The Environmental Health Bioinformatics (EHB) T32 training program leverages the unique confluence of strengths in Data Science and Environmental Health Science at NC State to train scientists fluent in this critical interdisciplinary space. The program includes several enhancements to further the environment for mentored research training and professional development. This data-intensive training program will produce scientists ready to meet the emerging challenges in environmental health research, including the ever-expanding exposome, understanding of variability between individuals, rational integration across massive data sets, and study designs that incorporate diverse community goals and needs.

Our overarching goal is to learn how to positively influence health trajectories, modify disease risk and reduce health disparities through dietary modification. Emerging data, including our own, suggest that prenatal stressors including prenatal depression, perceived stress, and exposure to environmental contaminants increase oxidative stress to contribute to adverse pregnancy, birth, and postnatal outcomes and a Mediterranean-style diet decreases these health effects. However, data are limited and frequently under-powered to investigate these effects in ethnic minorities. We propose to leverage data and biological samples from our existing cohort resources of the Newborn Epigenetics Study (NEST) and Stress and Health In Pregnancy (SHIP) where more than 1200 women and their children have been followed from 3 months gestation, and now range in age from 2 to 15 years. We will test the overarching hypothesis that Mediterranean style diet prenatal and postnatally mitigates health effects of prenatal stress via epigenetic mechanisms. Specifically, we will determine if a Med-style diet during pregnancy is associated with molecular and epigenetic readouts of oxidative stress, inflammation, gut microbial diversity and DNA methylation. DNA methylation, a specific form of epigenetic modification, in regulatory regions of our genome that impact metabolism and inflammation recently identified by our group. These data will provide the data necessary for clinical trials focused on dietary manipulation, to mitigate the effects of a wide range of prenatal exposures.

The increased prevalence of obesity in the US and elsewhere has led to the hypothesis that epigenetic mechanisms mediate associations between environmental cues and obesity outcomes. However, epigenetic regions that alter obesity risk are still largely unknown, and the current lack of a screening tool for comprehensive measurement of epigenetic modifications hampers the identification of associated regions. Such a screen that could be applied to any disease or exposure of interest would be of great utility for a broad range of human health studies. The interpretation of human epigenetic data generated using genome-scale approaches is hampered by several obstacles. Firstly, the available data are largely based on methylation differences measured in DNA obtained cross-sectionally at different ages throughout the life course, yet DNA methylation marks are known to vary by age. Also, methylation measurements are made in accessible peripheral cell types accessible from otherwise healthy individuals, and variance of epigenetic marks between cell types means that measurements from peripheral cells do not always correlate with those from cell types that contribute to diseases. Additionally, alteration to epigenetic marks can be caused by disease, and this temporal ambiguity between exposure and outcome complicates causal inference. To overcome these obstacles, we have comprehensively identified DNA methylation-controlled regulatory regions for genomically imprinted genes, mapping the first draft of the human ����������������imprint-ome���������������. Epigenetically regulated imprinted genes are estimated to comprise 1-2% (200-400 genes) of the human genome, and are critical in the development of the early embryo; however, only ~30 imprint control regions (ICRs), regulating 70 to 80 genes, presently defined. Monoallelic expression of imprinted genes is regulated by parent-of-origin specific DNA methylation at ICRs that is established prior to germ-layer specification and maintained in somatic tissues throughout life. Our overarching goal is to leverage the newly identified ICRs, develop a custom platform to measure them in human specimens, and statistically identify the subset of the human imprint-ome associated with one of the most common trace metals������������������cadmium, a heavy metal that is sequestered by the placenta, contributing to placental dysfunction. Cadmium related methylation will also be examined in relation to children������������������s metabolic outcomes. Once developed, this ICR custom platform will be invaluable in identifying regions of early epigenetic perturbation associated with other early-acquired diseases or exposures, creating new opportunities for early detection and understanding the fetal origins and consequences of these conditions.

The rapid increase in the prevalence of obesity in the last 30 years has led to the hypothesis that epigenetic mechanisms mediate associations between environmental cues and obesity outcomes. Nevertheless, epigenetic regions that alter obesity risk are still unknown. We presently lack a screening tool for comprehensive measurement of epigenetic modifications. Such a screen in any disease or exposure of interest would be of great utility for a broad range of human health studies. The interpretation of human epigenetic data generated using genome-scale approaches is hampered by three main obstacles. Firstly, available data are largely based on methylation differences measured in DNA obtained cross-sectionally at different ages throughout the life course, yet DNA methylation marks are known to vary by age. Secondly, although methylation is known to vary by cell and tissue types, measurements are made in accessible peripheral cell types accessible from otherwise healthy individuals, and do not always correlate with those of cell types that contribute to obesity. Thirdly, alteration to epigenetic marks can be caused by obesity, and this temporal ambiguity between exposure and outcome complicates causal inference. To overcome these obstacles, we will comprehensively identify regulatory DNA methylation for imprinted genes, creating the first draft of the human ����������������imprintome���������������. Epigenetically regulated imprinted genes are estimated to comprise 1-2% (200-400 genes) of the human genome, and are critical in the development of the early embryo; however, only ~30 imprint control regions (ICRs), regulating 70-80 genes, are known. Monoallelic expression of imprinted genes is regulated by parent-of-origin specific DNA methylation at ICRs that is established prior to germ-layer specification and maintained in somatic tissues throughout life. Therefore, methylation marks regulating the expression of these genes are functionally relevant, and are conserved across cell types, among individuals, and throughout aging. These unique features of ICRs provide a means to a comprehensive tool for multiplexed measurement of early acquired epigenetic modifications, and assess their link between exposures and disease. Our overarching goal is to use genomewide approaches to systematically identify all ICRs using a wide variety of samples, including multiple cell types from males and females from a wide age range. In this way, identification can be restricted to only differentially methylated regions (DMRs) that are consistent across cell type, sex, and age ������������������ the hallmark of ICRs. The ICR panel will then be evaluated in relationship to obesity, by identifying, in umbilical cord blood at birth, ICR patterns predictive of obesity later in childhood. Identifying altered imprint regulation will provide markers for prospective risk assessment, identify mechanisms contributing to obesity development, and inform future research into environmental exposures affecting obesity. Once developed, this ICR screening assay would also then be used to identify regions of early epigenetic perturbation associated with any disease or exposure, creating new opportunities for understanding the fetal origins of these conditions.

The mission of the Center for Human Health and the Environment (CHHE) is to advance understanding of environmental impacts on human health. Through a systems biology framework integrating all levels of biological organization, CHHE aims to elucidate the fundamental mechanisms through which environmental exposures/stressors interface with biomolecules, pathways, the genome, and epigenome to influence human disease. CHHE will develop three interdisciplinary research teams that represent NC State������������������s distinctive strengths. CHHE will implement specific mechanisms to promote intra- and inter-team interactions and build interdisciplinary bridges to advance basic science discovery and translational research in environmental health science along the continuum from genes to population. These teams are; - The Molecular/Cellular-Based Systems and Model Organisms Team will utilize cutting edge molecular/cellular-based systems and powerful vertebrate and invertebrate model organisms to define mechanisms, pathways, GxE interactions, and individual susceptibility to environmental agents. - The Human Population Science Team will integrate expertise on environmental exposures, epidemiology, genomics and epigenomics to identify key human pathways and link exposure and disease across populations. - Bioinformatics Team will develop novel analytics and computational tools to translate Big Data generated across high-throughput and multiscale experiments into systems-level discoveries To further increase the impact and translational capacity of these teams, CHHE will develop three new facility cores that will provide instrumentation, expertise, and training to facilitate basic mechanism- to population-based research. - The Integrative Health Sciences Facility Core will expand the ability of CHHE members to translate basic science discoveries across species and provide mechanistic insights into epidemiological studies by partnering with: a) NC State������������������s Comparative Toxicogenomics Database (CTD); b) East Carolina University Brody School of Medicine and c) NC Dept. of Health and Human Services. - The Comparative Pathobiology Core will be located at NC State������������������s top-ranked College of Veterinary Medicine and its nationally recognized veterinary pathology group to facilitate assessment of the effects of environmental stressors in the many model organisms utilized by CHHE members. - The Systems Technologies Core will introduce state-of-the-art proteomics capabilities and dedicated bioinformatics support to expand the ability of CHHE members to analyze the Next Generation Sequencing data involving the genome, transcriptome and epigenome. As a land-grant university, NC State has an extensive and active Cooperative Extension Service network throughout North Carolina. CHHE will utilize this unique network to develop a highly effective, multi-directional Community Outreach and Engagement Core to disseminate findings that will contribute to addressing disparity in exposures and health outcomes and to educate communities about environmental influences on health. A strong Career Development Core for early stage scientists that is coordinated with a robust Pilot Project Program will support cutting-edge, collaborative and multidisciplinary environmental health projects to enhance the research success and impact of our membership. Through these activities and the purposeful interfacing of different disciplines CHHE will build on NC State������������������s unique research and community outreach strengths to become a premier transformative and synergistic EHS Core Center.

Non-communicable diseases including cardiovascular diseases, metabolic diseases and cancer are the leading causes of death in developed countries. These diseases are also predicted to be leading causes of death in developing countries by 2020. Stemming the increase in the prevalence of these diseases will require a more detailed understanding of their etiology using a life course approach. However, existing data linking early chemical and non-chemical stressors to these adult-onset diseases derives either from well-powered cross-section or retrospective cohort studies, or u

The premise of this application is that tobacco retail outlets (TROs) and the associated socio-economic environment are related to the levels of primary and secondary smoke exposure in the population, which has an impact on health and health related costs. Within the context of the Newborn Epigenetic Study (NEST), a Durham, NC based birth cohort, our group will integrate policy-level data related to community-wide smoking bans, geospatial-environmental data related TROs and neighborhood socioeconomic status, and individual-level data related to smoking, second-hand smoke exposure, and health care utilization and claims data. The integration of these data will lead to new insight that will further contribute to the empirical literature on drivers of smoking and second-hand smoke exposure and will help inform community-level policies that target tobacco use in public places and modification of laws regulating sales. The proposal is enhanced by the inclusion of a number of scientific rigorous methods and measures, including the innovative use of an analytic method to better characterize various aspects related to the socio-economic environment and how this relates to biological (cotinine) and behavioral data on smoking and second hand smoke exposure. Further, we have assembled a highly qualified team that has the requisite expertise for this project to be successful ������������������ expertise in geospatial analysis, tobacco regulatory policy, smoking behavior, and health services research.

Shift work, which is regularly experienced by millions of individuals (approximately 25% of the US workforce), is associated with increased risk of cancer, cardiovascular disease, metabolic disorders and neurodegenerative diseases. Evidence from our group and others indicate that disruption of the biological clock is a major environmental contributing factor to carcinogenesis. Yet, the underlying mechanisms are not well understood, which hampers efforts in prevention and mitigation of these devastating health risks. Although epigenetic modification of DNA is considered as one of the hallmarks of carcinogenesis, its connection with human circadian clock disruption and shift work is little known. The next logical step is to determine changes to differentially methylated regions (DMRs) and their role in DNA damage repair to identify molecular mechanisms, and search for biomarkers in order to better understand the environmental disease etiology. We must first ascertain whether simulated shift work induces epigenetic modification of DNA - one of the hallmarks of cancer. This will be executed by comparing 24 hour changes in DMRs of the whole genome, core clock genes, DNA damage repair genes, and other cancer hallmark genes in 14 simulated night and day shift workers. We will then be able to determine possible molecular mechanisms involved in elevated cancer risk as well as identify biomarkers and potential targets for treatment in real-world night shift workers.

Primary liver cancer, the vast majority of which is hepatocellular carcinoma (HCC) is one of the few cancers with increasing incidence in the US. Incidence of HCC has tripled since 1980, which is particularly worrisome given that HCC confers a median survival of less than two years. The steepest increases in incidence are in Southern rural states and among ethnic minorities. While the prevalence of HCC had paralleled high rates of viral hepatitis in the last several decades, recent increases in the prevalence of nonalcoholic fatty liver disease (NAFLD) and its progression to nonalcoholic steatohepatitis (NASH) with fibrosis and cirrhosis, has fueled HCC in recent years. Yet, these factors alone do not explain the substantial regional and ethnic variation in HCC progression. One understudied but potentially potent HCC risk factor with increasing prevalence that disproportionately affects ethnic minorities, is exposure to environmental contaminants. These contaminants degrade slowly and therefore persist in the environment, providing a stable exogenous source for human exposure. Toxic metal(oid)s such as cadmium and arsenic are classified as probable carcinogens, and emerging data from murine models suggest that exposure is associated with hepatic steatosis, cirrhosis and liver cancer. Per- and poly-fluoroalkyl substances (PFAS) exposure in humans is associated with obesity and NASH. Further, emerging evidence indicates that these environmental exposures can induce epigenetic alterations that may promote adverse effects on the liver, but we lack longitudinal human data. These data underscore the need for longitudinal human data to assess whether and how these contaminants impact HCC risk. To address these knowledge gaps, and in response to RFA-CA-20-049, we propose the Southeastern Liver Health Study, a longitudinal cohort study of two sub-cohorts comprising 16,000 males and females aged 40 years and older in two Southeastern states, North Carolina and Georgia. We will test the overarching hypothesis that cadmium alone or in a mixture with other toxic metals and PFAS increases the risk of progression from NAFLD to liver fibrosis and HCC. The cohort will be recruited from community clinics including Federally Qualified Health Centers and University Health Systems������������������ Primary Care Centers and Hepatology programs at Duke, UNC Chapel Hill and Emory. Sub-cohort I will comprise 10,000 otherwise healthy adults who will be followed for 1������������������5 years, anticipating that ~1,100 fibrosis cases, including cirrhosis, will develop, and sub-cohort II will comprise 6,000 advanced fibrosis cases, anticipating ~750 HCC cases will develop. We will nest case-control studies within the cohorts, evaluate associations between environmental exposures and HCC incidence, and identify epigenetic marks responsive to contaminants that predict progression to HCC. Impact: This will be the first large-scale effort to longitudinally determine the link between environmental contaminants, liver disease and cancer in a residentially and ethnically diverse population. Additionally, we will create a data and specimen repository that will provide the research community with an invaluable resource to study HCC and other cancers.

In the last 30 years, obesity prevalence has more than doubled among children and more than tripled among adolescents. While obesity rates have recently plateaued overall, socioeconomic and racial/ethnic disparities appear to be widening. Greater exposure to social adversity among individuals from low-income and racial/ethnic minority backgrounds may help explain these disparities. Animal and human studies demonstrate that early life experiences, including prenatal stress and adverse childhood experiences (ACE) are associated with greater risk for obesity. Obesity, in turn, is associated with poorer health, less educational attainment, and reduced quality of life, perpetuating health inequality across the life course. Emerging research in the field that suggests prenatal and early life stress may confer risk for obesity and other health problems through epigenetic mechanisms. To follow-up on these preliminary findings, we propose to leverage two ongoing prenatal cohorts in Florida and North Carolina. We will recruit a sample of 470 additional pregnant women enriched for adversity in pregnancy and follow their children to 24 months of age. We will assess the impact of mothers������������������ ACE and prenatal stress on measures of DNA methylation determined in human umbilical vein endothelial cells (HUVEC). We will also assess maternal and child postnatal psychosocial stress exposure, and child growth in the first 24 months of life. Children who are overweight at any point during the first two years of life have an approximately six-fold increased risk for obesity at five years of age, and are at risk for chronic health problems across the lifecycle.