Integrated analysis of multi-omics data on epigenetic changes caused by combined exposure to environmental hazards

Interior decorative volatile organic compounds exposure induces sleep disorders through aberrant branched chain amino acid transaminase 2 mediated glutamatergic signaling resulting from a neuroinflammatory cascade

Air pollution has been recognized as a contributing factor to sleep disorders (SD), which have been correlated with an elevated susceptibility to a variety of human diseases. Nevertheless, research has not definitively established a connection between SD and interior decorative volatile organic compounds (ID-VOCs), a significant indoor air pollutant. In this study, we employed a mouse model exposed to ID-VOCs to explore the impacts of ID-VOCs exposure on sleep patterns and the potential underlying mechanism. Of the 23 key compositions of ID-VOCs identified, aromatic hydrocarbons were found to be the most prevalent. Exposure to ID-VOCs in mice resulted in SD, characterized by prolonged wake fullness and decreased sleep during the light period. ID-VOCs exposure triggered neuroinflammatory responses in the suprachiasmatic nucleus (SCN), with microglia activation leading to the overproduction of inflammatory cytokines such as tumor necrosis factor-α (TNF-α), interleukin-1α (IL-1α), and complement component 1q (C1q), ultimately inducing A1 astrocytes. Consequently, the upregulation of branched chain amino acid transaminase 2 (BCAT2) in A1 astrocytes resulted in elevated extracellular glutamate and disruption of the wake-sleep transition mechanism, which might be the toxicological mechanism of SD caused by ID-VOCs.

Association of volatile organic compounds exposure with the risk of depression in U.S. adults: a cross‑sectional study from NHANES 2013-2016

BACKGROUND

Volatile organic compounds (VOCs) are a broad class of chemicals, and previous studies showed that VOCs could increase the risk of central nervous system disorders. However, few studies have comprehensively explored their association with depression among general adults.

OBJECTIVE

We aimed to explore the association between blood VOCs and depression risk based on a large cross-sectional study of the National Health and Nutrition Examination Survey (NHANES).

METHODS

We analyzed data from 3449 American adults in the NHANES 2013-2016. Survey-weighted logistic regression model was used to explore the association of ten blood VOCs with depression. Subsequently, the relative importance of the selected VOCs was determined using the XGBoost model. The weighted quantile sum (WQS) regression model was used to explore the overall association of 10 blood VOCs with depression. Subgroup analyses were performed to identify high-risk populations. Finally, restricted cubic spline (RCS) analysis was utilized to explore the dose-response relationship between blood VOCs and the risk of depression.

RESULTS

XGBoost Algorithm model identified blood 2,5-dimethylfuran was the most critical variable in depression. The logistic regression model showed that blood benzene, blood 2,5-dimethylfuran, and blood furan showed a positive correlation with depression. In subgroup analysis, we found that the effects of the above VOCs on depression existed among the female, young middle-aged, and overweight-obese population. Mixture VOCs exposure was positively associated with depression risk (OR = 2.089, 95% CI: 1.299-3.361), and 2,5-dimethylfuran had the largest weights in WQS regression. RCS displayed that blood benzene, blood 2,5-dimethylfuran, and blood furan were positively associated with depression.

CONCLUSION

The results of this study indicated that VOCs exposure was associated with an increased prevalence of depression in U.S. adults. Women, young and middle-aged, and overweight-obese populations are more vulnerable to VOCs.

Systems bioengineering approaches for developmental toxicology

Developmental toxicology is the field of study that examines the effects of chemical and physical agents on developing organisms. By using principles of systems biology and bioengineering, a systems bioengineering approach could be applied to study the complex interactions between developing organisms, the environment, and toxic agents. This approach would result in a holistic understanding of the effects of toxic agents on organisms, by considering the interactions between different biological systems and the impacts of toxicants on those interactions. It would be useful in identifying key biological pathways and mechanisms affected by toxic agents, as well as in the development of predictive models to assess potential risks of exposure to toxicants during development. In this review, we discuss the relevance of systems bioengineering to the field of developmental toxicity and provide up-to-date examples that illustrate the use of engineering principles for this application.

Toxicomethylomics revisited: A state-of-the-science review about DNA methylation modifications in blood cells from workers exposed to toxic agents

Introduction

Epigenetic marks have been proposed as early changes, at the subcellular level, in disease development. To find more specific biomarkers of effect in occupational exposures to toxicants, DNA methylation studies in peripheral blood cells have been performed. The goal of this review is to summarize and contrast findings about DNA methylation in blood cells from workers exposed to toxicants.

Methods

A literature search was performed using PubMed and Web of Science. After first screening, we discarded all studies performed in vitro and in experimental animals, as well as those performed in other cell types other than peripheral blood cells. Results: 116 original research papers met the established criteria, published from 2007 to 2022. The most frequent investigated exposures/labor group were for benzene (18.9%) polycyclic aromatic hydrocarbons (15.5%), particulate matter (10.3%), lead (8.6%), pesticides (7.7%), radiation (4.3%), volatile organic compound mixtures (4.3%), welding fumes (3.4%) chromium (2.5%), toluene (2.5%), firefighters (2.5%), coal (1.7%), hairdressers (1.7%), nanoparticles (1.7%), vinyl chloride (1.7%), and others. Few longitudinal studies have been performed, as well as few of them have explored mitochondrial DNA methylation. Methylation platforms have evolved from analysis in repetitive elements (global methylation), gene-specific promoter methylation, to epigenome-wide studies. The most reported observations were global hypomethylation as well as promoter hypermethylation in exposed groups compared to controls, while methylation at DNA repair/oncogenes genes were the most studied; studies from genome-wide studies detect differentially methylated regions, which could be either hypo or hypermethylated.

Discussion

Some evidence from longitudinal studies suggest that modifications observed in cross-sectional designs may be transitory; then, we cannot say that DNA methylation changes are predictive of disease development due to those exposures.

Conclusion

Due to the heterogeneity in the genes studied, and scarcity of longitudinal studies, we are far away from considering DNA methylation changes as biomarkers of effect in occupational exposures, and nor can we establish a clear functional or pathological correlate for those epigenetic modifications associated with the studied exposures.

Evaluation of HKUST-1 as Volatile Organic Compound Adsorbents for Respiratory Filters

Cyclohexane is a representative of volatile organic compounds (VOCs). VOCs can cause serious health problems in case of continuous exposure; therefore, it is essential to develop efficient personal protective equipment. Historically, activated carbons are used as VOC adsorbents. However, the emergence of promising novel adsorbents, such as metal-organic frameworks, has pushed the research to study their behavior under the same conditions. In this work, the use of the well-known HKUST-1 MOF of different particle sizes (20 μm, 300-600 μm, and 1-1.18 mm) for the adsorption of low-grade (5000 ppm) cyclohexane combined with different water concentrations (dry, 27 and 80% RH) in a fixed bed is proposed. The results were compared under the same conditions for a typically used activated carbon, PICACTIF TA 60. HKUST-1 has higher affinity to cyclohexane than PICACTIF for the whole pressure range studied, especially at low partial pressures. It begins to adsorb much earlier (0.0025 kPa) than the activated carbon (0.01 kPa). However, a different adsorption behavior is evidenced for both materials in the presence of water vapor since HKUST-1 is very hydrophilic in the zone near to the copper open metal sites, whereas PICACTIF is hydrophobic. After three consecutive cycles, good stability results were obtained for the MOF, comparable to activated carbon, even in the presence of water. As the main finding, although the unstability of HKUST-1 is well established under high humid conditions, the kinetic of degradation has not been established so far. Here, it is shown that the time usage of HKUST-1 as the adsorbent for respiratory mask (single pass) is not affected by the degradation of the structure, which may occur on a longer time scale. Finally, shaping by tableting provides good results since it is possible to increase the MOF density by around 69% with minor loss of adsorption capacity. The best fraction is 300-600 μm, reaching cyclohexane breakthrough times around 85 min/cm³ at 80% RH, comparable with PICACTIF-activated carbon and promising for practical applications.

High-throughput screening paradigms in ecotoxicity testing: Emerging prospects and ongoing challenges

The rapidly increasing number of new production chemicals coupled with stringent implementation of global chemical management programs necessities a paradigm shift towards boarder uses of low-cost and high-throughput ecotoxicity testing strategies as well as deeper understanding of cellular and sub-cellular mechanisms of ecotoxicity that can be used in effective risk assessment. The latter will require automated acquisition of biological data, new capabilities for big data analysis as well as computational simulations capable of translating new data into in vivo relevance. However, very few efforts have been so far devoted into the development of automated bioanalytical systems in ecotoxicology. This is in stark contrast to standardized and high-throughput chemical screening and prioritization routines found in modern drug discovery pipelines. As a result, the high-throughput and high-content data acquisition in ecotoxicology is still in its infancy with limited examples focused on cell-free and cell-based assays. In this work we outline recent developments and emerging prospects of high-throughput bioanalytical approaches in ecotoxicology that reach beyond in vitro biotests. We discuss future importance of automated quantitative data acquisition for cell-free, cell-based as well as developments in phytotoxicity and in vivo biotests utilizing small aquatic model organisms. We also discuss recent innovations such as organs-on-a-chip technologies and existing challenges for emerging high-throughput ecotoxicity testing strategies. Lastly, we provide seminal examples of the small number of successful high-throughput implementations that have been employed in prioritization of chemicals and accelerated environmental risk assessment.

Two novel zinc-based MOFs as luminescence sensors to detect phenylglyoxylic acid

Automobile exhaust gases, plastic pollutants, smoking, and other harmful substances can cause serious harm to human beings and the environment. Styrene, as a common airborne toxin, enters the human body through breathing or the skin and is discharged in the form of phenylglyoxylic acid (PGA). Therefore, specific, sensitive and trace detection of PGA is particularly important. Here, two zinc-based metal-organic frameworks {[Zn₂L₁(DMF)₂H₂O](DMF)₂H₂O}_n, {[Zn₄(L₂)₂(DMF)₂(H₂O)₃](DMF)₈}_n (L₁ = 2,5-bis((3-carboxylphenyl)amino)terephthalic acid, L₂ = 2,5-bis((4-carboxyphenyl)amino)terephthalic acid) have been reported as 1 and 2, respectively. Both 1 and 2 present 3D structures, which can both be simplified as 4,4,4-c net topology. It is worth mentioning that 2 has two different kinds of Zn SBUs as connecting nodes in the structure. Besides, compared with the other materials for the detection of PGA, 1 and 2 exhibit relatively low detection limits (LODs), both in water and in urine (where the LODs for 1 in water and urine were 0.33 μM and 0.43 μM in the range of 0-0.39 mM, and those for 2 were 0.28 μM and 0.49 μM in the range of 0-0.59 mM, respectively). In addition, the sensors have excellent anti-interference ability, high stability, rapid response, and can easily distinguish between different concentrations of PGA with the naked eye. The developed paper probes were suitable for practical sensing applications for portable detection of PGA in urine.

Analysis of multi-omics data on the relationship between epigenetic changes and nervous system disorders caused by exposure to environmentally harmful substances

Environmentally hazardous substances and exposure to these can cause various diseases. Volatile organic compounds can easily evaporate into the atmosphere, thereby exerting toxic effects through either the skin or respiratory tract exposures. Toluene, a neurotoxin, has been widely used in various industries. However, it has a detrimental effect on the nervous system (such as hallucinations or memory impairment), while data on the mechanism underlaying its harmful effects remain limited. Therefore, this study investigates the effect of toluene on the nervous system via epigenetic and genetic changes of toluene-exposed individuals. We identified significant epigenetic changes and confirmed that the affected abnormally expressed genes negatively influenced the nervous system. In particular, we confirmed that the miR-15 family, upregulated by toluene, downregulated ABL2, which could affect the R as signaling pathway resulting in neuronal structural abnormalities. Our study suggests that miR-15a-5p, miR-15b-5p, miR-16-5p, miR-301a-3p, and lncRNA NEAT1 may represent effective epigenomic markers associated with neurodegenerative diseases caused by toluene.

Epigenetic Regulation in Exposome-Induced Tumorigenesis: Emerging Roles of ncRNAs

Environmental factors, including pollutants and lifestyle, constitute a significant role in severe, chronic pathologies with an essential societal, economic burden. The measurement of all environmental exposures and assessing their correlation with effects on individual health is defined as the exposome, which interacts with our unique characteristics such as genetics, physiology, and epigenetics. Epigenetics investigates modifications in the expression of genes that do not depend on the underlying DNA sequence. Some studies have confirmed that environmental factors may promote disease in individuals or subsequent progeny through epigenetic alterations. Variations in the epigenetic machinery cause a spectrum of different disorders since these mechanisms are more sensitive to the environment than the genome, due to the inherent reversible nature of the epigenetic landscape. Several epigenetic mechanisms, including modifications in DNA (e.g., methylation), histones, and noncoding RNAs can change genome expression under the exogenous influence. Notably, the role of long noncoding RNAs in epigenetic processes has not been well explored in the context of exposome-induced tumorigenesis. In the present review, our scope is to provide relevant evidence indicating that epigenetic alterations mediate those detrimental effects caused by exposure to environmental toxicants, focusing mainly on a multi-step regulation by diverse noncoding RNAs subtypes.

Sample management: a primary critical starting point for successful omics studies

Biological samples collected from cohort studies are widely utilized in molecular genetic studies and are typically stored long term for future applications, such as omics analyses. The extent of sample availability is determined by proper sample handling, and it is of primary importance for successful omics studies. However, questions on whether samples in long-term storage are properly available for omics experiments has been raised, because the quality and availability of such samples remain unknown until their actual utilization. In that perspective, several guidelines for proper sample management have been suggested. In addition, several researchers assessed how improper management damages sample using mock sample and suggested a set of requirements for sample handling. In this review, we present several considerations for sample handling eligible for omics studies. Focusing on birth cohorts, we describe the types of samples collected from which omics data were generated. This review ultimately aims to provide proper guidelines for sample handling for successful human omics studies.

Prenatal Exposure to Heavy Metals Affects Gestational Age by Altering DNA Methylation Patterns

Environmental exposure is known to have toxic effects. Maternal environmental exposure not only affects mothers but also their fetuses in utero, which may interrupt their early development. Preterm birth, one of the outcomes of prenatal exposure, is a significant factor in lifelong health risks. To understand the effects of prenatal exposome on preterm birth, we studied the association between maternal and prenatal heavy metal exposure and gestational age, using resources from the MOthers' and Children's Environmental Health (MOCEH) study in South Korea. Additionally, a methylation assay was performed to analyze epigenetic mediation using genomic DNA derived from the cord blood of 384 participants in the MOCEH study. The results suggest that maternal cadmium exposure is associated with a decrease in gestational age through an alteration in DNA methylation at a specific CpG site, cg21010642. The CpG site was annotated to a gene involved in early embryonic development. Therefore, irregular methylation patterns at this site may contribute to premature birth by mediating irregular biological mechanisms.