Genomics in environmental health research--opportunities and challenges

Evaluation of Early Biomarkers of Atherosclerosis Associated with Polychlorinated Biphenyl Exposure: An in Vitro and in Vivo Study

BACKGROUND

Miscellaneous cardiovascular risk factors have been defined, but the contribution of environmental pollutants exposure on cardiovascular disease (CVD) remains underappreciated.

OBJECTIVE

We investigated the potential impact of typical environmental pollutant exposure on atherogenesis and its underlying mechanisms.

METHODS

We used human umbilical vein endothelial cells (HUVECs) and apolipoprotein E knockout (ApoE-/-) mice to investigate how 2,3,5-trichloro-6-phenyl-[1,4]-benzoquinone (PCB29-pQ, a toxic polychlorinated biphenyl metabolite) affects atherogenesis and identified early biomarkers of CVD associated with PCB29-pQ exposures. Then, we used long noncoding RNAs (lncRNAs) HDAC7-AS1-overexpressing ApoE-/- mice and apolipoprotein E/caveolin 1 double-knockout (ApoE-/-/CAV1-/-) mice to address the role of these early biomarkers in PCB29-pQ-induced atherogenesis. Plasma samples from patients with coronary heart disease (CHD) were also used to confirm our findings.

RESULTS

Our data indicate that lncRNA HDAC7-AS1 bound to MIR-7-5p via argonaute 2 in PCB29-pQ-challenged HUVECs. Our mRNA sequencing assay identified transforming growth factor-β2 (TGF-β2) as a possible target gene of MIR-7-5p; HDAC7-AS1 sponged MIR-7-5p and inhibited the binding of TGF-β2 to MIR-7-5p. The effect of PCB29-pQ-induced endothelial injury, vascular inflammation, development of plaques, and atherogenesis in ApoE-/- mice was greater with MIR-7-5p-mediated TGF-β2 inhibition, whereas HDAC7-AS1-overexpressing ApoE-/- mice and ApoE-/-/CAV1-/- mice showed the opposite effect. Consistently, plasma levels of HDAC7-AS1 and MIR-7-5p were found to be significantly associated individuals diagnosed with CHD.

DISCUSSIONS

These findings demonstrated that a mechanism-based, integrated-omics approach enabled the identification of potentially clinically relevant diagnostic indicators and therapeutic targets of CHD mediated by environmental contaminants using in vitro and in vivo models of HUVECs and ApoE-/- and ApoE-/-/CAV1-/- mice. https://doi.org/10.1289/EHP9833.

Toxicogenomic Analysis

The biological functions of a cell may change in response to exposure to toxic agents. Toxicogenomics employs the recent developments in genomics, transcriptomics, and proteomics to study how a chemical impacts gene/protein expression and cell functions. We describe a method for transcriptomic analysis by RNA sequencing based on Illumina HiSeq, NextSeq, or NovaSeq Systems followed by real-time qPCR validation. We also depict a method for proteomic analysis by "one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis" (1D SDS-PAGE) and a sample preparation procedure for "liquid chromatography in tandem with mass spectrometry" (LC-MS/MS), and we present some generic points to consider during LC-MS/MS.

Blood transcriptomics: applications in toxicology

The number of new chemicals that are being synthesized each year has been steadily increasing. While chemicals are of immense benefit to mankind, many of them have a significant negative impact, primarily owing to their inherent chemistry and toxicity, on the environment as well as human health. In addition to chemical exposures, human exposures to numerous non-chemical toxic agents take place in the environment and workplace. Given that human exposure to toxic agents is often unavoidable and many of these agents are found to have detrimental human health effects, it is important to develop strategies to prevent the adverse health effects associated with toxic exposures. Early detection of adverse health effects as well as a clear understanding of the mechanisms, especially at the molecular level, underlying these effects are key elements in preventing the adverse health effects associated with human exposure to toxic agents. Recent developments in genomics, especially transcriptomics, have prompted investigations into this important area of toxicology. Previous studies conducted in our laboratory and elsewhere have demonstrated the potential application of blood gene expression profiling as a sensitive, mechanistically relevant and practical surrogate approach for the early detection of adverse health effects associated with exposure to toxic agents. The advantages of blood gene expression profiling as a surrogate approach to detect early target organ toxicity and the molecular mechanisms underlying the toxicity are illustrated and discussed using recent studies on hepatotoxicity and pulmonary toxicity. Furthermore, the important challenges this emerging field in toxicology faces are presented in this review article.

Developmental origin of chronic diseases: toxicological implication

Human epidemiological and experimental animal studies show that suboptimal environments in fetal and neonatal life exerts a profound influence on physiological function and risk of disease in adult life. The molecular, cellular, metabolic, endocrine and physiological adaptations to intrauterine nutritional conditions result in permanent alterations of cellular proliferation and differentiation of tissues and organ systems, which in turn can manifest by pathological consequences or increased vulnerability to chronic diseases in adulthood. Intrauterine growth restriction (IUGR) due to intrauterine development derangements is considered the important factor in development of such diseases as essential hypertension, diabetes mellitus, ischemic diseases of the heart, osteoporosis, respiratory, neuropsychiatric and immune system diseases.

An early life exposures to dietary and environmental exposures can have a important effect on epigenetic code, resulting in diseases developed later in life. The concept of the "developmental programming" and Developmental Origins of Adult Diseases (DOHaD) has become well accepted because of the compelling animal studies that have precisely defined the outcomes of specific exposures.

The environmental pollullutants and other chemical toxicants may influence crucial cellular functions during critical periods of fetal development and permanently alter the structure or function of specific organ systems. Developmental epigenetics is believed to establish "adaptive" phenotypes to meet the demands of the later-life environment. Resulting phenotypes that match predicted later-life demands will promote health, while a high degree of mismatch will impede adaptability to later-life challenges and elevate disease risk. The rapid introduction of synthetic chemicals, environmental pollutants and medical interventions, may result in conflict with the programmed adaptive changes made during early development, and explain the alarming increases in some diseases.

Inter- and intra-individual variations of urinary endogenous metabolites in healthy male college students using (1)H NMR spectroscopy

BACKGROUND

Most human metabolomics studies have shown that spectral outputs of (1)H nuclear magnetic resonance fingerprinting are strongly influenced by inter- and intra-individual variations; however, few studies have been performed to evaluate the inter- and intra-individual variations in urinary endogenous metabolites.

METHODS

We recruited 30 male college students to evaluate the factors affecting intra- and inter-individual variations in urinary endogenous metabolites. Statistical analysis for variations in urinary metabolites was performed after eliminating outliers found in principal component analysis (PCA) plots.

RESULTS

Inter-individual variations were relatively low for 2-oxoglutarate, succinate, citrate, dimethylglycine, and taurine, but high for trimethylaminoxide (TMAO), hippurate, and lactate. Intra-individual variations for 2-oxoglutarate, citrate, dimethylglycine, and taurine were relatively low, but high for TMAO and hippurate. The factors affecting inter-individual variation of lactate were age, body mass index, beverages, and alcohol, whereas the factors affecting intra-individual variation of lactate were age and fish. Kim Chi intake affected the inter-individual variation of succinate, citrate, TMAO, and hippurate; however, it did not affect the intra-individual variation of endogenous metabolites.

CONCLUSIONS

Our results showed that inter- and intra-individual variations in urinary endogenous metabolites were very large, and significant factors affecting inter- and intra-individual variation were diverse, even after eliminating outliers in PCA analysis.

Proteomic applications in ecotoxicology

Within the growing body of proteomics studies, issues addressing problems of ecotoxicology are on the rise. Generally speaking, ecotoxicology uses quantitative expression changes of distinct proteins known to be involved in toxicological responses as biomarkers. Unlike these directed approaches, proteomics examines how multiple expression changes are associated with a contamination that is suspected to be detrimental. Consequently, proteins involved in toxicological responses that have not been described previously may be revealed. Following identification of key proteins indicating exposure or effect, proteomics can potentially be employed in environmental risk assessment. To this end, bioinformatics may unveil protein patterns specific to an environmental stress that would constitute a classifier able to distinguish an exposure from a control state. The combined use of sets of marker proteins associated with a given pollution impact may prove to be more reliable, as they are based not only on a few unique markers which are measured independently, but reflect the complexity of a toxicological response. Such a proteomic pattern might also integrate some of the already established biomarkers of environmental toxicity. Proteomics applications in ecotoxicology may also comprise functional examination of known classes of proteins, such as glutathione transferases or metallothioneins, to elucidate their toxicological responses.

The National Children's Study: a 21-year prospective study of 100,000 American children

Prospective, multiyear epidemiologic studies have proven to be highly effective in discovering preventable risk factors for chronic disease. Investigations such as the Framingham Heart Study have produced blueprints for disease prevention and saved millions of lives and billions of dollars. To discover preventable environmental risk factors for disease in children, the US Congress directed the National Institute of Child Health and Human Development, through the Children's Health Act of 2000, to conduct the National Children's Study. The National Children's Study is hypothesis-driven and will seek information on environmental risks and individual susceptibility factors for asthma, birth defects, dyslexia, attention-deficit/hyperactivity disorder, autism, schizophrenia, and obesity, as well as for adverse birth outcomes. It will be conducted in a nationally representative, prospective cohort of 100,000 US-born children. Children will be followed from conception to 21 years of age. Environmental exposures (chemical, physical, biological, and psychosocial) will be assessed repeatedly during pregnancy and throughout childhood in children's homes, schools, and communities. Chemical assays will be performed by the Centers for Disease Control and Prevention, and banks of biological and environmental samples will be established for future analyses. Genetic material will be collected on each mother and child and banked to permit study of gene-environment interactions. Recruitment is scheduled to begin in 2007 at 7 Vanguard Sites and will extend to 105 sites across the United States. The National Children's Study will generate multiple satellite studies that explore methodologic issues, etiologic questions, and potential interventions. It will provide training for the next generation of researchers and practitioners in environmental pediatrics and will link to planned and ongoing prospective birth cohort studies in other nations. Data from the National Children's Study will guide development of a comprehensive blueprint for disease prevention in children.

How omics technologies can contribute to the ‘3R’ principles by introducing new strategies in animal testing

In Europe, in light of ethical, political and commercial pressure, every effort should be made to replace animals with alternatives (e.g. in vitro models), to reduce the number of animals used in experiments to a minimum and to refine current testing strategies in a way that ensures animals undergo minimum pain and distress. Methods currently used in toxicology for mandatory safety tests rely heavily on the dosing of animals, followed by the detection and pathological evaluation of manifested toxic lesions. Through the integration of so-called 'omics' technologies, a global analysis of treatment-related changes on the molecular level becomes feasible and therefore might provide a means for predicting toxicity before classical toxicological endpoints. This Opinion article summarizes the key features of pushing the '3R' principles in animal testing, discusses the possible impact on safety testing in toxicology and describes the potential of using omics technologies for improved toxicity prediction to meet ethical, political and commercial expectations.

Biologic monitoring of exposure to environmental chemicals throughout the life stages: requirements and issues for consideration for the National Children's Study

Biomonitoring of exposure is a useful tool for assessing environmental exposures. The matrices available for analyses include blood, urine, breast milk, adipose tissue, and saliva, among others. The sampling can be staged to represent the particular time period of concern: preconceptionally from both parents, from a pregnant woman during each of the three trimesters, during and immediately after childbirth, from the mother postnatally, and from the child as it develops to 21 years of age. The appropriate sample for biomonitoring will depend upon matrix availability, the time period of concern for a particular exposure or health effect, and the different classes of environmental chemicals to be monitored. This article describes the matrices available for biomonitoring during the life stages being evaluated in the National Children's Study; the best biologic matrices for exposure assessment for each individual chemical class, including consideration of alternative matrices; the analytical methods used for analysis, including quality control procedures and less costly alternatives; the costs of analysis; optimal storage conditions; and chemical and matrix stability during long-term storage.

Do we need genomic research for the prevention of common diseases with environmental causes?

Concerns have been raised about the value of genomic research for prevention and public health, especially for complex diseases with risk factors that are amenable to environmental modification. Given that gene-environment interactions underlie almost all human diseases, the public health significance of genomic research on common diseases with modifiable environmental risks is based not necessarily on finding new genetic "causes" but on improving existing approaches to identifying and modifying environmental risk factors to better prevent and treat disease. Such applied genomic research for environmentally caused diseases is important, because 1) it could help stratify disease risks and differentiate interventions for achieving population health benefits; 2) it could help identify new environmental risk factors for disease or help confirm suspected environmental risk factors; and 3) it could aid our understanding of disease occurrence in terms of transmission, natural history, severity, etiologic heterogeneity, and targets for intervention at the population level. While genomics is still in its infancy, opportunities exist for developing, testing, and applying the tools of genomics to clinical and public health research, especially for conditions with known or suspected environmental causes. This research is likely to lead to population-wide health promotion and disease prevention efforts, not only to interventions targeted according to genetic susceptibility.

Environmental exposures, toxicologic mechanisms, and adverse pregnancy outcomes

Environmental risk factors (defined as those agents and stresses that are generally the responsibility of environmental agencies) are often tangible indicators of economic and social disparity in the United States. Many site-specific analyses have reported that communities of color and poverty are exposed more often and more intensively to such environmental hazards as lead, air pollution, agrochemicals, incinerator emissions, and releases from hazardous waste sites. Thus, exposures to these toxicants may explain part of the socioeconomic disparity that is observed in terms of risks of adverse pregnancy outcomes. The purpose of this study was to describe the associations between certain environmental exposures and reproductive outcomes through a discussion of both epidemiologic and animal model studies. In addition, we list potential sources of exposure data and describe physiologic changes in pregnancy that may increase the likelihood of both external exposures and increased internal dose. Several models for further study of environmental risk factors are suggested to increase our understanding of gene-environment interactions toward the goal of indentifying preventable risk factors to improve reproductive outcomes of particular concern to disadvantaged populations.

Systems biology: new approaches to old environmental health problems

The environment plays a pivotal role as a human health determinant and presence of hazardous pollutants in the environment is often implicated in human disease. That pollutants cause human diseases however is often controversial because data connecting exposure to environmental hazards and human diseases are not well defined, except for some cancers and syndromes such as asthma. Understanding the complex nature of human-environment interactions and the role they play in determining the state of human health is one of the more compelling problems in public health. We are becoming more aware that the reductionist approach promulgated by current methods has not, and will not yield answers to the broad questions of population health risk analysis. If substantive applications of environment-gene interactions are to be made, it is important to move to a systems level approach, to take advantage of epidemiology and molecular genomic advances. Systems biology is the integration of genomics, transcriptomics, proteomics, and metabolomics together with computer technology approaches to elucidate environmentally caused disease in humans. We discuss the applications of environmental systems biology as a route to solution of environmental health problems.