Epigenetics and environmental chemicals

Timing of dietary effects on the epigenome and their potential protective effects against toxins

Exposure to toxins causes lasting damaging effects on the body. Numerous studies in humans and animals suggest that diet has the potential to modify the epigenome and these modifications can be inherited transgenerationally, but few studies investigate how diet can protect against negative effects of toxins. Potential evidence in the primary literature supports that caloric restriction, high-fat diets, high protein-to-carbohydrate ratios, and dietary supplementation protect against environmental toxins and strengthen these effects on their offspring's epigenome. Most notably, the timing when dietary interventions are given - during a parent's early development, pregnancy, and/or lifetime - result in similar transgenerational epigenetic durations. This implies the existence of multiple opportunities to strategically fortify the epigenome. This narrative review explores how to best utilize dietary modifications to modify the epigenome to protect future generations against negative health effects of persistent environmental toxins. Furthermore, by suggesting an ideal diet with specific micronutrients, macronutrients, and food groups, epigenetics can play a key role in the field of preventive medicine. Based on these findings, longitudinal research should be conducted to determine if a high protein, high-fat, and low-carbohydrate diet during a mother's puberty or pregnancy can epigenetically protect against alcohol, tobacco smoke, and air pollution across multiple generations.

Advancing translational exposomics: bridging genome, exposome and personalized medicine

Understanding the interplay between genetic predisposition and environmental and lifestyle exposures is essential for advancing precision medicine and public health. The exposome, defined as the sum of all environmental exposures an individual encounters throughout their lifetime, complements genomic data by elucidating how external and internal exposure factors influence health outcomes. This treatise highlights the emerging discipline of translational exposomics that integrates exposomics and genomics, offering a comprehensive approach to decipher the complex relationships between environmental and lifestyle exposures, genetic variability, and disease phenotypes. We highlight cutting-edge methodologies, including multi-omics technologies, exposome-wide association studies (EWAS), physiology-based biokinetic modeling, and advanced bioinformatics approaches. These tools enable precise characterization of both the external and the internal exposome, facilitating the identification of biomarkers, exposure-response relationships, and disease prediction and mechanisms. We also consider the importance of addressing socio-economic, demographic, and gender disparities in environmental health research. We emphasize how exposome data can contextualize genomic variation and enhance causal inference, especially in studies of vulnerable populations and complex diseases. By showcasing concrete examples and proposing integrative platforms for translational exposomics, this work underscores the critical need to bridge genomics and exposomics to enable precision prevention, risk stratification, and public health decision-making. This integrative approach offers a new paradigm for understanding health and disease beyond genetics alone.

The mediating mechanism of Oct4 in the process of cleft palate induced by 2, 3, 7, 8-tetrachlorodibenz-p-dioxin (TCDD) and all-trans retinoic acid

2, 3, 7, 8-tetrachlorodiphenyl-p-dioxin (TCDD) and all-trans retinoic acid (atRA) have been shown to be inducers of cleft palate (CP). Relevant studies have shown that Oct transcription factor 4 (Oct4) can regulate the expression of the aromatic hydrocarbon receptor (AhR), a target gene of TCDD, as well as influence the retinoic acid signaling pathway. However, the mechanism of Oct4 regulating the interaction between TCDD and atRA in CP pathogenesis remains unclear. In order to solve the above problems, mouse embryonic palatal mesenchymal (MEPM) cells were used for further study. The results show that, TCDD and atRA induce a similar pattern of CP in vivo and significantly inhibit the proliferation of MEPM cells. In vitro, TCDD exposure led to up-regulation of AhR and cytochrome P450 1A1 (CYP1A1) expression and down-regulation of cellular retinoic acid binding protein 2 (CRABP2) and retinoic acid receptor-alpha (RARA) expression in MEPM cells. In addition, atRA exposure resulted in decreased expression of AhR and CYP1A1, and increased protein levels of RARA and CRABP2. When Oct4 was overexpressed, the down-regulation of CRABP2 and RARA by TCDD and the down-regulation of AhR by RA were reversed. The cross results of mass spectrometry and Biogrid database show that HSP90AB1 can bind to Oct4 and AhR. Co-immunoprecipitation (Co-IP) results showed that Oct4 and CRABP2 were combined, which further suggested the mediating effects of Oct4 in CP development. In summary, we hypothesize that AhR-HSP90AB1-Oct4-CRABP2 axis may play the key role mediating the interaction between TCDD and atRA in CP pathogenesis.

Dual-directional epi-genotoxicity assay for assessing chemically induced epigenetic effects utilizing the housekeeping TK gene

Numerous chemicals are associated with carcinogenesis through epigenetic alterations in cells. To detect global epigenetic changes induced by carcinogens, the housekeeping gene can serve as a reporter locus, offering a baseline for identifying shifts in epigenetic marks. To investigate this potential, we developed a simple, cost-effective, and quantitative reporter system to assess chemically induced epigenetic effects, utilizing the thymidine kinase (TK) gene mutation assay as a foundation. Using a standard genotoxicity test cell line, human lymphoblast TK6, we edited the CpG promoter loci of the endogenous TK gene using the CRISPR/dCas9-SunTag-DNMT3A system. This epi-genotoxicity assay, employing modified mTK6 cells, provides a simple method for quantifying chemically induced epigenetic effects. The assay successfully detects both increased TK reversion rates induced by DNMT inhibitors, such as 5-Aza-2'-deoxycytidine and GSK-3484862, and, for the first time, a significant reduction in TK revertant frequency caused by the non-genotoxic carcinogen 12-O-tetradecanoylphorbol-13-acetate (TPA). Chromatin immunoprecipitation and western blotting analyses revealed that TPA treatment led to a global decrease in H3K27Ac levels, likely driven by TPA-mediated inflammation. These results demonstrate the utility of the epi-genotoxicity assay as a valuable tool for evaluating dual-directional epigenetic changes triggered by chemical exposure.

Exposome-wide association study of environmental chemical exposures and epigenetic aging in the national health and nutrition examination survey

Epigenetic clocks can serve as pivotal biomarkers linking environmental exposures with biological aging. However, research on the influence of environmental exposures on epigenetic aging has largely been limited to a small number of chemicals and specific populations. We harnessed data from the National Health and Nutrition Examination Survey 1999-2000 and 2001-2002 cycles to examine exposome-wide associations between environmental exposures and epigenetic aging. A total of 8 epigenetic aging biomarkers were obtained from whole blood in 2,346 participants ranging from 50-84 years of age. A total of 64 environmental exposures including phthalates, metals, pesticides, dioxins, and polychlorinated biphenyls (PCBs) were measured in blood and urine. Associations between log2-transformed/standardized exposure measures and epigenetic age acceleration (EAA) were assessed using survey-weighted generalized linear regression. A 1 standard deviation (SD) increase in log2 serum cadmium levels was associated with higher GrimAge acceleration (beta = 1.23 years, p = 3.63e-06), higher GrimAge2 acceleration (beta = 1.27 years, p = 1.62e-05), and higher DunedinPoAm (beta = 0.02, p = 2.34e-05). A 1 SD increase in log2 serum cotinine levels was associated with higher GrimAge2 acceleration (beta = 1.40 years, p = 6.53e-04) and higher DunedinPoAm (beta = 0.03, p = 6.31e-04). Associations between cadmium and EAA across several clocks persisted in sensitivity models adjusted for serum cotinine levels, and other associations involving lead, dioxins, and PCBs were identified. Several environmental exposures are associated with epigenetic aging in a nationally representative US adult population, with particularly strong associations related to cadmium and cotinine across several epigenetic clocks.

Effects of POPs-induced SIRT6 alteration on intestinal mucosal barrier function: A comprehensive review

Persistent organic pollutants (POPs) are pervasive organic chemicals with significant environmental and ecological ramifications, extending to adverse human health effects due to their toxicity and persistence. The intestinal mucosal barrier, a sophisticated defense mechanism comprising the epithelial layer, mucosal chemistry, and cellular immunity, shields the host from external threats and fosters a symbiotic relationship with intestinal bacteria. Sirtuin 6 (SIRT6), a sirtuin family member, is pivotal in genome and telomere stability, inflammation regulation, and metabolic processes. Result shows POPs have been implicated in the intestinal diseases, particularly in intestinal barrier dysfunction, through mechanisms such as cellular damage, epigenetic alterations, inflammation, microbiota changes, and metabolic disruptions. While the impact of SIRT6 expression changes on intestinal barrier functions has been reviewed, the mechanisms linking POPs to SIRT6 remain elusive. This review summarized the latest research results on the effects of POPs on intestinal barrier, discussed the role of SIRT6 from multiple mechanism perspectives, proposed new research directions on POPs, SIRT6 and intestinal health, and explored the therapeutic potential of SIRT6.

Analysis of the relationship between environmental particulate matter exposure and congenital diseases, as well as the epidemiological trends and burden of impact on newborns

BACKGROUND

With the rise in air pollution levels, there is a growing concern about its impact on public health, particularly on the development of fetuses and newborns. This study investigates the causal relationship between environmental particulate and congenital diseases in newborns, using a Mendelian randomization approach with GWAS data.

METHODS

The study employed Mendelian randomization, utilizing single nucleotide polymorphisms as instrumental variables, to estimate the causal effect of environmental Particulate on congenital diseases. Data from the UK Biobank and FinnGen databases were used to identify independent SNPs associated with environmental particulate. Two-sample Mendelian randomization methods were applied, and the Global Burden of Disease (GBD) database was leveraged to analyze the trends and burden of neonatal diseases from 1990 to 2021 and to forecast the burden for 2022-2052.

RESULTS

Significant causal associations were identified between PM2.5, PM10 and specific congenital malformations, including gallbladder, bile duct, liver anomalies, and malformations of the reproductive organs and broad ligaments. A review of GBD data indicates a decline in the prevalence of neonatal DALYs and YLDs attributed to ambient particulate matter over the past three decades. This may be attributed to improvements in air quality and the implementation of pollution control measures. However, forecasting models indicated potential future risks, suggesting that the burden of disease in newborns due to particulate matter exposure remains a concern.

CONCLUSION

The study provides evidence of a causal link between environmental particulate and congenital diseases in newborns, highlighting the importance of air pollution reduction for the health of newborns. Despite the observed decline in disease burden, the potential future risks underscore the necessity for continued air quality management and the need for further research to understand the complex interactions between environmental particulate, genetic factors, and fetal development.

Dietary fiber intake moderates the impact of blood cadmium on depression: a nationally representative cross-sectional study

BACKGROUND

Cadmium (Cd) is a very poisonous pollutant in the environment that has harmful implications on the neurological system. While high fiber intake is beneficial for mental health, it remains unknown whether the recommended basis for dietary fiber intake (DFI) (14 g/1000 kcal per day) can alleviate Cd-induced depression.

METHODS

The investigation employed data from the National Health and Nutrition Examination Survey (NHANES) conducted between the years 2005 and 2020. The research encompassed individuals who had information on blood Cd concentrations, two 24-hour dietary recalls, and depression diagnosis. We deployed weighted logistic regression analyses to estimate the association of exposure to Cd and DFI with depression risk.

RESULTS

The adjusted ORs (95% CI) for depression were 1.33 (95% CI: 1.08, 1.65) and 1.64 (95% CI: 1.38, 1.94) for the third and fourth quartiles of blood Cd concentrations, respectively (Ptrend < 0.001). Doubling DFI was connected with a 0.78-fold (95% CI: 0.71, 0.85) decrease in the risk of depression. Participants below recommended DFI levels had a greater depression risk with higher blood Cd concentrations: OR of 1.39 (95% CI: 1.11, 1.73) for the third and 1.67 (95% CI: 1.40, 1.98) for the fourth quartile. No significant association between Cd exposure and depression was perceived for participants meeting recommended DFI levels.

CONCLUSIONS

Higher blood Cd burden was associated with elevated depression risk, while recommended DFI could alleviate this effect. High-fiber dietary pattern may counteract the deleterious effect of environmental pollutants such as Cd on depression.

CLINICAL TRIAL NUMBER

Not applicable.

Exposure to a Titanium Dioxide Product Alters DNA Methylation in Human Cells

The safety of titanium dioxide (TiO2), widely used in foods and personal care products, has been of ongoing concern. Significant toxicity of TiO2 has been reported, suggesting a risk to human health. To evaluate its potential epigenotoxicity, the effect of exposure to a TiO2 product to which humans could be exposed on DNA methylation, a primary epigenetic mechanism, was investigated using two human cell lines (Caco-2 (colorectal) and HepG2 (liver)) relevant to human exposure. Global methylation was determined by enzyme-linked immunosorbent assay-based immunochemical analysis. Gene promoter methylation was evaluated using EpiTect Methyl II Signature PCR System Array technology. Expression of DNA methyltransferases, MBD2, and URHF1 was quantified by qRT-PCR. A decrease in global DNA methylation was observed in both cell lines. Across the cell lines, seven genes (BNIP3, DNAJC15, GADD45G, GDF15, INSIG1, SCARA3, and TP53) were identified in which promoters were methylated. Changes in promoter methylation were associated with gene expression. Results also revealed aberrant expression of regulatory genes, DNA methyltransferases, MBD2, and UHRF1. Findings from the study clearly demonstrate the impact of TiO2 exposure on DNA methylation in two cell types, supporting the potential involvement of this epigenetic mechanism in its biological responses. Hence, epigenetic studies are critical for complete assessment of potential risk from exposure.

Parental arsenic exposure and tissue-specific DNA methylation in Bangladeshi infants with spina bifida

An emerging hypothesis linking arsenic toxicity involves altered epigenetic mechanisms, such as DNA methylation. In this study, we examined the relationship between parents' arsenic exposure and DNA methylation in tissues obtained from 28 infants with spina bifida from Bangladesh. We analyzed arsenic in parents' toenails using inductively coupled plasma mass spectrometry (ICP-MS). DNA methylation was measured in infants' dural tissue, buccal swabs, and whole blood using the Illumina Infinium MethylationEPIC BeadChip. We performed epigenome-wide association analyses (EWAS) and tested differentially methylated regions (DMRs). In EWAS, DNA methylation at cg24039697 in dural tissue was positively associated (β = 0.59, p = 7.6 × 10-9) with father's toenail arsenic concentrations, adjusting for covariates. We did not identify any CpG sites related to father's arsenic exposure in the other tissues, or any CpG sites related to mother's arsenic exposure. Gene ontology analysis identified many biological pathways of interest, including the Wnt signaling pathways. We identified several DMRs across the tissues related to arsenic exposure that included probes mapping to genes that have previously been identified in studies of neural tube defects. This study emphasizes the potential impact of arsenic exposure in fathers, often understudied in epidemiological studies, on DNA methylation in a unique neurological tissue specific to spina bifida.

Prenatal Perfluoroalkyl Substance Exposure in Association with Global Histone Post-Translational Methylation in 2-Year-Old Children

Perfluoroalkyl substances (PFASs) have elimination half-lives in years in humans and are persistent in the environment. PFASs can cross the placenta and impact fetal development. Exposure to PFASs may lead to adverse effects through epigenetic mechanisms. This study aimed to investigate whether prenatal exposure to perfluorooctyl sulfonate (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), and perfluoroundecanoic acid (PFUA) was associated with global histone methylation level changes among the 130 2-year-old children followed-up in a birth cohort study in Taiwan. PFOS, PFOA, PFNA, and PFUA were measured by UHPLC/MS/MS in cord blood. Global histone methylation levels were measured from the blood leukocytes of 2-year-old children by Western blotting. Multivariable regression analyses were applied to adjust for potential confounding effects. Among the 2-year-old children, an IQR increase in the natural log-transformed PFUA exposure was associated with an increased H3K4me3 level by 2.76-fold (95%CI = (0.79, 4.73), p = 0.007). PFOA and PFNA exposures was associated with a decreased H3K27me3 level by 2.35-fold (95%CI = (-4.29, -0.41), p = 0.01) and 2.01-fold (95%CI = (-4.00, -0.03), p = 0.04), respectively. Our findings suggest that prenatal PFAS exposure affected histone post-translational modifications.

Genetics, Epigenetics, and the Environment: Are Precision Medicine, Provider Compassion, and Social Justice Effective Public Health Measures to Mitigate Disease Risk and Severity?

Environmental forces impacting public health include exposure to toxic substances, adverse childhood experiences (ACEs), diet, and exercise. Here, we examine the first two of these forces in some detail since they may be amenable to correction through cultural, medical, and practitioner intervention. At the same time, changing people's dietary and exercise routines are likely more resistant to these interventions and are referred to only incidentally in this review. That is, societal efforts could prevent exposure to toxicants and ACEs-not necessarily requiring cooperation by the affected individuals-whereas changing diet and exercise practices requires an individual's discipline. Toxic substances considered in this review include endocrine disruptors, arsenics, 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), the organic solvent, Trichloroethylene (TCE), and the Benzo[a]pyrene (B[a]P) produced from incomplete combustion of tobacco and other organic materials. Exposure to each of these toxic substances may have serious adverse health effects, especially in genetically more susceptible individuals. For example, children of mothers exposed to the endocrine disruptor, Atrazine, have significantly lower birth length, weight, and head circumference. Moreover, male offspring exhibit genital abnormalities, and all of these effects may be transgenerational. However, analyses of interactions among genes, the environment, and epigenetic modifications have already revealed distinctive individual risks of adverse reactions to toxic exposure. So, interventions through precision medicine might improve the health of those exposed individuals. Adults previously exposed to more than one ACE (e.g., child abuse and inter-parental violence) are more likely to develop anxiety, cancer, and diabetes. Detecting ACE exposures in children in the general population is fraught with difficulty. Thus, the risks of ACEs to our health remain even more insidious than exposures to toxicants. Nevertheless, higher provider compassion is associated with significantly better clinical outcomes for patients with these afflictions. For all these reasons, the first major aim of this review is to recount several of the major forces contributing to or impairing public health. Our second major aim is to examine mitigating influences on these forces, including social justice and provider compassion in the setting of precision medicine. Idealistically, these mitigators might eventually lead to the development of more cooperative and compassionate cultures and societies.

Time-course characterization of whole-transcriptome dynamics of HepG2/C3A spheroids and its toxicological implications

Physiologically relevant in vitro models are a priority in predictive toxicology to replace and/or reduce animal experiments. The compromised toxicant metabolism of many immortalized human liver cell lines grown as monolayers as compared to in vivo metabolism limits their physiological relevance. However, recent efforts to culture liver cells in a 3D environment, such as spheroids, to better mimic the in vivo conditions, may enhance the toxicant metabolism of human liver cell lines. In this study, we characterized the dynamic changes in the transcriptome of HepG2/C3A hepatocarcinoma cell spheroids maintained in a clinostat system (CelVivo) to gain insight into the metabolic capacity of this model as a function of spheroid size and culture time. We assessed morphological changes (size, necrotic core), cell health, and proliferation rate from initial spheroid seeding to 35 days of continuous culture in conjunction with a time-course (0, 3, 7, 10, 14, 21, 28 days) of the transcriptome (TempO-Seq, BioSpyder). The phenotypic characteristics of HepG2/C3A growing in spheroids were comparable to monolayer growth until ∼Day 12 (Day 10-14) when a significant decrease in cell doubling rate was noted which was concurrent with down-regulation of cell proliferation and cell cycle pathways over this time period. Principal component analysis of the transcriptome data suggests that the Day 3, 7, and 10 spheroids are pronouncedly different from the Day 14, 21, and 28 spheroids in support of a biological transition time point during the long-term 3D spheroid cultures. The expression of genes encoding cellular components involved in toxicant metabolism and transport rapidly increased during the early time points of spheroids to peak at Day 7 or Day 10 as compared to monolayer cultures with a gradual decrease in expression with further culture, suggesting the most metabolically responsive time window for exposure studies. Overall, we provide baseline information on the cellular and molecular characterization, with a particular focus on toxicant metabolic capacity dynamics and cell growth, of HepG2/C3A 3D spheroid cultures over time.

Prevalence and risk of occurrence of visible birth defects in mining areas in South Kivu: A hospital-based cross-sectional study

BACKGROUND

Possible contamination related to mining activities might contribute with other risk factors in increasing the burden of birth defects (BDs) in many developing countries including the Democratic Republic of Congo. The subsequent prevalence is frequently underestimated. Implementation of focused public health interventions is hindered by the paucity of comprehensive data. We assessed the potential impact of mining on the prevalence and occurrence of visible BDs in neonates in South Kivu (SK).

METHODS

A hospital-based cross-sectional study was conducted among 65,474 newborns registered in 7 hospitals in SK from 2016-2021. Hospitals were categorized based on mining activities in their respective catchment areas. Living in a mining zone was the exposure, whereas the outcome was visible BDs. Prevalence was estimated per 100,000 live births, and risk of occurrence with odds ratio (OR) and their 95% confidence interval.

RESULTS

261 neonates with visible BDs were recorded accounting for a prevalence of 399 cases per 100,000 live births. The prevalence ranges between 217 and 1365 cases per 100,000 live births. An increased risk was found in mining zones(OR=2.07; 95%CI=1.59-2.68), Mubumbano(OR=1.72, 95%CI=1.22-2.43), and Mwenga(OR=3.89, 95%CI=2.73-5.54), whereas a reduced risk was reported in non-mining zones(OR=0.48, 95%CI=0.37-0.62) in Katana (OR=0.49, 95%CI=0.33-0.73). Musculoskeletal(28.74%) and central nervous systems(19.92%) were the most common BDs. A significant difference in prevalence for BDs involving the face, GI system and abdominal wall, musculoskeletal, central nervous and genitourinary systems between mining and non-mining zones was found(p<0.001).

CONCLUSION

There is an excessive risk for visible BDs in areas with hazardous mining activities in SK region.​​ More complex studies are needed to define the possible causal relationship. Moreover, findings generated herein should be corroborated by other research design, periodically monitored by public health authorities, and used to inform initiatives promoting enhanced environmental health, access to pediatric surgical care, and public health campaigns aimed at decreasing risk of BDs.

Benzene exposure and pediatric leukemia: From molecular clues to epidemiological insights

According to the International Agency for Research on Cancer, leukemia ranks 14th in incidence and 11th in mortality and has a 5-year prevalence of approximately 1300,000 cases. Acute lymphoblastic leukemia is the most common hematopoietic syndrome in children during the first 5 years of life and represents approximately 75 % of all neoplasms among the pediatric population. The development of leukemia is strongly governed by DNA alterations that accelerate the growth of bone marrow cells. Currently, the most examined factor in pediatric leukemia is exposure to multiple compounds, such as hydrocarbons. Benzene, an aromatic hydrocarbon, can cause health challenges and is categorized as a carcinogen. Benzene toxicity has been widely associated with occupational exposure. Importantly, studies are underway to generate evidence that can provide clues regarding the risk of environmental benzene exposure and hematological problems in children. In this review, we summarize the existing evidence regarding the effects of benzene on pediatric leukemia, the associations between the effect of benzene on carcinogenesis, and the presence of certain molecular signatures in benzene-associated pediatric leukemia. Although there is sufficient evidence regarding the effects of benzene on carcinogenesis and leukemia, epidemiological research has primarily focused on occupational risk. Moreover, most benzene-induced molecular and cytogenetic alterations have been widely described in adults but not in the pediatric population. Thus, epidemiological efforts are crucial in the pediatric population in terms of epidemiological, clinical, and biomedical research.

Could environmental exposure and climate change Be a key factor in the rising incidence of early onset colorectal cancer?

The emergence of early onset colorectal cancer (EOCRC) is believed to result from the complex interplay between external environmental factors and internal molecular processes. This review investigates the potential association between environmental exposure to chemicals and climate change and the increased incidence of EOCRC, focusing on their effects on gut microbiota (GM) dynamics. The manuscript explores the birth cohort effect, suggesting that individuals born after 1950 may be at higher risk of developing EOCRC due to cumulative environmental exposures. Furthermore, we also reviewed the impact of environmental pollution, including particulate matter and endocrine disrupting chemicals (EDCs), as well as global warming, on GM disturbance. Environmental exposures have the potential to disrupt GM composition and diversity, leading to dysbiosis, chronic inflammation, and oxidative stress, which are known risk factors associated with EOCRC. Particulate matter can enter the gastrointestinal tract, modifying GM composition and promoting the proliferation of pathogenic bacteria while diminishing beneficial bacteria. Similarly, EDCs, can induce GM alterations and inflammation, further increasing the risk of EOCRC. Additionally, global warming can influence GM through shifts in gut environmental conditions, affecting the host's immune response and potentially increasing EOCRC risk. To summarize, environmental exposure to chemicals and climate change since 1950 has been implicated as contributing factors to the rising incidence of EOCRC. Disruptions in gut microbiota homeostasis play a crucial role in mediating these associations. Consequently, there is a pressing need for enhanced environmental policies aimed at minimizing exposure to pollutants, safeguarding public health, and mitigating the burden of EOCRC.

Bisphenol A (BPA) and neurological disorders: An overview

The human body is commonly exposed to bisphenol A (BPA), which is widely used in consumer and industrial products. BPA is an endocrine-disrupting chemical that has adverse effects on human health. In particular, many studies have shown that BPA can cause various neurological disorders by affecting brain development and neural function during prenatal, infancy, childhood, and adulthood exposure. In this review, we discussed the correlation between BPA and neurological disorders based on molecular cell biology, neurophysiology, and behavioral studies of the effects of BPA on brain development and function. Recent studies, both animal and epidemiological, strongly indicate that BPA significantly impacts brain development and function. It hinders neural processes, such as proliferation, migration, and differentiation during development, affecting synaptic formation and activity. As a result, BPA is implicated in neurodevelopmental and neuropsychiatric disorders like autism spectrum disorder (ASD), attention-deficit hyperactivity disorder (ADHD), and schizophrenia.

Genetic variants reduced POPs-related colorectal cancer risk via altering miRNA binding affinity and m6A modification

Exposure to persistent organic pollutants (POPs) may contribute to colorectal cancer risk, but the underlying mechanisms of crucial POPs exposure remain unclear. Hence, we systematically investigated the associations among POPs exposure, genetics and epigenetics and their effects on colorectal cancer. A case-control study was conducted in the Chinese population for detecting POPs levels. We measured the concentrations of 24 POPs in the plasma using gas chromatography-tandem mass spectrometry (GC-MS/MS) and evaluated the clinical significance of POPs by calculating the area under the receiver operating characteristic curve (AUC). To assess the associations between candidate genetic variants and colorectal cancer risk, unconditional logistic regression was used. Compared with healthy control individuals, individuals with colorectal cancer exhibited higher concentrations of the majority of POPs. Exposure to PCB153 was positively associated with colorectal cancer risk, and PCB153 demonstrated superior accuracy (AUC=0.72) for predicting colorectal cancer compared to other analytes. On PCB153-related genes, the rs67734009 C allele was significantly associated with reduced colorectal cancer risk and lower plasma levels of PCB153. Moreover, rs67734009 exhibited an expression quantitative trait locus (eQTL) effect on ESR1, of which the expression level was negatively related to PCB153 concentration. Mechanistically, the risk allele of rs67734009 increased ESR1 expression via miR-3492 binding and m6A modification. Collectively, this study sheds light on potential genetic and epigenetic mechanisms linking PCB153 exposure and colorectal cancer risk, thereby providing insight into the accurate protection against POPs exposure.

Integrating Multi-Omics with environmental data for precision health: A novel analytic framework and case study on prenatal mercury induced childhood fatty liver disease

BACKGROUND

Precision Health aims to revolutionize disease prevention by leveraging information across multiple omic datasets (multi-omics). However, existing methods generally do not consider personalized environmental risk factors (e.g., environmental pollutants).

OBJECTIVE

To develop and apply a precision health framework which combines multiomic integration (including early, intermediate, and late integration, representing sequential stages at which omics layers are combined for modeling) with mediation approaches (including high-dimensional mediation to identify biomarkers, mediation with latent factors to identify pathways, and integrated/quasi-mediation to identify high-risk subpopulations) to identify novel biomarkers of prenatal mercury induced metabolic dysfunction-associated fatty liver disease (MAFLD), elucidate molecular pathways linking prenatal mercury with MAFLD in children, and identify high-risk children based on integrated exposure and multiomics data.

METHODS

This prospective cohort study used data from 420 mother-child pairs from the Human Early Life Exposome (HELIX) project. Mercury concentrations were determined in maternal or cord blood from pregnancy. Cytokeratin 18 (CK-18; a MAFLD biomarker) and five omics layers (DNA Methylation, gene transcription, microRNA, proteins, and metabolites) were measured in blood in childhood (age 6-10 years).

RESULTS

Each standard deviation increase in prenatal mercury was associated with a 0.11 [95% confidence interval: 0.02-0.21] standard deviation increase in CK-18. High dimensional mediation analysis identified 10 biomarkers linking prenatal mercury and CK-18, including six CpG sites and four transcripts. Mediation with latent factors identified molecular pathways linking mercury and MAFLD, including altered cytokine signaling and hepatic stellate cell activation. Integrated/quasi-mediation identified high risk subgroups of children based on unique combinations of exposure levels, omics profiles (driven by epigenetic markers), and MAFLD.

CONCLUSIONS

Prenatal mercury exposure is associated with elevated liver enzymes in childhood, likely through alterations in DNA methylation and gene expression. Our analytic framework can be applied across many different fields and serve as a resource to help guide future precision health investigations.

Impact of antenatal exposure to a mixture of persistent organic pollutants on intellectual development

OBJECTIVE

Strong experimental evidence exists that several endocrine disrupting chemicals (EDCs) have neurobehavioral toxicity. However, evidence of associations between prenatal exposure and child's cognitive development is inconsistent. Moreover, toxicants are generally analyzed one by one without considering aggregate effects. We examined here the impact of a prenatal exposure to a mixture of persistent organic pollutants (POPs) on intellectual abilities in preschool children, and compared their effects to those described in the literature.

METHODS

Sixty-two children were included in a longitudinal cohort. Four organochlorine pesticides, four polychlorinated biphenyls (PCBs) and seven perfluorinated compounds (PFCs) were measured in cord blood. Intellectual abilities were assessed at 6 years of age using the Wechsler Preschool and Primary Scale of Intelligence 4th ed. (WPPSI-IV). We examined the associations between a mixture of POPs and cognitive performances using principal components approach (PCA) and weighted quantile sum (WQS) regression taking sex difference into account.

RESULTS

No negative correlation was found when analyses were performed on boys and girls together. In sex-stratified analyses, lower scores in full scale intelligence quotient (FSIQ) and fluid reasoning index (FRI) were observed in boys most exposed to a mixture of POPs. Increase of the WQS index was also associated with lower verbal comprehension index (VCI) scores in girls only. No other negative correlation was found using both WQS and PCA models.

CONCLUSION

Our study suggests deleterious associations between antenatal exposure to a mixture of POPs and sex-specific cognitive level, clarifying some trends described in the literature.

Multiomics Screening Identified CpG Sites and Genes That Mediate the Impact of Exposure to Environmental Chemicals on Cardiometabolic Traits

An understanding of the molecular mechanism whereby an environmental chemical causes a disease is important for the purposes of future applications. In this study, a multiomics workflow was designed to combine several publicly available datasets in order to identify CpG sites and genes that mediate the impact of exposure to environmental chemicals on cardiometabolic traits. Organophosphate and prenatal lead exposure were previously reported to change methylation level at the cg23627948 site. The outcome of the analyses conducted in this study revealed that, as the cg23627948 site becomes methylated, the expression of the GNA12 gene decreases, which leads to a higher body fat percentage. Prenatal perfluorooctane sulfonate exposure was reported to increase the methylation level at the cg21153102 site. Findings of this study revealed that higher methylation at this site contributes to higher diastolic blood pressure by changing the expression of CHP1 and GCHFR genes. Moreover, HKR1 mediates the impact of B12 supplementation → cg05280698 hypermethylation on higher kidney function, while CTDNEP1 mediates the impact of air pollution → cg03186999 hypomethylation on higher systolic blood pressure. This study investigates CpG sites and genes that mediate the impact of environmental chemicals on cardiometabolic traits. Furthermore, the multiomics approach described in this study provides a convenient workflow with which to investigate the impact of an environmental factor on the body's biomarkers, and, consequently, on health conditions, using publicly available data.

β-Hexachlorocyclohexane triggers neuroinflammatory activity, epigenetic histone post-translational modifications and cognitive dysfunction

Persistent organic pollutants (POPs), which encompass pesticides and industrial chemicals widely utilized across the globe, pose a covert threat to human health. β-hexachlorocyclohexane (β-HCH) is an organochlorine pesticide with striking stability, still illegally dumped in many countries, and recognized as responsible for several pathogenetic mechanisms. This study represents a pioneering exploration into the neurotoxic effects induced by the exposure to β-HCH specifically targeting neuronal cells (N2a), microglia (BV-2), and C57BL/6 mice. As shown by western blot and qPCR analyses, the administration of β-HCH triggered a modulation of NF-κB, a key factor influencing both inflammation and pro-inflammatory cytokines expression. We demonstrated by proteomic and western blot techniques epigenetic modifications in H3 histone induced by β-HCH. Histone acetylation of H3K9 and H3K27 increased in N2a, and in the prefrontal cortex of C57BL/6 mice administered with β-HCH, whereas it decreased in BV-2 cells and in the hippocampus. We also observed a severe detrimental effect on recognition memory and spatial navigation by the Novel Object Recognition Test (NORT) and the Object Place Recognition Task (OPRT) behavioural tests. Cognitive impairment was linked to decreased expression of the genes BDNF and SNAP-25, which are mediators involved in synaptic function and activity. The obtained results expand our understanding of the harmful impact produced by β-HCH exposure by highlighting its implication in the pathogenesis of neurological diseases. These findings will support intervention programs to limit the risk induced by exposure to POPs. Regulatory agencies should block further illicit use, causing environmental hazards and endangering human and animal health.

Food, nutrition, and autism: from soil to fork

Food and nutrition-related factors have the potential to impact development of autism spectrum disorder (ASD) and quality of life for people with ASD, but gaps in evidence exist. On 10 November 2022, Tufts University's Friedman School of Nutrition Science and Policy and Food and Nutrition Innovation Institute hosted a 1-d meeting to explore the evidence and evidence gaps regarding the relationships of food and nutrition with ASD. This meeting report summarizes the presentations and deliberations from the meeting. Topics addressed included prenatal and child dietary intake, the microbiome, obesity, food-related environmental exposures, mechanisms and biological processes linking these factors and ASD, food-related social factors, and data sources for future research. Presentations highlighted evidence for protective associations with prenatal folic acid supplementation and ASD development, increases in risk of ASD with maternal gestational obesity, and the potential for exposure to environmental contaminants in foods and food packaging to influence ASD development. The importance of the maternal and child microbiome in ASD development or ASD-related behaviors in the child was reviewed, as was the role of discrimination in leading to disparities in environmental exposures and psychosocial factors that may influence ASD. The role of child diet and high prevalence of food selectivity in children with ASD and its association with adverse outcomes were also discussed. Priority evidence gaps identified by participants include further clarifying ASD development, including biomarkers and key mechanisms; interactions among psychosocial, social, and biological determinants; interventions addressing diet, supplementation, and the microbiome to prevent and improve quality of life for people with ASD; and mechanisms of action of diet-related factors associated with ASD. Participants developed research proposals to address the priority evidence gaps. The workshop findings serve as a foundation for future prioritization of scientific research to address evidence gaps related to food, nutrition, and ASD.

DNA methylation is associated with hair trace elements in female adolescents from two vulnerable populations in the Colombian Caribbean

Exposure to trace elements (TEs) influences DNA methylation patterns, which may be associated with disease development. Vulnerable populations, such as adolescents undergoing maturity, are susceptible to the effects of TE exposure. The aim of this study was to analyze the association of hair TE concentration with DNA methylation in a sample from female adolescents living in two communities in the Colombian Caribbean coast. Hair and blood samples were obtained from 45 females, between 13 and 16 years of age. Seventeen TEs were quantified in hair samples. DNA methylation was measured in leukocytes using the Infinium MethylationEPIC BeadChip. Linear models were employed to identify differentially methylated positions (DMPs) adjusting for age, body mass index, mother's education, and cell type composition. Among the tested elements, vanadium, chromium, nickel, copper, zinc, yttrium, tin, and barium were significantly associated with DMPs (false discovery rate < 0.05), registering 225, 1, 2, 184, 1, 209 189, and 104 hits, respectively. Most of the DMPs were positively associated with TEs and located in open sea regions. The greatest number of DMPs was annotated to the HOXA3 and FOXO3 genes, related to regulation of gene expression and oxidative stress, respectively. These findings suggest that DNA methylation may be involved in linking exposure to TEs among female adolescents to downstream health risks.

Genetic and epigenetic modulations in toxicity: The two-sided roles of heavy metals and polycyclic aromatic hydrocarbons from the environment

This study emphasizes the importance of considering the metabolic and toxicity mechanisms of environmental concern chemicals in real-life exposure scenarios. Furthermore, environmental chemicals may require metabolic activation to become toxic, and competition for binding sites on receptors can affect the severity of toxicity. The multicomplex process of chemical toxicity is reflected in the activation of multiple pathways during toxicity of which AhR activation is major. Real-life exposure to a mixture of concern chemicals is common, and the composition of these chemicals determines the severity of toxicity. Nutritional essential elements can mitigate the toxicity of toxic heavy metals, while the types and ratio of composition of PAH can either increase or decrease toxicity. The epigenetic mechanisms of heavy metals and PAH toxicity involves either down-regulation or up-regulation of some non-coding RNAs (ncRNAs) whereas specific small RNAs (sRNAs) may have dual role depending on the tissue and circumstance of expression. Similarly, decrease DNA methylation and histone modification are major players in heavy metals and PAH mediated toxicity and FLT1 hypermethylation is a major process in PAH induced carcinogenesis. Overall, this review provides the understanding of the metabolism of environmental concern chemicals, emphasizing the importance of considering mixed compositions and real-life exposure scenarios in assessing their potential effects on human health and diseases development as well as the dual mechanism of toxicity via genetic or epigenetic axis.

New approach methods to assess developmental and adult neurotoxicity for regulatory use: a PARC work package 5 project

In the European regulatory context, rodent in vivo studies are the predominant source of neurotoxicity information. Although they form a cornerstone of neurotoxicological assessments, they are costly and the topic of ethical debate. While the public expects chemicals and products to be safe for the developing and mature nervous systems, considerable numbers of chemicals in commerce have not, or only to a limited extent, been assessed for their potential to cause neurotoxicity. As such, there is a societal push toward the replacement of animal models with in vitro or alternative methods. New approach methods (NAMs) can contribute to the regulatory knowledge base, increase chemical safety, and modernize chemical hazard and risk assessment. Provided they reach an acceptable level of regulatory relevance and reliability, NAMs may be considered as replacements for specific in vivo studies. The European Partnership for the Assessment of Risks from Chemicals (PARC) addresses challenges to the development and implementation of NAMs in chemical risk assessment. In collaboration with regulatory agencies, Project 5.2.1e (Neurotoxicity) aims to develop and evaluate NAMs for developmental neurotoxicity (DNT) and adult neurotoxicity (ANT) and to understand the applicability domain of specific NAMs for the detection of endocrine disruption and epigenetic perturbation. To speed up assay time and reduce costs, we identify early indicators of later-onset effects. Ultimately, we will assemble second-generation developmental neurotoxicity and first-generation adult neurotoxicity test batteries, both of which aim to provide regulatory hazard and risk assessors and industry stakeholders with robust, speedy, lower-cost, and informative next-generation hazard and risk assessment tools.

What does scientometry tell us about mercury toxicology and its biological impairments?

Mercury is a toxic pollutant that poses risks to both human and environmental health, making it a pressing public health concern. This study aimed to summarize the knowledge on mercury toxicology and the biological impairments caused by exposure to mercury in experimental studies and/or diagnosis in humans. The research was conducted on the main collection of Web of Science, employing as a methodological tool a bibliometric analysis. The selected articles were analyzed, and extracted data such as publication year, journal, author, title, number of citations, corresponding author's country, keywords, and the knowledge mapping was performed about the type of study, chemical form of mercury, exposure period, origin of exposure, tissue/fluid of exposure measurement, mercury concentration, evaluation period (age), mercury effect, model experiments, dose, exposure pathway, and time of exposure. The selected articles were published between 1965 and 2021, with Clarkson TW being the most cited author who has also published the most articles. A total of 38% of the publications were from the USA. These studies assessed the prenatal and postnatal effects of mercury, emphasizing the impact of methylmercury on neurodevelopment, including motor and cognitive evaluations, the association between mercury and autism, and an evaluation of its protective effects against mercury toxicity. In observational studies, the blood, umbilical cord, and hair were the most frequently used for measuring mercury levels. Our data analysis reveals that mercury neurotoxicology has been extensively explored, but the association among the outcomes evaluated in experimental studies has yet to be strengthened. Providing metric evidence on what is unexplored allows for new studies that may help governmental and non-governmental organizations develop guidelines and policies.

Determination of diethylstilbestrol in environmental water based on electrochemical senser modified with vanadium based metal organic framework material composite

In this research, the MIL-47/ACET/Nafion/GCE electrochemical senser for the determination of diethylstilbestrol (DES) was prepared with vanadyl sulfate (VOSO4·nH2O) and terephthalic acid (H2BDC) as the main raw materials, compounded with acetylene black (ACET) and perfluorosulfonic acid polymer (Nafion). The compound DES belongs to the category of estrogens, and prolonged exposure to the environment can have detrimental effects on the physiological functioning of both humans and animals. Due to the strong DES enrichment performance of MIL-47(V-MOFs) with large specific surface area, in addition to the excellent conductivity and electrocatalysis of composite materials, this modified senser had good electrochemical response to DES. With differential pulse voltammetry, in optimum condition of 0.1 M NaH2PO4-Na2HPO4at pH = 7.0, potential interval of -1.0 to 1.0 V, enrichment time of 120 s and enrichment potential of 0.2 V, there was a good linear relationship between peak current and the concentration of DES over the range of 0.1 and 50μM, and the limit of detection was 0.008μM. The sensor accurately detected DES in actual water samples, with recovery rates ranging from 89.21% to 105.3%. The electrochemical sensor was simple to prepare and had practical significance for the detection of DES in water. The research results of the sensor provide another alternative analytical means for the sensitive detection of DES in the environment, which is important for maintaining public health.

Early-life environmental effects on birds: epigenetics and microbiome as mechanisms underlying long-lasting phenotypic changes

Although the long-lasting effects of variation in early-life environment have been well documented across organisms, the underlying causal mechanisms are only recently starting to be unraveled. Yet understanding the underlying mechanisms of long-lasting effects can help us predict how organisms will respond to changing environments. Birds offer a great system in which to study developmental plasticity and its underlying mechanisms owing to the production of large external eggs and variation in developmental trajectories, combined with a long tradition of applied, physiological, ecological and evolutionary research. Epigenetic changes (such as DNA methylation) have been suggested to be a key mechanism mediating long-lasting effects of the early-life environment across taxa. More recently, changes in the early-life gut microbiome have been identified as another potential mediator of developmental plasticity. As a first step in understanding whether these mechanisms contribute to developmental plasticity in birds, this Review summarizes how changes in early-life environment (both prenatal and postnatal) influence epigenetic markers and the gut microbiome. The literature shows how both early-life biotic (such as resources and social environment) and abiotic (thermal environment and various anthropogenic stressors) factors modify epigenetic markers and the gut microbiome in birds, yet data concerning many other environmental factors are limited. The causal links of these modifications to lasting phenotypic changes are still scarce, but changes in the hypothalamic-pituitary-adrenal axis have been identified as one putative pathway. This Review identifies several knowledge gaps, including data on the long-term effects, stability of the molecular changes, and lack of diversity in the systems studied, and provides directions for future research.

MicroRNAs in Tetrahymena thermophila: An epigenetic regulatory mechanism in the response to cadmium stress

Among the epigenetic mechanisms based on non-coding RNA are microRNAs (miRNAs) that are involved in the post-transcriptional regulation of mRNAs. In many organisms, the expression of genes involved in the cellular response to biotic or abiotic stress depends on the regulation, generally inhibitory, performed by miRNAs. For the first time in the eukaryotic microorganism (ciliate-model) Tetrahymena thermophila, miRNAs involved in the post-transcriptional regulation of transcripts linked to the response to cadmium have been isolated and analyzed. Forty de novo miRNAs (we named tte-miRNAs) have been isolated from control and Cd-treated populations (1 or 24 h exposures). An exhaustive comparative analysis of the features of these mature tte-miRNAs and their precursor sequences (pre-tte-miRNAs) confirms that they are true miRNAs. In addition to the three types of miRNA isoforms previously described in other organisms, two new types are also described among the tte-miRNAs studied. A certain percentage of the pre-tte-miRNA sequences are in introns from genes with many introns, and have been defined as 5', 3'-tailed mirtrons. A qRT-PCR analysis of selected tte-miRNAs together with some of their targets has validated them. Cd is one of the most toxic metals for the cell, which must defend itself against its toxicity by various mechanisms, such as expulsion by membrane pumps, chelation by metallothioneins, among others. Like other toxic metals, Cd also causes a well-known series of cellular effects such as intense proteotoxicity. Many of the targets that are regulated by the tte-miRNAs are transcripts encoding proteins that fit into these defense mechanisms and toxic metal effects.

A geospatial assessment of industrial releases and pediatric neuroblastic tumours at diagnosis: A retrospective case series

Environmental risk factors associated with malignancy of pediatric neuroblastic tumours are not well-known and few studies have examined the relationship between industrial emissions and neuroblastic tumour diagnosis. A retrospective case series of 310 patients was evaluated at a tertiary hospital in Toronto, Canada between January 2008, and December 2018. Data from the National Pollutant Release Inventory (NPRI) were used to estimate exposure for a dozen chemicals with known or suspected carcinogenicity or embryotoxicity. Comparative analysis and predictive logistic regression models for malignant versus benign neuroblastic tumours included variables for residential proximity, number, and type of industries, mean total emissions within 2 km, and inverse distance weighted (IDW) quantity of chemical-specific industrial emissions estimated within 10 and 50 km of cases. No significant difference was seen between malignant and benign cases with respect to the mean nearest residential distance to industry, the number or type of industry, or the mean total quantity of industrial emissions within a 2 km radius of residential location of cases. However, there were statistically significant differences in the interpolated IDW emissions of dioxins and furans released between 1993 and 2019 within 10 km. Concentrations were significantly higher in malignant neuroblastic tumours at 1.65 grams (g) toxic equivalent (TEQ) (SD 2.01 g TEQ) compared to benign neuroblastic tumours at 1.13 g TEQ (SD 0.84 g TEQ) (p = 0.05). Within 50 km 3 years prior to diagnosis, malignant cases were exposed to higher levels of aluminum, benzene, and nitrogen dioxide (p = 0.02, p = 0.04, and p = 0.02 respectively). Regression analysis of the IDW emissions within a 50 km radius revealed higher odds of exposure to benzene for malignant neuroblastic tumours (OR = 1.03, CI: 1.01-1.05, p = 0.01). These preliminary findings suggest a potential role of industrial emissions in the development of malignant pediatric neuroblastic tumours and underscore the need for further research to investigate these associations.

Wonder symphony: epigenetics and the enchantment of the arts

Epigenetics, the study of heritable changes in gene expression without altering the DNA sequence, has gained significant attention due to its implications for gene regulation and chromatin stability. Epigenetic mechanisms play a fundamental role in gene-environment interactions, shaping individual development and adaptation. DNA methylation, histone modifications, and non-coding RNAs are key epigenetic regulators. Epigenetic changes can be triggered by environmental factors, including stress, toxins, and social interactions, influencing health and well-being. Positive experiences, such as engagement with the arts, have been linked to emotional responses and neurotransmitter release. While the impacts of detrimental factors on epigenetics have been widely studied, the effects of positive influences are less explored. Specifically, visual art and music have profound effects on emotions, cognition, and mood regulation. Exposure to arts enhances memory, reduces stress, and fosters social inclusion. Recent research has begun to explore the links between positive experiences and epigenetic modifications, suggesting that aesthetic experiences, including visual art and music fruition, might induce dynamic and/or stable changes in gene expression profiles. However, this field is in its infancy, and more research is needed to establish clear connections. Collaborative efforts among genetics, epigenetics, neuroscience, psychology, and the arts are essential for a comprehensive understanding. Longitudinal studies tracking sustained exposure to positive experiences and examining the influence of childhood artistic education on the biological bases of therapeutic effects of art and music are promising avenues for future research. Ultimately, understanding how positive experiences influence epigenetics could provide insights into the long-term enhancement of human well-being.

The Effects of Environmental Exposure on Epigenetic Modifications in Allergic Diseases

Allergic diseases are one of the most common chronic conditions and their prevalence is on the rise. Environmental exposure, primarily prenatal and early life influences, affect the risk for the development and specific phenotypes of allergic diseases via epigenetic mechanisms. Exposure to pollutants, microorganisms and parasites, tobacco smoke and certain aspects of diet are known to drive epigenetic changes that are essential for immune regulation (e.g., the shift toward T helper 2-Th2 cell polarization and decrease in regulatory T-cell (Treg) differentiation). DNA methylation and histone modifications can modify immune programming related to either pro-allergic interleukin 4 (IL-4), interleukin 13 (IL-13) or counter-regulatory interferon γ (IFN-γ) production. Differential expression of small non-coding RNAs has also been linked to the risk for allergic diseases and associated with air pollution. Certain exposures and associated epigenetic mechanisms play a role in the susceptibility to allergic conditions and specific clinical manifestations of the disease, while others are thought to have a protective role against the development of allergic diseases, such as maternal and early postnatal microbial diversity, maternal helminth infections and dietary supplementation with polyunsaturated fatty acids and vitamin D. Epigenetic mechanisms are also known to be involved in mediating the response to common treatment in allergic diseases, for example, changes in histone acetylation of proinflammatory genes and in the expression of certain microRNAs are associated with the response to inhaled corticosteroids in asthma. Gaining better insight into the epigenetic regulation of allergic diseases may ultimately lead to significant improvements in the management of these conditions, earlier and more precise diagnostics, optimization of current treatment regimes, and the implementation of novel therapeutic options and prevention strategies in the near future.

Impact of Maternal Mediterranean-Type Diet Adherence on Microbiota Composition and Epigenetic Programming of Offspring

Understanding how maternal diet affects in utero neonatal gut microbiota and epigenetic regulation may provide insight into disease origins and long-term health. The impact of Mediterranean diet pattern adherence (MDA) on fetal gut microbiome and epigenetic regulation was assessed in 33 pregnant women. Participants completed a validated food frequency questionnaire in each trimester of pregnancy; the alternate Mediterranean diet (aMED) score was applied. Umbilical cord blood, placental tissue, and neonatal meconium were collected from offspring. DNA methylation patterns were probed using the Illumnia EPICarray Methylation Chip in parturients with high versus low MDA. Meconium microbial abundance in the first 24 h after birth was identified using 16s rRNA sequencing and compared among neonates born to mothers with high and low aMED scores. Twenty-one mothers were classified as low MDA and 12 as high MDA. Pasteurellaceae and Bacteroidaceae trended towards greater abundance in the high-MDA group, as well as other short-chain fatty acid-producing species. Several differentially methylated regions varied between groups and overlapped gene regions including NCK2, SNED1, MTERF4, TNXB, HLA-DPB, BAG6, and LMO3. We identified a beneficial effect of adherence to a Mediterranean diet on fetal in utero development. This highlights the importance of dietary counseling for mothers and can be used as a guide for future studies of meconium and immuno-epigenetic modulation.

HPV38 impairs UV-induced transcriptional activation of the IL-18 pro-inflammatory cytokine

IMPORTANCE

Here, we demonstrate that the direct binding of p53 on the IL-18 promoter region regulates its gene expression. However, the presence of E6 and E7 from human papillomavirus type 38 impairs this mechanism via a new inhibitory complex formed by DNA methyltransferase 1 (DNMT1)/PKR/ΔNp73α, which binds to the region formerly occupied by p53 in primary keratinocytes.

MicroRNAs as Potential Biomarkers of Environmental Exposure to Polycyclic Aromatic Hydrocarbons and Their Link with Inflammation and Lung Cancer

Exposure to atmospheric air pollution containing volatile organic compounds such as polycyclic aromatic hydrocarbons (PAHs) has been shown to be a risk factor in the induction of lung inflammation and the initiation and progression of lung cancer. MicroRNAs (miRNAs) are small single-stranded non-coding RNA molecules of ~20-22 nucleotides that regulate different physiological processes, and their altered expression is implicated in various pathophysiological conditions. Recent studies have shown that the regulation of gene expression of miRNAs can be affected in diseases associated with outdoor air pollution, meaning they could also be useful as biomarkers of exposure to environmental pollution. In this article, we review the published evidence on miRNAs in relation to exposure to PAH pollution and discuss the possible mechanisms that may link these compounds with the expression of miRNAs.

Exploring the promising potential of induced pluripotent stem cells in cancer research and therapy

The advent of iPSCs has brought about a significant transformation in stem cell research, opening up promising avenues for advancing cancer treatment. The formation of cancer is a multifaceted process influenced by genetic, epigenetic, and environmental factors. iPSCs offer a distinctive platform for investigating the origin of cancer, paving the way for novel approaches to cancer treatment, drug testing, and tailored medical interventions. This review article will provide an overview of the science behind iPSCs, the current limitations and challenges in iPSC-based cancer therapy, the ethical and social implications, and the comparative analysis with other stem cell types for cancer treatment. The article will also discuss the applications of iPSCs in tumorigenesis, the future of iPSCs in tumorigenesis research, and highlight successful case studies utilizing iPSCs in tumorigenesis research. The conclusion will summarize the advancements made in iPSC-based tumorigenesis research and the importance of continued investment in iPSC research to unlock the full potential of these cells.

Mining toxicogenomic data for dose-responsive pathways: implications in advancing next-generation risk assessment

Introduction: While targeted investigation of key toxicity pathways has been instrumental for biomarker discovery, unbiased and holistic analysis of transcriptomic data provides a complementary systems-level perspective. However, in a systematic context, this approach has yet to receive comprehensive and methodical implementation. Methods: Here, we took an integrated bioinformatic approach by re-analyzing publicly available MCF7 cell TempO-seq data for 44 ToxCast chemicals using an alternative pipeline to demonstrate the power of this approach. The original study has focused on analyzing the gene signature approach and comparing them to in vitro biological pathway altering concentrations determined from ToxCast HTS assays. Our workflow, in comparison, involves sequential differential expression, gene set enrichment, benchmark dose modeling, and identification of commonly perturbed pathways by network visualization. Results: Using this approach, we identified dose-responsive molecular changes, biological pathways, and points of departure in an untargeted manner. Critically, benchmark dose modeling based on pathways recapitulated points of departure for apical endpoints, while also revealing additional perturbed mechanisms missed by single endpoint analyses. Discussion: This systems-toxicology approach provides multifaceted insights into the complex effects of chemical exposures. Our work highlights the importance of unbiased data-driven techniques, alongside targeted methods, for comprehensively evaluating molecular initiating events, dose-response relationships, and toxicity pathways. Overall, integrating omics assays with robust bioinformatics holds promise for improving chemical risk assessment and advancing new approach methodologies (NAMs).

PVC pellet leachates affect adult immune system and embryonic development but not reproductive capacity in the sea urchin Paracentrotus lividus

Microplastic pollution is a major concern of our age, eliciting a range of effects on organisms including during embryonic development. Plastic preproduction pellets stunt the development of sea urchins through the leaching of teratogenic compounds. However, the effect of these leachates on adult sea urchins and their fertility is unknown. Here we investigate the effect of PVC leachates on the capacity to produce normal embryos, and demonstrate that adults kept in contaminated water still produce viable offspring. However, we observe a cumulative negative effect by continued exposure to highly polluted water: adult animals had lower counts and disturbed morphological profiles of immune cells, were under increased oxidative stress, and produced embryos less tolerant of contaminated environments. Our findings suggest that even in highly polluted areas, sea urchins are fertile, but that sublethal effects seen in the adults may lead to transgenerational effects that reduce developmental robustness of the embryos.

Prenatal cadmium exposure has inter-generational adverse effects on Sertoli cells through the follicle-stimulating hormone receptor pathway

In brief

Exposure to cadmium (Cd) during pregnancy can potentially harm the reproductive system of male offspring. This article shows that pregnant woman should be protected from cadmium exposure.

Abstract

Exposure to cadmium (Cd) during pregnancy can potentially harm the reproductive system of male offspring, although the full extent of its heritable effects remains partially unresolved. In this study, we examined the inter-generational impacts of Cd using a distinct male-lineage generational model. Pregnant Sprague-Dawley female rats (F0) were administered control or cadmium chloride (0.5, 1 and 2 mg/day) via intra-gastric administration from gestation day 1 to 20. Subsequently, the first filial generation (F1) male rats were mated with untreated females (not exposed to Cd) to produce the second filial generation (F2). Histopathological analysis of the F1 and F2 generations revealed abnormal testicular development, while ultrastructural examination indicated damage to Sertoli cells. Cd exposure also led to alterations in serum hormone levels (gonadotropin-releasing hormone, follicle-stimulating hormone) and reduced follicle-stimulating hormone receptor (FSHR) protein expression in Sertoli cells in the F1 generation. Furthermore, Cd affected the mRNA and protein expression of FSHR pathway factors and DNA methyltransferase, albeit with distinct patterns and inconsistencies observed between the F1 and F2 generations. Overall, our findings indicate that prenatal Cd exposure, using a male-lineage transmission model, can induce inter-generational effects on male reproduction, particularly by causing toxicity in Sertoli cells. This effect appears to be primarily mediated through disruptions in the FSHR pathway and changes in DNA methyltransferase activity in the male testes.

Influence of chemical dose and exposure duration on protein synthesis in green sea turtle primary cells

Understanding the impacts of chemical exposure in marine wildlife is challenging, due to practical and ethical constraints that preclude traditional toxicology research on these animals. This study addressed some of these limitations by presenting an ethical and high throughput cell-based approach to elucidate molecular-level effects of contaminants on sea turtles. The experimental design addressed basic questions of cell-based toxicology, including chemical dose and exposure time. Primary green turtle skin cells were exposed to polychlorinated biphenyl (PCB) 153 and perfluorononanoic acid (PFNA) for 24 and 48 h, at three sub-lethal, environmentally relevant concentrations (1, 10 and 100 μg/L). Sequential window acquisition of all theoretical mass spectra (SWATH-MS) identified over 1000 differentially abundant proteins within the 1% false discovery rate (FDR) threshold. The 24 h exposure resulted in a greater number of differentially abundant proteins, compared to 48 h exposure, for both contaminants. However, there were no statistically significant dose-response relationships for the number of differentially synthesised proteins, nor differences in the proportion of increased vs decreased proteins between or within exposure times. Known in vivo markers of contaminant exposure, superoxide dismutase and glutathione S-transferase, were differentially abundant following exposure to PCB153 and PFNA. SIGNIFICANCE: Cell-based (in vitro) proteomics provides an ethical and high throughput approach to understanding the impacts of chemical contamination on sea turtles. Through investigating effects of chemical dose and exposure duration on unique protein abundance in vitro, this study provides an optimised framework for conducting cell-based studies in wildlife proteomics, and highlights that proteins detected in vitro could act as biomarkers of chemical exposure and effect in vivo.

The effects of mutations on gene expression and alternative splicing

Understanding the relationship between mutations and their genomic and phenotypic consequences has been a longstanding goal of evolutionary biology. However, few studies have investigated the impact of mutations on gene expression and alternative splicing on the genome-wide scale. In this study, we aim to bridge this knowledge gap by utilizing whole-genome sequencing data and RNA sequencing data from 16 obligately parthenogenetic Daphnia mutant lines to investigate the effects of ethyl methanesulfonate-induced mutations on gene expression and alternative splicing. Using rigorous analyses of mutations, expression changes and alternative splicing, we show that trans-effects are the major contributor to the variance in gene expression and alternative splicing between the wild-type and mutant lines, whereas cis mutations only affected a limited number of genes and do not always alter gene expression. Moreover, we show that there is a significant association between differentially expressed genes and exonic mutations, indicating that exonic mutations are an important driver of altered gene expression.

The Effect of Nanomaterials on DNA Methylation: A Review

DNA methylation is an epigenetic mechanism that involves the addition of a methyl group to a cytosine residue in CpG dinucleotides, which are particularly abundant in gene promoter regions. Several studies have highlighted the role that modifications of DNA methylation may have on the adverse health effects caused by exposure to environmental toxicants. One group of xenobiotics that is increasingly present in our daily lives are nanomaterials, whose unique physicochemical properties make them interesting for a large number of industrial and biomedical applications. Their widespread use has raised concerns about human exposure, and several toxicological studies have been performed, although the studies focusing on nanomaterials' effect on DNA methylation are still limited. The aim of this review is to investigate the possible impact of nanomaterials on DNA methylation. From the 70 studies found eligible for data analysis, the majority were in vitro, with about half using cell models related to the lungs. Among the in vivo studies, several animal models were used, but most were mice models. Only two studies were performed on human exposed populations. Global DNA methylation analyses was the most frequently applied approach. Although no trend towards hypo- or hyper-methylation could be observed, the importance of this epigenetic mechanism in the molecular response to nanomaterials is evident. Furthermore, methylation analysis of target genes and, particularly, the application of comprehensive DNA methylation analysis techniques, such as genome-wide sequencing, allowed identifying differentially methylated genes after nanomaterial exposure and affected molecular pathways, contributing to the understanding of their possible adverse health effects.

Molecular and phenotypic effects of early exposure to an environmentally relevant pesticide mixture in the Pacific oyster, Crassostrea gigas

Early life stages are crucial for organism development, especially for those displaying external fertilization, whose gametes and early stages face environmental stressors such as xenobiotics. The pacific oyster, Crassostrea gigas, is considered a model species in ecotoxicology because of its ecological characteristics (benthic, sessile, filter feeding). So far studies have investigated the impact of xenobiotics at embryotoxic, genotoxic and physiological endpoints, sometimes at the multigenerational scale, highlighting the role of epigenetic mechanisms in transmitting alterations induced by exposure to single xenobiotics. However, to date, little is known about the impact of environmentally-mimicking contaminants cocktails. Thus, we examined the impact of an early exposure to environmentally relevant mixture on the Pacific oyster life history. We studied transcriptomic, epigenetic and physiological alterations induced in oysters exposed to 18 pesticides and metals at environmental concentration (nominal sum concentration: 2.85 μg.L-1, measured sum concentration: 3.74 ± 0.013 μg.L-1) during embryo-larval stage (0-48 h post fertilization, hpf). No significant differences in embryo-larval abnormalities at 24 hpf were observed during larval and spat rearing; the swimming behaviour of exposed individuals was disturbed, while they were longer and heavier at specific time points, and exhibited a lower epinephrine-induced metamorphosis rate as well as a higher survival rate in the field. In addition, RNA-seq analyses of gastrula embryos revealed the differential expression of development-related genes (e.g. Hox orthologues and cell cycle regulators) between control and exposed oysters. Whole-genome DNA methylation analyses demonstrated a significant modification of DNA methylation in exposed larvae marked by a demethylation trend. Those findings suggest that early exposure to an environmentally relevant pesticide mixture induces multi-scale latent effects possibly affecting life history traits in the Pacific oyster.

Paternal exposure to arsenic and sperm DNA methylation of imprinting gene Meg3 in reproductive-aged men

BACKGROUND

Prenatal exposure to arsenic and mercury have been associated with adverse pregnancy outcomes that might be in part mediated by dynamic modification of imprinting gene that are emerging mechanism.

OBJECTIVES

The objective of this study was to examine the impacts of paternal exposure to arsenic and co-exposure to arsenic and mercury on human sperm DNA methylation status of imprinting genes, respectively.

METHODS

A total of 352 male subjects (23-52 years old) were recruited and demographic data were obtained through questionnaires. Urinary arsenic and mercury levels were measured using hydride generation-atomic fluorescence spectrometer. Multivariate regression model was employed to investigate the relationship between urinary arsenic levels and sperm DNA methylation status at H19, Meg3 and Peg3, measured by pyrosequencing, and evaluating the interaction with mercury.

RESULTS

After adjusting potential confounds factors by multivariate regression model, the results indicated a significantly positive relationship between urinary arsenic levels and the methylation status of Meg3 at both mean level (β =  + 0.125, p < 0.001) and all individual CpGs, i.e., CpG1 (β =  + 0.094, p < 0.001), CpG2 (β =  + 0.132, p < 0.001), CpG3 (β =  + 0.121, p < 0.001), CpG4 (β =  + 0.142, p < 0.001), CpG5 (β =  + 0.111, p < 0.001), CpG6 (β =  + 0.120, p < 0.001), CpG7 (β =  + 0.143, p < 0.001), CpG8 (β =  + 0.139, p < 0.001) of Meg3 DMRs. The interaction effects analysis indicated the interaction effects of arsenic and mercury on Meg3 were not existing.

CONCLUSIONS

Paternal nonoccupational exposure to arsenic induces the altered DNA methylation status of Meg3 in human sperm DNA. In addition, the interaction effects of arsenic and mercury on Meg3 were not existing. These findings would implicate the sensibility of sperm epigenome for environmental pollutions.

A review of the order mysida in marine ecosystems: What we know what is yet to be known

Mysids have a high ecological importance, particularly by their role in marine food chains as a link between the benthic and pelagic realms. Here we describe the relevant taxonomy, ecological aspects such as distribution and production, and their potential as ideal test organisms for environmental research. We also highlight their importance in estuarine communities, trophic webs, and their life history, while demonstrating their potential in addressing emergent problems. This review emphasizes the importance of mysids in understanding the impacts of climate change and their role in the ecology of estuarine communities. Although there is a dearth of research in genomic studies, this review emphasizes the relevance of mysids and their potential as a model organism in environmental assessment studies of prospective or retrospective nature and highlights the need for further research to enhance our understanding of this group's ecological significance.

Targeted DNA Demethylation: Vectors, Effectors and Perspectives

Aberrant DNA hypermethylation at regulatory cis-elements of particular genes is seen in a plethora of pathological conditions including cardiovascular, neurological, immunological, gastrointestinal and renal diseases, as well as in cancer, diabetes and others. Thus, approaches for experimental and therapeutic DNA demethylation have a great potential to demonstrate mechanistic importance, and even causality of epigenetic alterations, and may open novel avenues to epigenetic cures. However, existing methods based on DNA methyltransferase inhibitors that elicit genome-wide demethylation are not suitable for treatment of diseases with specific epimutations and provide a limited experimental value. Therefore, gene-specific epigenetic editing is a critical approach for epigenetic re-activation of silenced genes. Site-specific demethylation can be achieved by utilizing sequence-dependent DNA-binding molecules such as zinc finger protein array (ZFA), transcription activator-like effector (TALE) and clustered regularly interspaced short palindromic repeat-associated dead Cas9 (CRISPR/dCas9). Synthetic proteins, where these DNA-binding domains are fused with the DNA demethylases such as ten-eleven translocation (Tet) and thymine DNA glycosylase (TDG) enzymes, successfully induced or enhanced transcriptional responsiveness at targeted loci. However, a number of challenges, including the dependence on transgenesis for delivery of the fusion constructs, remain issues to be solved. In this review, we detail current and potential approaches to gene-specific DNA demethylation as a novel epigenetic editing-based therapeutic strategy.

iGEM as a human iPS cell-based global epigenetic modulation detection assay provides throughput characterization of chemicals affecting DNA methylation

Chemical-induced dysregulation of DNA methylation during the fetal period is known to contribute to developmental disorders or increase the risk of certain diseases later in life. In this study, we developed an iGEM (iPS cell-based global epigenetic modulation) detection assay using human induced pluripotent stem (hiPS) cells that express a fluorescently labeled methyl-CpG-binding domain (MBD), which enables a high-throughput screening of epigenetic teratogens/mutagens. 135 chemicals with known cardiotoxicity and carcinogenicity were categorized according to the MBD signal intensity, which reflects the degree of nuclear spatial distribution/concentration of DNA methylation. Further biological characterization through machine-learning analysis that integrated genome-wide DNA methylation, gene expression profiling, and knowledge-based pathway analysis revealed that chemicals with hyperactive MBD signals strongly associated their effects on DNA methylation and expression of genes involved in cell cycle and development. These results demonstrated that our MBD-based integrated analytical system is a powerful framework for detecting epigenetic compounds and providing mechanism insights of pharmaceutical development for sustainable human health.

ALS is imprinted in the chromatin accessibility of blood cells

Amyotrophic Lateral Sclerosis (ALS) is a complex and incurable neurodegenerative disorder in which genetic and epigenetic factors contribute to the pathogenesis of all forms of ALS. The interplay of genetic predisposition and environmental footprints generates epigenetic signatures in the cells of affected tissues, which then alter transcriptional programs. Epigenetic modifications that arise from genetic predisposition and systemic environmental footprints should in theory be detectable not only in affected CNS tissue but also in the periphery. Here, we identify an ALS-associated epigenetic signature ('epiChromALS') by chromatin accessibility analysis of blood cells of ALS patients. In contrast to the blood transcriptome signature, epiChromALS includes also genes that are not expressed in blood cells; it is enriched in CNS neuronal pathways and it is present in the ALS motor cortex. By combining simultaneous ATAC-seq and RNA-seq with single-cell sequencing in PBMCs and motor cortex from ALS patients, we demonstrate that epigenetic changes associated with the neurodegenerative disease can be found in the periphery, thus strongly suggesting a mechanistic link between the epigenetic regulation and disease pathogenesis.