Integrative exposomic, transcriptomic, epigenomic analyses of human placental samples links understudied chemicals to preeclampsia

Seminar: Functional Exposomics and Mechanisms of Toxicity-Insights from Model Systems and NAMs

BACKGROUND

Significant progress has been made over the past decade in measuring the chemical components of the exposome, providing transformative population-scale frameworks in probing the etiologic link between environmental factors and disease phenotypes. While the analytical technologies continue to evolve with reams of data being generated, there is an opportunity to complement exposome-wide association studies (ExWAS) with functional analyses to advance etiologic search at organismal, cellular, and molecular levels.

OBJECTIVES

Exposomics is a transdisciplinary field aimed at enabling discovery-based analysis of the nongenetic factors that contribute to disease, including numerous environmental chemical stressors. While advances in exposure assessment are enhancing population-based discovery of exposome-wide effects and chemical exposure agents, functional screening and elucidation of biological effects of exposures represent the next logical step toward precision environmental health and medicine. In this work, we focus on the use, strategies, and prospects of alternative approaches and model systems to enhance the current human exposomics framework in biomarker search and causal understanding, spanning from bench-based nonmammalian organisms and cell culture to computational new approach methods (NAMs).

DISCUSSION

We visit the definition of the functional exposome and exposomics and discuss a need to leverage alternative models as opposed to mammalian animals for delineating exposome-wide health effects. Under the "three Rs" principle of reduction, replacement, and refinement, model systems such as roundworms, fruit flies, zebrafish, and induced pluripotent stem cells (iPSCs) are advantageous over mammals (e.g., rodents or higher vertebrates). These models are cost-effective, and cell-specific genetic manipulations in these models are easier and faster, compared to mammalian models. Meanwhile, in silico NAMs enhance hazard identification and risk assessment in humans by bridging the translational gaps between toxicology data and etiologic inference, as represented by in vitro to in vivo extrapolation (IVIVE) and integrated approaches to testing and assessment (IATA) under the adverse outcome pathway (AOP) framework. Together, these alternatives offer a strong toolbox to support functional exposomics to study toxicity and causal mediators underpinning exposure-disease links. https://doi.org/10.1289/EHP13120.

Neonatal Encephalopathy is a Complex Phenotype Representing Reproductive and Pregnancy Exposome Effects on the Maternal-Placental-Fetal Triad

Reproductive, pregnancy, and placental exposomes influence the fetal neural exposome through toxic stressor interplay, impairing the maternal-placental-fetal (MPF) triad. Neonatal encephalopathy represents different clinical presentations based on complex time-dependent etiopathogenetic mechanisms including hypoxia-ischemia that challenge diagnosis and prognosis. Reproductive, pregnancy, and placental exposomes impair the fetal neural exposome through toxic stressor interplay within the MPF triad. Long intervals often separate disease onset from phenotype. Interdisciplinary fetal-neonatal neurology training, practice, and research closes this knowledge gap. Maintaining reproductive health preserves MPF triad health with life-course benefits.

Exploring applications of non-targeted analysis in the characterization of the prenatal exposome

Capturing the breadth of chemical exposures in utero is critical in understanding their long-term health effects for mother and child. We explored methodological adaptations in a Non-Targeted Analysis (NTA) pipeline and evaluated the effects on chemical annotation and discovery for maternal and infant exposure. We focus on lesser-known/underreported chemicals in maternal and umbilical cord serum analyzed with liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF/MS). The samples were collected from a demographically diverse cohort of 296 maternal-cord pairs (n = 592) recruited in San Francisco Bay area. We developed and evaluated two data processing pipelines, primarily differing by detection frequency cut-off, to extract chemical features from non-targeted analysis (NTA). We annotated the detected chemical features by matching with EPA CompTox Chemicals Dashboard (n = 860,000 chemicals) and Human Metabolome Database (n = 3140 chemicals) and applied a Kendrick Mass Defect filter to detect homologous series. We collected fragmentation spectra (MS/MS) on a subset of serum samples and matched to an experimental MS/MS database within the MS-Dial website and other experimental MS/MS spectra collected from standards in our lab. We annotated ~72 % of the features (total features = 32,197, levels 1-4). We confirmed 22 compounds with analytical standards, tentatively identified 88 compounds with MS/MS spectra, and annotated 4862 exogenous chemicals with an in-house developed annotation algorithm. We detected 36 chemicals that appear to not have been previously reported in human blood and 9 chemicals that were reported in less than five studies. Our findings underline the importance of NTA in the discovery of lesser-known/unreported chemicals important to characterize human exposures.

De facto Water Reuse: Investigating the Fate and Transport of Chemicals of Emerging Concern from Wastewater Discharge through Drinking Water Treatment Using Non-targeted Analysis and Suspect Screening

Wastewater is a source for many contaminants of emerging concern (CECs), and surface waters receiving wastewater discharge often serve as source water for downstream drinking water treatment plants. Nontargeted analysis and suspect screening methods were used to characterize chemicals in residence-time-weighted grab samples and companion polar organic chemical integrative samplers (POCIS) collected on three separate hydrologic sampling events along a surface water flow path representative of de facto water reuse. The goal of this work was to examine the fate of CECs along the study flow path as water is transported from wastewater effluent through drinking water treatment. Grab and POCIS samples provided a comparison between residence-time-weighted single-point and integrative sample results. This unique and rigorous study design, coupled with advanced analytical chemistry tools, provided important insights into chemicals found in drinking water and their potential sources, which can be used to help prioritize chemicals for further study. K-means clustering analysis was used to identify patterns in chemical occurrences across both sampling sites and sampling events. Chemical features that occurred frequently or survived drinking water treatment were prioritized for identification, resulting in the probable identification of over 100 CECs in the watershed and 28 CECs in treated drinking water.

[New advances in exposomics-analysis methods and research paradigms based on chromatography-mass spectrometry]

The occurrence and development of human diseases are influenced by both genetic and environmental factors. Research models that describe disease occurrence only from the perspective of genetics present certain limitations. In recent years, effects of environment factors on the occurrence and development of diseases have attracted extensive attentions. Exposomics focuses on the measurement of all exposure factors in an individual's life and how these factors are related to disease development. Exposomics provides new ideas to promote studies on the relationship between human health and environmental factors. Environmental exposures are characterized with different physical and chemical properties, as well as very low concentrations in vivo, which contribute great challenges in the comprehensive measurement of chemical residues in the human body. Chromatography-mass spectrometry-based technologies combine the high-efficiency separation ability of chromatography with the high resolution and sensitive detection characteristics of mass spectrometry; the combination of these techniques can achieve the high-coverage, high-throughput, and sensitive detection of environmental exposures, thus providing a powerful tool for measuring chemical exposures. Exposomics-analysis methods based on chromatography-mass spectrometry mainly include targeted quantitative analysis, suspect screening, and non-targeted screening. To explore the relationship between environmental exposure and the occurrence and development of diseases, researchers have developed research paradigms, including exposome wide association study, mixed-exposure study, exposomics and multi-omics (genome, transcriptome, proteome, metabolome)-association study, and so on. The emergence of these methods has brought about unprecedented developments in exposomics studies. In this manuscript, analytical methods based on chromatography-mass spectrometry, exposomics research paradigms, and their relevant prospects are reviewed.

Interdisciplinary fetal-neonatal neurology training applies neural exposome perspectives to neurology principles and practice

An interdisciplinary fetal-neonatal neurology (FNN) program over the first 1,000 days teaches perspectives of the neural exposome that are applicable across the life span. This curriculum strengthens neonatal neurocritical care, pediatric, and adult neurology training objectives. Teaching at maternal-pediatric hospital centers optimally merges reproductive, pregnancy, and pediatric approaches to healthcare. Phenotype-genotype expressions of health or disease pathways represent a dynamic neural exposome over developmental time. The science of uncertainty applied to FNN training re-enforces the importance of shared clinical decisions that minimize bias and reduce cognitive errors. Trainees select mentoring committee participants that will maximize their learning experiences. Standardized questions and oral presentations monitor educational progress. Master or doctoral defense preparation and competitive research funding can be goals for specific individuals. FNN principles applied to practice offer an understanding of gene-environment interactions that recognizes the effects of reproductive health on the maternal-placental-fetal triad, neonate, child, and adult. Pre-conception and prenatal adversities potentially diminish life-course brain health. Endogenous and exogenous toxic stressor interplay (TSI) alters the neural exposome through maladaptive developmental neuroplasticity. Developmental disorders and epilepsy are primarily expressed during the first 1,000 days. Communicable and noncommunicable illnesses continue to interact with the neural exposome to express diverse neurologic disorders across the lifespan, particularly during the critical/sensitive time periods of adolescence and reproductive senescence. Anomalous or destructive fetal neuropathologic lesions change clinical expressions across this developmental-aging continuum. An integrated understanding of reproductive, pregnancy, placental, neonatal, childhood, and adult exposome effects offers a life-course perspective of the neural exposome. Exosome research promises improved disease monitoring and drug delivery starting during pregnancy. Developmental origins of health and disease principles applied to FNN practice anticipate neurologic diagnoses with interventions that can benefit successive generations. Addressing health care disparities in the Global South and high-income country medical deserts require constructive dialogue among stakeholders to achieve medical equity. Population health policies require a brain capital strategy that reduces the global burden of neurologic diseases by applying FNN principles and practice. This integrative neurologic care approach will prolong survival with an improved quality of life for persons across the lifespan confronted with neurological disorders.

A Critical Review on the Opportunity to Use Placenta and Innovative Biomonitoring Methods to Characterize the Prenatal Chemical Exposome

Adverse effects associated with chemical exposures during pregnancy include several developmental and reproductive disorders. However, considering the tens of thousands of chemicals present on the market, the effects of chemical mixtures on the developing fetus is still likely underestimated. In this critical review, we discuss the potential to apply innovative biomonitoring methods using high-resolution mass spectrometry (HRMS) on placenta to improve the monitoring of chemical exposure during pregnancy. The physiology of the placenta and its relevance as a matrix for monitoring chemical exposures and their effects on fetal health is first outlined. We then identify several key parameters that require further investigations before placenta can be used for large-scale monitoring in a robust manner. Most critical is the need for standardization of placental sampling. Placenta is a highly heterogeneous organ, and knowledge of the intraplacenta variability of chemical composition is required to ensure unbiased and robust interindividual comparisons. Other important variables include the time of collection, the sex of the fetus, and mode of delivery. Finally, we discuss the first applications of HRMS methods on the placenta to decipher the chemical exposome and describe how the use of placenta can complement biofluids collected on the mother or the fetus.

Wrangling Whole Mixtures Risk Assessment: Recent Advances in Determining Sufficient Similarity

Human health risk assessments for complex mixtures can address real-world exposures and protect public health. While risk assessors typically prefer whole mixture approaches over component-based approaches, data from the precise exposure of interest are often unavailable and surrogate data from a sufficiently similar mixture(s) are required. This review describes recent advances in determining sufficient similarity of whole, complex mixtures spanning the comparison of chemical features, bioactivity profiles, and statistical evaluation to determine "thresholds of similarity". Case studies, including water disinfection byproducts, botanical ingredients, and wildfire emissions, are used to highlight tools and methods. Limitations to application of sufficient similarity in risk-based decision making are reviewed and recommendations presented for developing best practice guidelines.

Cutting-edge computational chemical exposure research at the U.S. Environmental Protection Agency

Exposure science is evolving from its traditional "after the fact" and "one chemical at a time" approach to forecasting chemical exposures rapidly enough to keep pace with the constantly expanding landscape of chemicals and exposures. In this article, we provide an overview of the approaches, accomplishments, and plans for advancing computational exposure science within the U.S. Environmental Protection Agency's Office of Research and Development (EPA/ORD). First, to characterize the universe of chemicals in commerce and the environment, a carefully curated, web-accessible chemical resource has been created. This DSSTox database unambiguously identifies >1.2 million unique substances reflecting potential environmental and human exposures and includes computationally accessible links to each compound's corresponding data resources. Next, EPA is developing, applying, and evaluating predictive exposure models. These models increasingly rely on data, computational tools like quantitative structure activity relationship (QSAR) models, and machine learning/artificial intelligence to provide timely and efficient prediction of chemical exposure (and associated uncertainty) for thousands of chemicals at a time. Integral to this modeling effort, EPA is developing data resources across the exposure continuum that includes application of high-resolution mass spectrometry (HRMS) non-targeted analysis (NTA) methods providing measurement capability at scale with the number of chemicals in commerce. These research efforts are integrated and well-tailored to support population exposure assessment to prioritize chemicals for exposure as a critical input to risk management. In addition, the exposure forecasts will allow a wide variety of stakeholders to explore sustainable initiatives like green chemistry to achieve economic, social, and environmental prosperity and protection of future generations.