A network biology-based approach to evaluating the effect of environmental contaminants on human interactome and diseases

Community-Engaged Research and the Use of Open Access ToxVal/ToxRef In Vivo Databases and New Approach Methodologies (NAM) to Address Human Health Risks From Environmental Contaminants

BACKGROUND

The paper analyzes opportunities for integrating Open access resources (Abstract Sifter, US EPA and NTP Toxicity Value and Toxicity Reference [ToxVal/ToxRefDB]) and New Approach Methodologies (NAM) integration into Community Engaged Research (CEnR).

METHODS

CompTox Chemicals Dashboard and Integrated Chemical Environment with in vivo ToxVal/ToxRef and NAMs (in vitro) databases are presented in three case studies to show how these resources could be used in Pilot Projects involving Community Engaged Research (CEnR) from the University of California, Davis, Environmental Health Sciences Center.

RESULTS

Case #1 developed a novel assay methodology for testing pesticide toxicity. Case #2 involved detection of water contaminants from wildfire ash and Case #3 involved contaminants on Tribal Lands. Abstract Sifter/ToxVal/ToxRefDB regulatory data and NAMs could be used to screen/prioritize risks from exposure to metals, PAHs and PFAS from wildfire ash leached into water and to investigate activities of environmental toxins (e.g., pesticides) on Tribal lands. Open access NAMs and computational tools can apply to detection of sensitive biological activities in potential or known adverse outcome pathways to predict points of departure (POD) for comparison with regulatory values for hazard identification. Open access Systematic Empirical Evaluation of Models or biomonitoring exposures are available for human subpopulations and can be used to determine bioactivity (POD) to exposure ratio to facilitate mitigation.

CONCLUSIONS

These resources help prioritize chemical toxicity and facilitate regulatory decisions and health protective policies that can aid stakeholders in deciding on needed research. Insights into exposure risks can aid environmental justice and health equity advocates.

Network Toxicology and Molecular Docking to Investigate the Non-AChE Mechanisms of Organophosphate-Induced Neurodevelopmental Toxicity

Organophosphate pesticides (OPs) are toxic substances that contaminate aquatic environments, interfere with the development of the nervous system, and induce Neurodevelopmental Toxicity (NDT) in animals and humans. The canonical mechanism of OP neurotoxicity involves the inhibition of acetylcholinesterase (AChE), but other mechanisms non-AChE are also involved and not fully understood. We used network toxicology and molecular docking to identify molecular targets and toxicity mechanisms common to OPs. Targets related to diazinon-oxon, chlorpyrifos oxon, and paraoxon OPs were predicted using the Swiss Target Prediction and PharmMapper databases. Targets related to NDT were compiled from GeneCards and OMIM databases. In order to construct the protein-protein interaction (PPI) network, the common targets between OPs and NDT were imported into the STRING. Network topological analyses identified EGFR, MET, HSP90AA1, and SRC as hub nodes common to the three OPs. Using the Reactome pathway and gene ontology, we found that signal transduction, axon guidance, cellular responses to stress, and glutamatergic signaling activation play key roles in OP-induced NDT.

Role of macrophage AHR/TLR4/STAT3 signaling axis in the colitis induced by non-canonical AHR ligand aflatoxin B1

Here we report that macrophage AHR/TLR/STAT signaling axis is implicated in the colon colitis induced by non-canonical AHR ligand aflatoxin B1 (AFB1). In BALB/c mice gavaged with 5, 25 and 50 µg/kg body weight/day AFB1, we observed severe colitis featured by over-recruitment of myeloid lineage immune cells such as monocytes/macrophage in colon lamina propria. Stressed and damaged colon epithelial cells were observed in low-dose group, while twisted and shortened intestinal crypts being found in middle dose group. Severe tissue damage was induced in the high-dose group. Dose-dependent increases of ROS, NO, and decrease of mitochondrial ROS-suppressor STAT3 were observed in the exposure groups. Further investigation in AFB1-treated human macrophage model found: (1) functional adaptations such as elevation of TNF-alpha and IL-6 secretion, stimulation of phagocytosis, elevation of LTE4 level; (2) overall inflammatory status confirmed by RNA-sequence analysis, in line with up-regulation of immune functional proteins such as ICAM-1, IDO-1, NF-kB-p65, NLRP3, COX-2 and iNOS; (3) mRNA disruption of mitochondrial oxidative phosphorylation complex I units and STATs; (4) perturbation of AHR/TLR/STAT3 signaling axis, including elevated AHR, TLR2, TLR4, and decreased STAT3, p-STAT3 Ser727. Mechanism investigation revealed regulatory links of ligand-dependent AHR/TLR4/STAT3. AHR-TLR4 together regulate MyD88, and STAT3 may be directly regulated by MyD88 (TLR4 downstream molecule) upon AHR/TLR4 binding with ligands. Solely protein level changes of AHR/TLR4 cannot regulate STAT3. Our study suggests that macrophage AHR/TLR4/STAT3 is involved with the colitis induced by sub-acute exposure to AFB1. Future follow-up study will focus on the intervention of the colitis using AHR-anti-inflammatory ligands.

Emerging contaminant triclosan incites endocrine disruption, reproductive impairments and oxidative stress in the commercially important carp, Catla (Labeo catla): An insight through molecular, histopathological and bioinformatic approach

Triclosan (TCS), a broad-spectrum antimicrobial agent is ubiquitous in aquatic ecosystems; however, the mechanisms regarding TCS-induced reproductive toxicity in the teleost still remains uncertain. In this context, Labeo catla were subjected to sub-lethal doses of TCS for 30 days and variations in expression of genes and hormones comprising the hypothalamic-pituitary-gonadal (HPG) axis along with alterations in sex steroids were evaluated. Moreover, manifestation of oxidative stress, histopathological alterations, in silico docking and the potential to bioaccumulate were also investigated. Exposure to TCS may lead to an inevitable onset of the steroidogenic pathway through its interaction at several loci along the reproductive axis: TCS stimulated synthesis of kisspeptin 2 (Kiss 2) mRNAs which in turn prompts the hypothalamus to secrete gonadotropin-releasing hormone (GnRH), resulting in elevated serum 17β-estradiol (E₂) as a consequence; TCS exposure increased aromatase synthesis by brain, which by converting androgens to oestrogens may raise E₂ levels; Moreover, TCS treatment resulted in elevated production of GnRH and gonadotropins by the hypothalamus and pituitary, respectively resulting in the induction of E₂. The elevation in serum E₂ may be linked to abnormally elevated levels of vitellogenin (Vtg) with harmful consequences evident as hypertrophy of hepatocytes and increment in hepatosomatic indices. Additionally, molecular docking studies revealed potential interactions with multiple targets viz. Vtg and luteinizing hormone (LH). Furthermore, TCS exposure induced oxidative stress and caused extensive damage to tissue architecture. This study elucidated molecular mechanisms underlying TCS-induced reproductive toxicity and the need for regulated use and efficient alternatives which could suffice for TCS.

Differently surface-labeled polystyrene nanoplastics at an environmentally relevant concentration induced Crohn's ileitis-like features via triggering intestinal epithelial cell necroptosis

Nanoplastics (NPs), regarded as the emerging contaminants, can enter and be mostly accumulated in the digest tract, which pose the potential threat to intestinal health. In this study, mice were orally exposed to polystyrene (PS), PS-COOH and PS-NH₂ NPs with the size of ∼100 nm at a human equivalent dose for 28 consecutive days. All three kinds of PS-NPs triggered Crohn's ileitis-like features, such as ileum structure impairment, increased proinflammatory cytokines and intestinal epithelial cell (IEC) necroptosis, and PS-COOH/PS-NH₂ NPs exhibited higher adverse effects on ileum tissues. Furthermore, we found PS-NPs induced necroptosis rather than apoptosis via activating RIPK3/MLKL pathway in IECs. Mechanistically, we found that PS-NPs accumulated in the mitochondria and subsequently caused mitochondrial stress, which initiated PINK1/Parkin-mediated mitophagy. However, mitophagic flux was blocked due to lysosomal deacidification caused by PS-NPs, and thus led to IEC necroptosis. We further found that mitophagic flux recovery by rapamycin can alleviate NP-induced IEC necroptosis. Our findings revealed the underlying mechanisms concerning NP-triggered Crohn's ileitis-like features and might provide new insights for the further safety assessment of NPs.

Multitrait Pseudomonas sp. isolated from the rhizosphere of Bergenia ciliata acts as a growth-promoting bioinoculant for plants

Multifunctional plant growth-promoting bioinoculants are used to enhance growth, harvest yields, and add economic value to agricultural crops. In this study, such bioinoculant, BC-II-20 (Pseudomonas sp.), was isolated from the rhizospheric soil of a medicinal plant Bergenia ciliata from the Garhwal Himalayas, Uttarakhand, India. After characterization, supplementation with Pseudomonas sp. was used to study growth stimulation in a commercially important medicinal plant, Andrographis paniculata (Kalmegh), and it depicted enhanced physiological growth parameters under controlled conditions. Bacterial seed priming and also supplementation led to early and increased germination and plants displayed better vegetative growth during the entire growth stages. Early initiation of flowers and the appearance of pods occurred in inoculated plants, ultimately leading to the reduction in the life cycle of the plant. At the time of harvesting, there was an increase in the physiological parameters such as shoot length (38%), root length (14%), fresh weight (57%), dry weight (60%), number of panicles, and root branching. Photosynthetic efficiency was also higher, and ultimately, overall plant growth was improved by bacterial inoculation. The eco-friendly and sustainable use of this bioinoculant will provide an alternative to harmful chemical fertilizers and has become increasingly important. In conclusion, we reported a promising bioinoculant having plant growth-promoting traits, which promotes growth and development in A. paniculata and may be applied to other plants also.

Genome-wide evaluation of transcriptomic responses of human tissues to smoke: A systems biology study

The harmful compounds in various sources of smoke threaten human health. So far, many studies have investigated the effects of compounds of smoke on transcriptome changes in different human tissues. However, no study has been conducted on the effects of these compounds on transcriptome changes in different human tissues simultaneously. Hence, the present study was conducted to identify smoke-related genes (SRGs) and their response mechanisms to smoke in various human cells and tissues using systems biology based methods. A total of 6,484 SRGs were identified in the studied tissues, among which 4,095 SRGs were up-regulated and 2,389 SRGs were down-regulated. Totally, 459 SRGs were smoke-related transcription factors (SRTFs). Gene regulatory network analysis showed that the studied cells and tissues have different gene regulation and responses to compounds of smoke. The comparison of different tissues revealed no common SRG among the all studied tissues. However, the CYP1B1 gene was common among seven cells and tissues, and had the same expression trend. Network analysis showed that the CYP1B1 is a hub gene among SRGs in various cells and tissues. To the best of our knowledge, for the first time, our results showed that compounds of smoke induce and increase the expression of CYP1B1 key gene in all target and non-target tissues of human. Moreover, despite the specific characteristics of CYP1B1 gene and its identical expression trend in target and non-target tissues, it can be used as a biomarker for diagnosis and prognosis.

Introduction to Environmental Harmful Factors

In this Chapter, we systematically and comprehensively described various environmental harmful factors. They were classified into four aspects: physical factors, chemical factors, biological factors, and physiological and psychological stress factors. Their classification, modes of presence, toxicity and carcinogenicity, routes of exposure to human and toxic effects on the female reproductive health were introduced. It is expected that the exposure routes could be controlled and eliminated, and the pathogenic mechanism of environmental harmful factors should be investigated and explained to protect female reproductive health.

Spatial and temporal variation, source profile of PCDD/Fs in the atmosphere of a municipal waste incinerator in China

The mass concentrations, toxic equivalent quantity (TEQ) concentrations and congener profiles of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in the stack flue gas and ambient air of municipal solid waste incinerator (MSWI) were monitored in this study to evaluate the levels, emission characteristics, seasonal variation and emission sources of PCDD/Fs. Thirty-one ambient air samples were collected from four sites around MSWI during 2016-2017, and twelve stack flue gas samples were collected from one MSWI. Results showed that the PCDD/Fs concentrations of the stack flue gas ranged from 0.0077 to 0.021 ng I-TEQ/Nm³, with an average value of 0.016 ng I-TEQ/Nm³. The ambient air samples collected in 2016 and 2017 ranged from 0.017 to 0.27, and 0.035-0.27 pg I-TEQ/Nm³, with an average value of 0.078 and 0.10 pg I-TEQ/Nm³, respectively. The 2, 3, 4, 7, 8-PCDF always contributes most to toxicity both in stack flue gas and ambient air samples. PCDD/Fs in the ambient air of the study area showed significant seasonal differences, and the total concentration of PCDD/Fs was highest in winter, which was about 3.5-7.5 times that of summer. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) were used to determine the correlation between MSWI emissions and PCDD/Fs in ambient air. It is worth mentioning that MSWI is not the main source of PCDD/Fs in ambient air.

Broad range metabolomics coupled with network analysis for explaining possible mechanisms of Er-Zhi-Wan in treating liver-kidney Yin deficiency syndrome of Traditional Chinese medicine

ETHNOPHARMACOLOGICAL RELEVANCE

Er-Zhi-Wan (EZW), a famous traditional Chinese formulation, is used to prevent, or to treat, various liver and kidney diseases for its actions of replenishing liver and kidney. However, the mechanisms of treating Liver-kidney Yin deficiency syndrome (LKYDS) of EZW have not been comprehensively investigated.

AIM OF THE STUDY

In this study, a broad range metabolomics strategy coupled with network analysis was established to investigate possible mechanisms of EZW in treating LKYDS.

MATERIALS AND METHOD

The rat models of LKYDS were established using the mixture of thyroxine and reserpine, and the changes of biochemical indices in serum and histopathology were detected to explore the effects of EZW. Next, a broad range metabolomics strategy based on RPLC-Q-TOF/MS and HILIC-Q-TOF/MS has been developed to find the possible significant metabolites in the serum and urine of LKYDS rats. Then, network analysis was applied to visualize the relationships between identified serum and urine metabolites and in detail to find hub metabolites, which might be responsible for the effect of EZW on rats of LKYDS. Furthermore, the shortest path of "disease gene-pathway protein-metabolite" was built to investigate the possible intervention path of EZW from the systematic perspective.

RESULTS

Five hub metabolites, namely, arachidonic acid, L-arginine, testosterone, taurine and oxoglutaric acid, were screened out and could be adjusted to recover by EZW. After that, the shortest path starting from disease genes and ending in metabolites were identified and disclosed, and the genes of aging such as CAV1 and ACO1 were selected to explain the pathological mechanism of LKYDS.

CONCLUSION

Broad range metabolomics coupled with network analysis could provide another perspective on systematically investigating the molecular mechanism of EZW in treating LKYDS at metabolomics level. In addition, EZW might prevent the pathological process of LKYDS through regulating the disturbed metabolic pathway and the aging genes such as CAV1 and ACO1, which may be potential targets for EZW in the treatment of LKYDS.

Study on the multivariate prediction model and exposure level of indoor and outdoor particulate concentration in severe cold region of China

Atmospheric particulate matter( PM₁₀, PM_2.5) has been the main pollutant in most cities of China in recent years, and the exposure concentration is related to the incidence of human diseases and mortality. The time spent indoors is more than 80% for modern people. Therefore, study on the correlation and exposure level of indoor and outdoor atmospheric particles is important. To research the exposure level in the heating season and non-heating season of indoor and outdoor particulate concentration in severe cold region of China, a total of 110 samples of four types of buildings (office, classroom, urban residence and rural residence) in Daqing, a typical city of severe cold region in China, were tested by particle monitor. Based on the indoor and outdoor environmental parameters, multiple linear regression (MLR) and principal component regression (PCR), established the indoor particulate concentration prediction models. The short and long term exposure of different people in different environments in severe cold region of China was analyzed based on the people's time-activity pattern with the measured data and model. The results showed that as for the short term indoor and outdoor exposure of different people, the average combined exposure of urban people in heating season is 60.0% higher than that in non-heating season, and rural people in heating season 30.2% higher than that in non-heating season. As for the long term indoor and outdoor exposure of different people, the annual average combined exposure of urban people was 9.6% higher than that of rural people. While all for urban and rural people, differences in respiratory rates between genders resulted in an average potential dose of 21. 8% higher in male than in female.

Association between prenatal exposure to multiple persistent organic pollutants (POPs) and growth indicators in newborns

Despite the fact that many of persistent organic pollutants (POPs) have been banned for decades, they still constitute a group of harmful substances to human health. Prenatal exposure can have adverse effects on one's health as well as on their newborns. The present cross-sectional study, which includes 87% of the births registered in La Palma Island (Canary Islands, Spain) during 2016 (n = 447), aims to evaluate the potential adverse health effects exerted by a wide range of POPs on newborns. We quantified blood cord levels of twenty organochlorine pesticides, eighteen polychlorinated biphenyls (PCBs), eight bromodiphenyl ethers (BDEs), and sixteen polycyclic aromatic hydrocarbons (PAHs) using the method of gas chromatography-mass spectrometry. By groups, p,p'-DDE, PCB-28, BDE-47, and phenanthrene were the most frequently detected compounds (median values = 0.148, 0.107, 0.065, and 0.380 ng/mL, respectively). p,p'-DDE was found to be significantly associated with an increase in neonatal birth weight, with a special emphasis on girls. An inverse association between PCB-28 and PCB-52 with birth weight was observed, and these associations were determined by the gender. A similar trend was obtained for BDE-47 but not for any of the PAHs. When assessing the effect of mixtures, boys exhibiting ≥ 3 OCPs were at lower risk of having higher birth weight (OR = 0.25; 95% CI = 0.07 - 0.89; P = 0.032). The effect of these pollutants on birth weight does not go in the same direction, a fact that is conditioned by several factors, including the chemical nature of the substance or the gender of the newborn. Additional research is needed to understand the role of POPs on fetal development.

Perspectives of Microbial Inoculation for Sustainable Development and Environmental Management

How to sustainably feed a growing global population is a question still without an answer. Particularly farmers, to increase production, tend to apply more fertilizers and pesticides, a trend especially predominant in developing countries. Another challenge is that industrialization and other human activities produce pollutants, which accumulate in soils or aquatic environments, contaminating them. Not only is human well-being at risk, but also environmental health. Currently, recycling, land-filling, incineration and pyrolysis are being used to reduce the concentration of toxic pollutants from contaminated sites, but too have adverse effects on the environment, producing even more resistant and highly toxic intermediate compounds. Moreover, these methods are expensive, and are difficult to execute for soil, water, and air decontamination. Alternatively, green technologies are currently being developed to degrade toxic pollutants. This review provides an overview of current research on microbial inoculation as a way to either replace or reduce the use of agrochemicals and clean environments heavily affected by pollution. Microorganism-based inoculants that enhance nutrient uptake, promote crop growth, or protect plants from pests and diseases can replace agrochemicals in food production. Several examples of how biofertilizers and biopesticides enhance crop production are discussed. Plant roots can be colonized by a variety of favorable species and genera that promote plant growth. Microbial interventions can also be used to clean contaminated sites from accumulated pesticides, heavy metals, polyaromatic hydrocarbons, and other industrial effluents. The potential of and key processes used by microorganisms for sustainable development and environmental management are discussed in this review, followed by their future prospects.