerobic bacterium that is a member of the viridans streptococcus group. It is found in human mouths in dental plaque, which accounts for both dental cavities and bacterial endocarditis, and which entails a mortality rate of 25%. Although a range of remedial mediators have been found to control this organism, the effectiveness of agents such as penicillin, amoxicillin, trimethoprim-sulfamethoxazole, and erythromycin, was observed. The emphasis of this investigation was on finding substitute and efficient remedial approaches for the total destruction of this bacterium. MATERIALS AND METHODS: In this computational study, various databases and online software were used to ascertain some specific targets of S. sanguinis. Particularly, the Kyoto Encyclopedia of Genes and Genomes databases were applied to determine human nonhomologous proteins, as well as the metabolic pathways involved with those proteins. Different software such as Phyre2, CastP, DoGSiteScorer, the Protein Function Predictor server, and STRING were utilized to evaluate the probable active drug binding site with its known function and protein-protein interaction. RESULTS: In this study, among 218 essential proteins of this pathogenic bacterium, 81 nonhomologous proteins were accrued, and 15 proteins that are unique in several metabolic pathways of S. sanguinis were isolated through metabolic pathway analysis. Furthermore, four essentially membrane-bound unique proteins that are involved in distinct metabolic pathways were revealed by this research. Active sites and druggable pockets of these selected proteins were investigated with bioinformatic techniques. In addition, this study also mentions the activity of those proteins, as well as their interactions with the other proteins. CONCLUSION: Our findings helped to identify the type of protein to be considered as an efficient drug target. This study will pave the way for researchers to develop and discover more effective and specific therapeutic agents against S. sanguinis.