A Systems Biology-Based Approach to Investigate Formaldehyde’s Effects on MicroRNA Expression Profiles

Formaldehyde is a common indoor and outdoor air pollutant that adversely impacts global public health. Many toxicological studies have shown that formaldehyde causes nasopharyngeal cancer, possibly through tissue damage, increased cell proliferation, and/or DNA damage. However, there is lack of knowledge regarding formaldehyde's effects at the systems biology level and whether epigenetic mechanisms may contribute to cellular responses. Furthermore, whether formaldehyde is capable of altering genomic and epigenomic processes throughout sites distal to the respiratory tract is unknown. This topic is of high interest, as the link between formaldehyde inhalation exposure and leukemia development is currently under heated debate. Epidemiological studies have shown evidence supporting a link between formaldehyde exposure and leukemia development, while toxicological investigations have yet to provide evidence supporting formaldehyde's ability to influence sites distant to the respiratory tract. Before this dispute is resolved, further evaluation of the biological mechanisms linking formaldehyde to disease is clearly necessary. In particular, formaldehyde-induced changes to epigenetic contributors to transcriptional programs are extremely understudied, where microRNA (miRNA) expression profiles have yet to be investigated in relation to formaldehyde. We set out to test the novel hypothesis that miRNAs have altered expression profiles within the respiratory and hematopoietic systems upon exposure to formaldehyde. Our studies were the first to show that formaldehyde significantly disrupts miRNA expression patterns in vitro, within cultured human lung cells, and in vivo, within the nasal epithelium of nonhuman primates. Using a rodent model, the impact of formaldehyde exposure on miRNA-related processes in direct contact and distant tissues, including the nasal mucosa, circulating white blood cells, and bone marrow, was evaluated. Formaldehyde was found to significantly alter miRNA expression profiles within the nose and blood, but not the bone marrow. Evaluating the epigenetic effects of formaldehyde exposure at the systems biology level, putative miRNA-mediated responses were mapped onto interacting networks. Signaling related to inflammation, cell death, and cancer was identified as enriched. Taken together, our research increases the knowledge of under-studied mechanisms linking formaldehyde exposure to disease, acting as an important foundation for future research in public health and toxicology.Doctor of Philosoph

A Systems Biology Approach to Investigate Human Lung Cell Response to Air Pollutants

Exposure to air pollution is associated with many diseases, such as asthma, bronchitis, and lung cancer. Despite these adverse health effects, the cellular mechanisms underlying air pollution-associated diseases remain largely unknown. In this study we set out to investigate the genome-wide responses of human lung cells exposed to multiple air pollutant conditions. We first employ a toxicogenomic approach to compare transcripts and molecular networks modulated upon exposure to freshly emitted air pollutants and photochemically altered pollutant mixtures, containing secondary pollutants. The results demonstrate that secondary pollutants initiate a more robust genomic response. After identifying this trend, we investigate potential mechanisms underlying responses to individual secondary pollutants. Here, we evaluate global microRNA expression modifications resulting from formaldehyde exposure. Our analysis reveals that formaldehyde induces significant changes in microRNA levels, which may in turn, regulate genes associated with inflammation and cancer. Together, these investigations reveal novel mechanisms potentially underlying air pollutant-induced disease

A Toxicogenomic Comparison of Primary and Photochemically Altered Air Pollutant Mixtures

Background: Air pollution contributes significantly to global increases in mortality, particularly within urban environments. Limited knowledge exists on the mechanisms underlying health effects resulting from exposure to pollutant mixtures similar to those occurring in ambient air. In order to clarify the mechanisms underlying exposure effects, toxicogenomic analyses are used to evaluate genomewide transcript responses and map these responses to molecular networks

Systems Biology and Birth Defects Prevention: Blockade of the Glucocorticoid Receptor Prevents Arsenic-Induced Birth Defects

Background: The biological mechanisms by which environmental metals are associated with birth defects are largely unknown. Systems biology–based approaches may help to identify key pathways that mediate metal-induced birth defects as well as potential targets for prevention

High-Throughput Screening Data Interpretation in the Context of In Vivo Transcriptomic Responses to Oral Cr(VI) Exposure

The toxicity of hexavalent chromium [Cr(VI)] in drinking water has been studied extensively, and available in vivo and in vitro studies provide a robust dataset for application of advanced toxicological tools to inform the mode of action (MOA). This study aimed to contribute to the understanding of Cr(VI) MOA by evaluating high-throughput screening (HTS) data and other in vitro data relevant to Cr(VI), and comparing these findings to robust in vivo data, including transcriptomic profiles in target tissues. Evaluation of Tox21 HTS data for Cr(VI) identified 11 active assay endpoints relevant to the Ten Key Characteristics of Carcinogens (TKCCs) that have been proposed by other investigators. Four of these endpoints were related to TP53 (tumor protein 53) activation mapping to genotoxicity (KCC#2), and four were related to cell death/proliferation (KCC#10). HTS results were consistent with other in vitro data from the Comparative Toxicogenomics Database. In vitro responses were compared to in vivo transcriptomic responses in the most sensitive target tissue, the duodenum, of mice exposed to ≤ 180 ppm Cr(VI) for 7 and 90 days. Pathways that were altered both in vitro and in vivo included those relevant to cell death/proliferation. In contrast, pathways relevant to p53/DNA damage were identified in vitro but not in vivo. Benchmark dose modeling and phenotypic anchoring of in vivo transcriptomic responses strengthened the finding that Cr(VI) causes cell stress/injury followed by proliferation in the mouse duodenum at high doses. These findings contribute to the body of evidence supporting a non-mutagenic MOA for Cr(VI)-induced intestinal cancer

Chemical Mixtures in Household Environments: In Silico Predictions and In Vitro Testing of Potential Joint Action on PPARγ in Human Liver Cells

There are thousands of chemicals that humans can be exposed to in their everyday environments, the majority of which are currently understudied and lack substantial testing for potential exposure and toxicity. This study aimed to implement in silico methods to characterize the chemicals that co-occur across chemical and product uses in our everyday household environments that also target a common molecular mediator, thus representing understudied mixtures that may exacerbate toxicity in humans. To detail, the Chemical and Products Database (CPDat) was queried to identify which chemicals co-occur across common exposure sources. Chemicals were preselected to include those that target an important mediator of cell health and toxicity, the peroxisome proliferator activated receptor gamma (PPARγ), in liver cells that were identified through query of the ToxCast/Tox21 database. These co-occurring chemicals were thus hypothesized to exert potential joint effects on PPARγ. To test this hypothesis, five commonly co-occurring chemicals (namely, benzyl cinnamate, butyl paraben, decanoic acid, eugenol, and sodium dodecyl sulfate) were tested individually and in combination for changes in the expression of PPARγ and its downstream target, insulin receptor (INSR), in human liver HepG2 cells. Results showed that these likely co-occurring chemicals in household environments increased both PPARγ and INSR expression more significantly when the exposures occurred as mixtures vs. as individual chemicals. Future studies will evaluate such chemical combinations across more doses, allowing for further quantification of the types of joint action while leveraging this method of chemical combination prioritization. This study demonstrates the utility of in silico-based methods to identify chemicals that co-occur in the environment for mixtures toxicity testing and highlights relationships between understudied chemicals and changes in PPARγ-associated signaling

Bayesian Matrix Completion for Hypothesis Testing

High-throughput screening (HTS) is a well-established technology that rapidly and efficiently screens thousands of chemicals for potential toxicity. Massive testing using HTS primarily aims to differentiate active vs inactive chemicals for different types of biological endpoints. However, even using high-throughput technology, it is not feasible to test all possible combinations of chemicals and assay endpoints, resulting in a majority of missing combinations. Our goal is to derive posterior probabilities of activity for each chemical by assay endpoint combination, addressing the sparsity of HTS data. We propose a Bayesian hierarchical framework, which borrows information across different chemicals and assay endpoints in a low-dimensional latent space. This framework facilitates out-of-sample prediction of bioactivity potential for new chemicals not yet tested. Furthermore, this paper makes a novel attempt in toxicology to simultaneously model heteroscedastic errors as well as a nonparametric mean function. It leads to a broader definition of activity whose need has been suggested by toxicologists. Simulation studies demonstrate that our approach shows superior performance with more realistic inferences on activity than current standard methods. Application to an HTS data set identifies chemicals that are most likely active for two disease outcomes: neurodevelopmental disorders and obesity. Code is available on Github

Formaldehyde and Epigenetic Alterations: MicroRNA Changes in the Nasal Epithelium of Nonhuman Primates

Background: Formaldehyde is an air pollutant present in both indoor and outdoor atmospheres. Because of its ubiquitous nature, it is imperative to understand the mechanisms underlying formaldehyde-induced toxicity and carcinogenicity. MicroRNAs (miRNAs) can influence disease caused by environmental exposures, yet miRNAs are understudied in relation to formaldehyde. Our previous investigation demonstrated that formaldehyde exposure in human lung cells caused disruptions in miRNA expression profiles in vitro

Formaldehyde Carcinogenicity Research: 30 Years and Counting for Mode of Action, Epidemiology, and Cancer Risk Assessment

Formaldehyde is a widely used high production chemical that is also released as a byproduct of combustion, off-gassing of various building products, and as a fixative for pathologists and embalmers. What is not often realized is that formaldehyde is also produced as a normal physiologic chemical in all living cells. In 1980, chronic inhalation of high concentrations of formaldehyde was shown to be carcinogenic, inducing a high incidence of nasal squamous cell carcinomas in rats. Some epidemiologic studies have also found increased numbers of nasopharyngeal carcinoma and leukemia in humans exposed to formaldehyde that resulted in formaldehyde being considered a Known Human Carcinogen. This article reviews the data for rodent and human carcinogenicity, early Mode of Action studies, more recent molecular studies of both endogenous and exogenous DNA adducts, and epigenetic studies. It goes on to demonstrate the power of these research studies to provide critical data to improve our ability to develop science-based cancer risk assessments, instead of default approaches. The complexity of constant physiologic exposure to a known carcinogen requires that new ways of thinking be incorporated into determinations of cancer risk assessment for formaldehyde, other endogenous carcinogens, and the role of background endogenous DNA damage and mutagenesis

Epigenetic Changes in Individuals with Arsenicosis

Inorganic arsenic (iAs) is an environmental toxicant currently poisoning millions of people worldwide, and chronically exposed individuals are susceptible to arsenicosis or arsenic poisoning. Using a state-of-the-art technique to map the methylomes of our study subjects, we identified a large interactome of hypermethylated genes that are enriched for their involvement in arsenic-associated diseases, such as cancer, heart disease, and diabetes. Notably, we have uncovered an arsenic-induced tumor suppressorome, a complex of 17 tumor suppressors known to be silenced in human cancers. This finding represents a pivotal clue in unraveling a possible epigenetic mode of arsenic-induced disease