David Threadgill - US grants

Abstract Threadgill 9729645 The ERB proteins are a family consisting of four different cell surface receptors with enzymatic kinase activity that are activated by extracellular peptide growth factors. Upon activation these receptors homodimerize with an identical family member or heterodimerize with a different family member transactivating their respective dimerization partner by phosphorylation. These phosphorylated dimers form active signaling complexes that transmit the extracellular signal into the cell. A considerable amount of signaling specificity potentially exists in the type of receptor dimer that is formed. In this grant molecular and genetic analyses will be used to investigate the importance of receptor homo vs heterodimerization in determining signaling specificity and to determine to what extent receptor kinase activity is required for signal transmission. First the mode of receptor phosphorylation will be established in an in vitro cell culture system. The importance of the kinase activity of ERB2 and ERB4 will be studied in an in vivo animal system by engineering specific kinase-inactivating mutations in mice. The experiments will indicate how tyrosine kinase activation influences receptor dimerization and signaling specificity. This research is looking at some cell surface receptors, and studying their early reaction to substances which bind to them, and the means by which they pass this information on to other pathways in the cell which bring about a final response. ***

DESCRIPTION: (adapted from the investigator's abstract) Cancer of the colon and rectum is the third most frequently diagnosed cancer in the United States and accounts for the second largest number of cancer deaths. Even with the widespread occurrence of colorectal cancer, we only know how a few key genes, primarily associated with familial forms of colorectal cancer, are involved in its initiation and progression. The major goals of this research are to study the mode of susceptibility to the sporadic development of colorectal cancer and to identify regions of the genome that modulate this susceptibility. They will use an innovative approach combining the power of mouse embryological manipulation and genetics to achieve these goals. These goals will be pursued in two specific aims. The first specific aim is to address the mode by which resistance/susceptibility to colorectal cancer development is determined using a carcinogen-induced mouse model of colorectal cancer. They will utilize chimeras, an analysis of crypt architecture, and immunodeficient mice to pursue this aim. The second specific aim will be to survey several inbred mouse strains to gather preliminary data on the variability of colorectal cancer resistance/ susceptibility genes and to perform a serial backcross experiment to localize subsets of these genes from two strains of mice. Having a better understanding of how genetic factors effect the development of cancer will greatly aid our prognostic predictions. Additionally, having susceptibility markers to sporadic cases of colorectal cancer will permit us to better evaluate the interaction of genetics and the environment in the initiation and progression of colorectal cancer.

DESCRIPTION (Investigator's abstract): Intrauterine growth retardation (IUGR) is a major risk factor for peri-natal mortality and physical and mental retardation. While the causes of IUGR are highly heterogeneous, a strong correlation exists between IUGR caused by retarded placental development and reduced placental epidermal growth factor receptor (EGFR) activation. Therefore, a thorough understanding of EGFR function during placental development is required in order to accurately interpret the causes, identify genetic risk factors, and to design treatments for IUGR. To analyze the role of Egfr during placental development, an extensive and highly integrated genetic and molecular analysis of Egfr function will be pursued. The proposed experiments will use innovative approaches to study the dependency of the Egfr null phenotype on the genetic background. The modifier genes underlying the background dependency will be regionally mapped using a series of inbred mouse strains that have shown a modification of the placental phenotype (Specific Aim 1). These studies will be augmented by detailed histological and gene expression microarray analysis (Specific Aim 2) and phenotypic analysis of an engineered Egfr allelic series (Specific Aim 3) to provide a detailed biological context for successful candidate gene cloning and validation of the modifiers (Specific Aim 4). Through a detailed analysis of Egfr function using this mouse model, we will gain a much deeper insight into how EGFR functions in human placental development and how, through genetic modifiers, the severity of IUGR is modified. Additionally, knowing the types of genes that can compensate for abnormal Egfr function may lead to targets for IUGR therapeutic intervention. Treatments for IUGR would increase the chances of a successful pregnancy and greatly enhance post-natal survival and quality of life for the affected neonates.

DESCRIPTION (provided by applicant): The epidermal growth factor receptor (Egfr) is a transmembrane receptor tryrosine kinase that is required in numerous tissues during development and is associated with many forms of cancer. From mouse knockout studies, the Egfr is known to be required for the maturation and/or maintenance of the mature intestinal tract. Furthermore, genetic evidence suggests that the Egfr is required during colorectal tumorigenesis. This is despite that fact that the gene encoding Egfr is not known to be mutated during colorectal cancer development. Although cancer of the colon and rectum is the third most frequently diagnosed cancer in the United States and accounts for the second largest number of cancer deaths, the role of only a few genes has been studied in detail; these genes are typically mutated during colorectal tumorigenesis or are associated with familial forms of the disease. Little is know about genes that appear to be required for the progression of tumorigenesis but do not become mutated themselves like Egfr. The objectives of the proposed research are therefore (1) to investigate the global importance of Egfr during development of colorectal cancer, (2) to determine the temporal requirement for Egfr during colorectal cancer development, (3) to define the mode of action of Egfr during tumorigenesis, and (4) to investigate the function of Egfr in non-epithelial compartments of the gastrointestinal tract.

The Genomics Core will provide experimental planing, scientific services and computational support for SPORE projects using DNA microarrays. The facility is contained within the UNC Genomics Core & Microarray Facility housed in the Lineberger Comprehensive Cancer Center and adjacent to the core director's lab. It maintains centralized equipment for microarray production, utilization, and analysis. The Core also produces customized microarrays and maintains libraries of long-oligos and cDNA for printing the custom microarrays. To maximize efficiency and generate consistent quality results, the Genomics Core will provide complete microarray research services to SPORE projects. Investigators will isolate RNA and submit samples. The facility will perform quality control on all samples and prepare fluorescent probes for hybridization with either in-house produced or commercial micorarrays. The Genomics Core will provides computer hardware and analysis programs to collect and pre-process raw data before being transmitted to the Bioinformatics Core for databasing and analysis. The Genomics Core will initially support three of the SPORE projects. Its use will most likely expand to other projects and development studies as needed.

Colorectal cancer afflicts 135,000 Americans per year and 38% of these patients will die of disseminated disease most commonly to liver lung and bone. Of the patients that die of this disease, 70% have liver metastases and a significant 10% have liver-only disease. Even in those patients with metastases to multiple organ sites, the extent of liver disease remains the primary determinant of survival. Over the last two decades we have empirically learned that patients with liver only metastases have improved survival when treated aggressively. Untreated, patients with hepatic only metastases have a median survival of only 12-21 months and the five year survival of patients with unresected metastasis is close to 0%. In sharp contrast, resection of metastases in patients with liver only disease yields five year survival rates of 20-40% and 10 year survival rates of 20%. Furthermore, the most common site of disease recurrence after resection is the liver. Consequently, liver metastases are a primary determinant of survival in patients with stage IV colorectal cancer. Building upon preliminary data linking ERBB receptor activity to colorectal cancer progression and metastasis, we hypothesize that small molecule ERBB inhibitors, if optimally employed, will retard the growth and dissemination of metastatic colorectal cancer. We also hypothesize that colorectal cancer can also arise independently of ERBB and that an understanding of these mechanisms will allow us to design better therapies. Thus, using a combination of clinical samples and pre-clinical mouse models, we propose to investigate the mechanism of how metastatic colon cancer uses EGFR and other ERBB receptor signaling to establish residency in the liver and to identify markers for response to dual EGFR/ERBB2 inhibitors during treatment of metastatic lesions. Experiments are planned to identify transcriptional profiles unique to EGFR independent colorectal cancer development.

DESCRIPTION (provided by applicant): The proposed studies will build upon our recent research into genetic networks. We will be extending these, with an initial emphasis on colon and breast cancer, to include serum, urine, and other physiological analyses to develop models of a 'cancer susceptibility state' in order build better mouse models to investigate cancer predisposition and the mechanism by which an individuals genetic makeup and environmental exposure influences susceptibility and eventual response to therapy. Our definition of the cancer susceptibility state will draw from high-throughput methods for defining RNA and protein expression and high-throughput methods for defining genes that control that expression. We will also be addressing several critical issues in cancer research including how diet influence genetic networks associated with cancer susceptibility, the role of obesity in contributing to cancer susceptibility, how environmental exposures differ from genetic induction, among others. This research is definitely a new paradigm for cancer research and should lead to new biomarkers for susceptibility, a better understanding of intermediate phenotypes contributing to cancer susceptibility, and the role of biological plasticity and network switching in cancer predisposition with direct applications to human biology.

Description (provided by applicant): The Transomics Research Core (TRC) has the following objectives: 1) to develop and deploy contemporary genome-scale 'omics' technologies, 2) to support and expand collaborations applying ?omics? technologies to environmental health and susceptibility research activities, 3) to educate center members about new ?omics? technologies and their applications to environmental health research, 4) to integrate large data collection with computational analysis, 5) to promote and support interdisciplinary research through pilot projects, 6) to sponsor visits by innovators of existing and future ?omics? technologies.

Since Gregor Mendel first elucidated the principles of genetics and inheritance, the experimental basis for understanding heritable traits, like susceptibility to disease has largely involved studying biological systems one component at a time. However, the one-at-a-time approach does not scale when faced with a genome consisting of -30,000 genes as occurs in humans and other mammals. This limitation is further compounded by the complex interaction between genes and the environment. Factorial experimentation, described in the 1930's by Sir Ronald Fisher, in which many or all components of a system are altered simultaneously through randomization, is far more efficient. Analyses of all genes concurrently will be essential if we are to imagine a time when we understand human (mammalian) biology sufficiently well to synthetically reassemble biological knowledge to accurately predict and intelligently alter traits with complex etiologies, like susceptibility to common diseases. With the realization that a new model population was needed to understand human diseases with complex etiologies, we designed the Collaborative Cross (CC). The CC provides a translational tool to integrate gene functional studies into genetic networks and variation maps of the biomolecular space, containing all the biomolecules between the primary DMAsequence and the terminal disease phenotypes of interest, using a realistic population structure, which will be essential to understand the intricacies of biological processes like altered disease susceptibility. The CC is a large, highly innovative panel of recombinant inbred (Rl)lines of mice that combines the genomes of eight genetically diverse founder strains - A/J, C57BL/6J, 12981/SvlmJ, NOD/LtJ, NZO/HILU, CAST/EiJ, PWK/PhJ, and WSB/EiJ - to capture almost 90%of the known variation present in laboratory mice. To achieve the goal of producing the CC, we have formed the Systems Genetics Resource Consortium that will 1) develop the CC and assocaited husbandry and phenotype databases, 2) genotype the CC during development to identify synthetic lethal events and for quality control, and 3) develop a web portal for the CC for community access to data and analytic programs.

[unreadable] DESCRIPTION (provided by applicant): Colorectal cancer (CRC) is the fourth most frequently diagnosed cancer and accounts for the second largest number of cancer deaths in Western societies. One of the major molecular targets to arrise over the last decade is the epidermal growth factor receptor (EGFR), a major mitogenic signal receptor used by many epithelial cell types. Supporting the importance of EGFR in CRC development, we and others have observed that inhibition of EGFR dramatically attenuates development of intestinal and colorectal tumors in the ApcMin mouse model. Yet, some tumors still arise, even with significant reductions in EGFR activity, implying the existence of compensatory mechanisms for the loss of EGFR. This observation is particularly relevant to human cancer therapy since no validated biomarkers or unique gene expression signatures exist that can partition CRCs based upon their likely sensitivity to EGFR inhibitors. Mouse models offer the potential to define the context and biomarkers for tumors likely to respond to EGFR inhibitor therapy. Equally importantly, mouse models have the potential to identify compensatory signaling networks utilized in the context of reduced EGFR activity, which will make excellent therapeutic targets for cancers resistant to EGFR inhibitor therapy. Other Egfr/Erbb-related genes are also expressed in CRCs, driving the development of pan-ERBB inhibitor therapies. However, scant data exists defining the in vivo functional role of Erbb genes during CRC development or their relationship to EGFR during tumorigenesis. We are uniquely positioned to address many of these open questions by exploiting several new mouse models we developed. These models are ideally suited to develop a gene expression biomarker for sensitivity to EGFR inhibition, to investigate the compensatory networks used by cancers when EGFR is inhibited, identifying leads for new therapeutic targets in cancers resistant to anti-EGFR therapy, and to expose the role and functional interactions among the Erbb genes during CRC development. PUBLIC HEALTH RELEVANCE: The identification of biomarkers that indicate which patients will respond to specific molecular-targeted therapies like those against EGFR is highly significant and relevant to improving the efficacy of clinical treatments. Similarly, the identification of pathways that compensate for the loss of targeted pathways offers in targets to improve therapeutic benefit. The use of novel mouse models as proposed in this application has the potential to provide these insights. [unreadable] [unreadable] [unreadable]

DESCRIPTION (provided by applicant): Colorectal cancer (CRC) is the fourth most commonly diagnosed malignancy in adults. Although significant progress has been made in early detection, diagnosis and treatment, CRC remains the second leading cause of cancer-related deaths in the U.S. and first after smoking-related deaths are excluded. One factor contributing to successful outcome from CRC is early detection, largely performed by periodic colonoscopy. Recently, there is growing appreciation that cancer morphology at the time of presentation can greatly impact the frequencies of detection. In particular, classical polypoid lesions (polyps) are detected and removed during colonoscopy at a much higher frequency than flat ployps, although there is growing evidence that the latter may have a higher propensity to become invasive at much smaller sizes. Little is known about how or why certain cancer pathologies form or even whether this is a stochastic process or if there are specific genetic or environmental factors contributing to distinct cancer morphologies. Fortuitously, we have discovered novel mouse models of human CRC that consistently and almost exclusively produce flat adenomas compared to the much more frequent polypoid adenoma that occurs in the vast majority of mouse models. These results strongly suggest that there are specific genetic factors that determine CRC morphology. Using these new mouse models, we propose to identify the molecular characteristics that distinguish polypoid from flat CRCs and to identify the genetic factors responsible for determining cancer morphology. Although we will largely rely on a discovery-driven genetic approach to achieve these goals, our underlying hypotheses are that a distinct set of cancer modifiers controls susceptibility to flat CRCs and that there there exists specific host genetic factors that determine the type of CRC morphology an individual will develop. Investigation of this hypothesis will be achieved by 1) molecularly characterizing factors contributing to distinct histopathologies, 2) determining the number and genetic locations of flat adenoma modifiers, and 3) fine mapping and identifying candidate modifiers genes. PUBLIC HEALTH RELEVANCE: The identification genetic factors that are responsible for specific subsets of colorectal cancers offers hope that personalized medicine can be applied to the treatment of colorectal cancer. The proposed studies are aimed at identifying genetic differences among individuals that predispose them to develop flat adenomas, a histologically distinct type of colorectal cancer that is difficult to detect during routine colonoscopy. The identification of genetic polymorphisms predisposing patient to flat adenomas will be useful as prognostic markers for individuals needing extra scrutiny during colonoscopy.

DESCRIPTION (provided by applicant): Tremendous advances in understanding the molecular alterations contributing to cancer development and progression, and in exploiting this knowledge to build better mouse models that accurately recapitulate many aspects of human cancer have been achieved. New mouse models of human cancer have been used to identify candidate susceptibility genes, targets for cancer therapy and biomarkers for prognosis. However, similarly remarkable advances have not been realized in the clinic, especially for colorectal cancer (CRC), which accounts for the fourth largest number of new cancer cases each year and the second largest number of cancer-related deaths. Rather, large population-based studies of CRC have repeatedly proven that interventions to reduce susceptibility and deployment of early detection programs have the largest impact on survival from CRC. Colorectal cancer is largely preventable with appropriate lifestyle changes and curable if detected early and removed surgically. Building on the knowledge that CRC prevention and early detection are likely to have the greatest impact clinically, we propose a radical new approach to modeling human cancer in mice. We have assembled an experienced team of investigators that will exploit existing mouse models to develop and test innovative approaches for prevention, and robust yet economical methods for early detection of CRC. The foundation of our pioneering approach is a remarkable new mouse population called the Collaborative Cross that accurately models both germline and somatic genetic heterogeneity present within patient populations. We will use this experimentally tractable population-level model with clinically relevant environments to identify robust yet safe approaches for CRC prevention. We will also exploit the cancer heterogeneity of this population-level model, our previous discoveries from large-scale mouse and human CRC comparative gene expression profiling, and the unique ecology of the gastrointestinal tract microbiota to develop passive biosensors for early cancer detection. In parallel, a new biomarker-based mini-cam will be engineered to detect the location of nascent CRCs. RELEVANCE: Our proposed studies are highly relevant to the health of the US population. Colon cancer causes the second largest number of cancer-related deaths. The only proven ways to reduce loss of human life and financial costs of this disease is prevention and early detection. Consequently, innovative new approaches, as presented in this project, are required to reduce the incidence of life-threatening colon cancer.

DESCRIPTION (provided by applicant): The Department of Genetics at North Carolina State University was founded in 1958 and has established a long and esteemed record of contributions to quantitative genetics using model organisms. The Department of Genetics is housed in the four-story South Gardner Hall and occupies approximately 35,000 square feet on the second and third floors. Much of the space was renovated in 2007. The department has common facilities including a media kitchen, growth and storage chambers and adjacent small animal and greenhouse space to support a variety of research activities using multi-cellular model organisms including Arabidobsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and Mus musculus. With the hiring of a new department head in 2008, a revitalization of the historical strengths in the department was begun with a focus on building a Research Core Center in Systems Genetics. The first targeted hires were for two population or quantitative geneticists. An open search was performed and seven candidates interviewed. Two outstanding candidates were selected but before offers could be finalized, hiring was frozen for lack of resources to adequately support start-up funding due to the worsening economy in the state of North Carolina. Consequently, the Department of Genetics and its Research Core Center in Systems Genetics is uniquely positioned to benefit from RFA-OD-09-005: Biomedical Research Core Centers to Enhance Research Resources, which will result in the hiring of one new Assistant Professor with a focus on population genetics. Additionally, a second position will be created and equipment purchased to support the new lab. This application is ideally matched with the goals of the American Recovery and Reinvestment Act of 2009.

DESCRIPTION (provided by applicant): This project addresses broad Challenge Area (03) Biomarker Discovery and Validation and specific challenge topic 03-DK-104: "Development of drug toxicity biomarkers for kidney, liver, and other organs of NIDDK interest for use in assessing human drug toxicity". Liver injury due to drug toxicity is a serious safety risk associated with drug development and poses a significant burden to physicians, the pharmaceutical industry, and regulatory agencies. Often, drug-induced liver injury (DILI) manifests as a rare, "idiosyncratic" event that occurs only in the rare, susceptible patient. This project will evaluate the use of a newly developed mouse model population, called the Collaborative Cross, to detect genetic variants that cause individuals to be susceptible to DILI. Once validated, this research tool will provide a unique means for evaluating the toxicity risk associated with pharmaceutical agents in susceptible patients as well as a means for which otherwise efficacious pharmaceutical agents may remain in public use, enabled by genetic testing. ABSTRACT Drug-induced liver injury (DILI) is the major adverse drug event that leads to regulatory actions on drugs, including failure to approve, restricted indications, and withdrawal from the marketplace. The most problematic form of DILI is "idiosyncratic", meaning the drug is safe for the vast majority of treated patients while causing catastrophic liver injury in the rare, susceptible patient. Genetic predisposition for complex traits, such as DILI, results from the combined effects of genetic variations within genes termed "quantitative trait loci" (QTL). Due to the rarity of these events, studies aimed at detection of causal risk alleles in human populations are often under-powered, thus hampering the ability to detect QTL. However, there are no animal models that have been validated for the ability to detect those genetic variants that confer an increased risk for liver toxicity for a given pharmaceutical. The project proposes a new paradigm for preclinical drug safety that is performed using a newly available mouse population, the Collaborative Cross, which was created specifically to model the genetically heterogeneous human population. The Collaborative Cross was developed using a breeding scheme that maximizes the genetic diversity between strains, allowing capture of 90% of the known genetic variation in mice. In three specific aims, our goal is to utilize the Collaborative Cross mouse population to identify genetic variants that predispose individuals for DILI. In Aim 1 - Determine the optimal drug and dose necessary to achieve a DILI response within the parental mouse strains of the Collaborative Cross - a dose- escalation study will be performed with ten drugs known to cause idiosyncratic hepatotoxicity. Phenotyping of liver injury markers will be performed to determine the optimal drug and dose needed for QTL analysis. Using the optimal drug and dose, Aim 2 - Determine genetic loci that modulate susceptibility to idiosyncratic DILI using the Collaborative Cross mouse strains - will be performed in 150 Collaborative Cross lines. These studies will utilize liver injury markers collected across the Collaborative Cross mouse population to interrogate genetic variations within the genome (i.e. single nucleotide polymorphisms;SNPs). The outcome of Aim 2 will be regions of the genome that are significantly associated with liver injury risk across mouse strains. To follow up on these studies, Aim 3 - Identify risk alleles for toxicity susceptibility within candidate gene regions - will be performed. Specific genetic variants that confer an increased risk of DILI, alone or in combination, will be identified by sequencing of target genes followed by correlation and risk ratio analysis of identified SNPs. These studies offer a unique opportunity to study the genetic architecture of predisposition to idiosyncratic DILI and have the potential to revolutionize how preclinical drug safety testing is performed. Successful completion of the proposed studies will provide a roadmap for improved drug safety testing, leading to safer drugs and a route to rescue efficacious drugs that cause toxicity in only a subset of the patient population PUBLIC HEALTH RELEVANCE: This project addresses a major challenge in the drug development process that greatly limits the utility and safety of drugs. Currently, most drugs are removed from the marketplace or are not approved for clinical use because of liver toxicity. No current platform exists to perform accurate preclinical testing of new drugs to identify those most likely to result in adverse events or to identify genetic factors that contribute to toxicity susceptibility. We are proposing a revolutionary new model based upon a mouse resource that was specifically developed to model the heterogeneous human population. The successful use of this new resource will dramatically improve drug develop, saving significant costs and greatly expanding the pharmaceutical industry.

DESCRIPTION (provided by applicant) The investigators propose a new Center for Translational Environmental Health Research (CTEHR) to promote integrated translational research, and catalyze interdisciplinary research in human environmental health. The CTEHR Mission is to improve our understanding of environmental influences on human health by integrating basic, biomedical and engineering research across translational boundaries from the laboratory to the clinic and to the community and back. To achieve its mission, the CTEHR will be initiated with four broad goals: Goal 1: Build capacity in translational environmental health sciences through member participation in Thematic Focus Areas and utilization of an Integrated Health Sciences Facility Core (IHSFC). Research in the five interrelated Thematic Focus Areas focuses on environmental stressors, modifiers of individual response and human health outcomes impacted by the environment. The IHSFC will provide unique resources and utilize Translational Navigators to facilitate utilization and promote translational environmental health research by CTEHR members. Goal 2: Integrate researchers and research activities across translational boundaries and develop promising new investigators in translational environmental health with a Career Development Program. The CTEHR Career Development Program will mentor junior investigators, and promote professional development all along the career spectrum with a new inter-Center Mentored Partnership Program. Goal 3: Enhance the capabilities of research programs in environmental health sciences with Facility Cores and a Pilot Project Program. CTEHR Facility Cores will build a Discovery Pipeline to provide resources supporting Hypothesis Generation and Hypothesis Testing studies that Translate into practice Center member research. The Pilot Project Program supports early-stage projects with potential to advance environmental health science research. Goal 4: Create a bridge between Center members, surrounding communities, and stakeholders to further scientific collaborations and dissemination of research results through the Community Outreach and Engagement Core (COEC). By fostering the involvement of Center scientists, Facility Core and Program personnel, the COEC will provide resources and expertise that enable individuals, communities and policy makers to make informed decisions about environmental exposures, and to mitigate environmental disease risks. The Texas Medical Center is the largest medical center in the world, with a wealth of investigators conducting world-class research relevant to human environmental health. However, no entity exists in this setting to integrate these talented investigators and harness the capabilities of this resource-rich environment to promote research and translation of the environmental health sciences. CTEHR will fill this need by serving as the focal point for environmental health research across the TMC and affiliated institutions.

? DESCRIPTION (provided by applicant): The environment is perhaps the major contributor to human disease, yet its effect is largely ignored in whole genome approaches to genetics. In this CEGS, we will attack head-on the mechanisms through which environment influences genomic function, focusing on two extremely important exposures highly relevant to human health: diet and its relationship to metabolic disease and cancer; and stress related to neuropsychiatric disease. This requires nearly complete control of the experimental system in a way that cannot be done in humans. Our first aim is develop a new foundational experimental mouse model for understanding gene-environment interaction (GxE). We will expose crosses of the genetically heterogeneous Collaborative Cross population of mice to three well-controlled diets - Western, Mediterranean, ketogenic - and measure phenotypes across organ systems representing metabolic and cardiovascular disease. We will also determine the effects of diet on azoxymethane-induced colon tumors; as well as stress on phenotypes relevant to neuropsychiatric disease. We will couple these analyses to whole genome bisulfite sequencing, chromatin accessibility analysis and transcriptomics of target tissues including liver, adipose tissue, colon, hippocampus, prefrontal cortex, and blood, measuring the nature and flow of information among environment, genome, epigenome, and transcriptome in determining phenotype. Our second aim is to develop new statistical methods as well as a novel mathematical framework for handling the interaction between genetics, epigenetics, and exposure, which will allow us to model how information is passed between these three domains to ultimately shape phenotype. These methods include causal inference testing, analysis of genomically discontiguous genotype-epigenotype relationships, and novel stochastic approaches based on fundamental concepts of statistical physics and information theory. Our third aim is to perform replication in naïve animals and in highly relevant human epidemiologic cohorts: DWH and ALSPAC for diet exposures and metabolic disorders; NHSII and EPIC for diet and colon cancer; and ALSPAC and PIRC for stress and behavioral traits. Our fourth aim is to develop and promulgate new measurement, analytical, and computational technologies for comprehensive genomic analysis of GxE. These include new biological resources and software packages, as well as biochemical, cellular and computational tools to test and improve the models and conclusions from the other Aims, and of broad general use to the genomics community, including: analysis of single or multiple marks for determining long-range GxE relationships; single cell and in situ analysis of gene expression and epigenetic modifications; and novel computational approaches including ultrafast alignment of large datasets. This highly interdisciplinary proposal involves completely novel combinations of mouse genomics, statistical physics, biostatistics, computer science, biochemistry, epidemiology, and single cell analysis, in order to understand the essential question of how genomic function is shaped by the environment.

Chromatin regions, genes and pathways that confer susceptibility to chemical-induced DNA damage ABSTRACT Genetic variability has a major impact on susceptibility to common diseases, responses to drugs and toxicants, and influences disease-related outcomes. In addition, the links between genetic variability, toxicity outcomes and epigenetics are being actively explored. However, studies of Gene × Environment × Epigenetics are difficult as they involve interrogation of multiple individuals, exposure doses/times, tissue types, -omics endpoints and various toxicity phenotypes. This proposal aims to identify and validate chromatin regions, genes and pathways that confer susceptibility to environmental chemical-induced and metabolism-associated DNA damage. We will perform a series of proof-of-principle studies of the interplay between DNA damage induced by 1,3-butadiene, a genotoxic carcinogen, genetics, and epigenetics. We have extensive experience performing toxicology studies in the mouse (Collaborative Cross, CC) and human (1000 Genomes lymphoblast cell lines) population-based models. First, we will determine expression and chromatin quantitative trait loci (QTL) of butadiene genotoxicity in mouse tissues. We will test the hypothesis that strain- and tissue-specific variation in butadiene-induced DNA damage is controlled by the genetic variability-dependent background states in chromatin and gene expression. We will use tissues (liver, lung and kidney) from a study of 50 CC strains exposed to butadiene and will evaluate butadiene DNA damage and identify regions of active/repressed enhancers and promoters. Second, we will determine dose- and time-effects of butadiene-induced DNA damage in the context of background and treatment-induced chromatin and transcriptional states. We will test the hypothesis that butadiene exposure modifies strain- and tissue-specific epigenetic states in a dose-dependent manner and that DNA damage-associated effects on chromatin persist. We will examine inter- vs intra-strain variability, dose- and time-dependency in select CC strains. Third, we will characterize the extent of population variability in response to butadiene metabolites in a human in vitro population model. We will test the hypothesis that human lymphoblasts can be used to map susceptibility loci for butadiene genotoxicity. Fourth, we will validate the discoveries of the transcriptional and epigenetic mediators of strain-dependent DNA damage by butadiene in a human in vitro population-based model. We will test the hypothesis that genetic background- dependent transcriptional and epigenetic states confer susceptibility/resistance to butadiene-induced DNA damage. We will evaluate chromatin states and expression coupled with assays for DNA adducts. Overall, this work will demonstrate the interplay among environment (i.e., chemical exposure), genetics, and epigenetics by studying effects of 1,3-butadiene, an industrial toxicant and model genotoxic carcinogen. Human relevance and feasibility are justified by the focus on a fundamental mechanism of toxicity and carcinogenesis, the fact that butadiene is a known human and rodent carcinogen, and our previous work demonstrating butadiene effects of chromatin, histone modifications and other epigenetic states in a strain- and tissue-dependent manner.

Overall ABSTRACT    The  vision  for  the  Texas  A&M  Center  for  Environmental  Health  Research  (TiCER)  is  to  nucleate  research  and  translational  activities  of  faculty  and  trainees  around  the  overarching  theme  ?Enhancing  Public  Health  by  Identifying, Understanding and Reducing Adverse Environmental Health Risks.? This vision will be achieved by  building  on  Texas  A&M  University?s  ongoing  investments  in  people  and  facilities  and  a  history  of  state-­wide  outreach to community stakeholders, with a particular focus on underserved populations. Existing environmental  health  investments  at  Texas  A&M  provide  infrastructure  and  a  diverse  expertise  base  ready  to  catalyze  innovative  investigations  into  environmental  health  concerns  of  affected  communities  and  populations,  build  multidisciplinary  collaborations  among  Center  members  to  elucidate  mechanistic  links  between  environmental  exposures  and  adverse  health  outcomes,  and  translate  mechanistic  data  to  actionable  outcomes.  The  Center  will  continue  recent  successes  in  mentoring  junior  faculty,  recruitment  of  additional  established  faculty  into  environmental health research, and fostering a multi-­disciplinary, team-­oriented intellectual environment among  a core group of 54 members representing 11 colleges at Texas A&M. The thematic areas the Center will expand  upon  are:  1)  Stressors  to  Responses;?  2)  Environment  and  Metabolism;?  3)  Individuals  to  Populations;?  and  4)  Community, Regulation and Policy. The Center?s vision will be fulfilled through a highly integrated set of Facility  Cores.  The  Integrated  Health  Sciences  Facility  Core  will  support  bi-­directional  translation  with  a  human  translational studies component, a mouse translational studies component and an in vitro translational studies  component.  Three  technology-­integrating,  research  facility  cores  (Data  Science,  Bio  Science,  and  Chem  Science) will ensure Center member access to unparalleled instrumentation and resources of Texas A&M, a top  tier  public  research  university  with  extensive  outreach  throughout  the  state  of  Texas.  The  facility  cores  will  enhance  the  capacity,  breadth,  collaborative  nature,  and  impact  of  environmental  health  research.  The  Administrative Core and Pilot Project Program will facilitate the Center?s function by ensuring continuation of the  highest levels of institutional support, fostering career development and promoting multidisciplinary team science  that generates knowledge in areas of community concern. The Community Engagement Core will be a critical  vehicle for implementation of a multi-­prong strategy of the Center by serving as a bi-­directional portal to connect  Center members, affected communities and other stakeholders that builds on a strong tradition of Texas A&M  in public and community service statewide with a research focus on the health and environmental concerns of  underserved  populations.  Overall,  the  Center  will  expand  the  established  investigator  base  and  expertise  that  can be deployed to increase the impact of environmental health research in Texas and beyond. 

Administrative Core ABSTRACT  The  Administrative  Core  will  provide  leadership  and  guidance  to  the  Texas  A&M  Center  for  Environmental  Health  Research  (TiCER)  to  ensure  excellence  of  research  integration,  community  engagement,  research  translation, and career development. The overall theme of the Center is ?Enhancing Public Health by Identifying,  Understanding, and Reducing Adverse Environmental Health Risks.? The Administrative Core will serve as the  focal point for the Center and provide the support infrastructure to promote cross-­discipline interactions among  all members, facility cores, and external stakeholders. The Administrative Core will be centrally located on the  Texas A&M University campus. The responsibilities of the Administrative Core, led by the Program Committee,  consisting of the Center Director, Deputy Director, Center Administrator, Facility Core principal investigators and  theme  leaders,  will  be:  (i)  planning  Center  activities;?  (ii)  evaluating  progress  and  considering  solutions  for  challenges;?  (iii)  improving  Center  integration;?  (iv)  advising  on  personnel  matters;?  (v)  assessing  quality  management/assurance;? (vi) organizing the annual retreat;? and (vii) evaluating community engagement, training,  and research translation activities. will be to facilitate regular interactions among Center members, track products  and outcomes, develop and plan future activities, and guide and sustain growth of environmental health research  at Texas A&M. The Program Committee will use an Internal Advisory Board of senior Texas A&M administrators  and an External Advisory Board of eminent environmental health researchers in advisory capacities to ensure  that  research,  outreach,  career  development,  and  translation  goals  and  objectives  are  being  met.  The  Center  will achieve its goals through four aims: 1) Provide effective center leadership;? 2) Maintain an active membership;?  3) Enhance coordination, integration, and translation of research;? and 4) Promote career development.   

Project Summary IMSD at Texas A&M University: Initiative for Maximizing Student Diversity in Biomedical Sciences This proposal is to establish a new IMSD T32 program at Texas A&M University. The overall mission of this program is to maximize student diversity in biomedical sciences at Texas A&M by focusing on recruitment and retention of underrepresented minority (URM) populations of trainees seeking a PhD degree who have the skills to successfully transition into careers in the biomedical research workforce. Funds are requested to support six pre-doctoral (Ph.D. candidates) URM trainees who are applying to one of the six major biomedical graduate training programs at Texas A&M University: Medical Sciences, Biomedical Sciences, Genetics, Toxicology, Biochemistry & Biophysics, and Biomedical Engineering. Texas A&M University will match NIH support with six additional fellowships. This program will serve as a hub for unifying training-oriented diversity initiatives in biomedical fields and establish a community of URM scholars at Texas A&M. Trainees will benefit from didactic, research, mentoring and career development elements offered by the existing training programs, and from the new initiatives focused specifically on this cohort of URM scholars. Our goal is to prepare trainees to function as independent researchers and/or practitioners in a multidisciplinary setting by providing training in classroom-, laboratory- and externship-based settings. To achieve this goal we have assembled a team of 40 outstanding investigators who specialize in diverse biomedical fields. The program will be led by an executive committee of co-PIs representing Office of Graduate & Professional Studies and participating Colleges (Medicine, Veterinary Medicine, Engineering, and Agriculture & Life Sciences). The preceptors have strong records of mentoring URM trainees and obtaining competitive support from Federal, State and other sources. This group is exceptionally well balanced with respect to expertise, sex, and academic career level. Internal and external oversight will be provided by eminent scholars with first-hand knowledge of diversity experiences in biomedical training and employment. Recruitment will be conducted through external advertisement, post-baccalaureate diversity programs, as well as Texas A&M research experience for undergraduates and masters programs. Support from this program will be offered only in the first year of the doctoral program at the time when trainees undertake two laboratory rotations, follow structured core academic curricula of their respective graduate programs, and participate in regular joint activities as a group. A distinctive feature of the program is a strongly encouraged hands-on summer (in the 1st year) externship through a broad and diverse network of academic laboratories, state and federal governmental agencies, as well as industry and non-governmental organizations. Following the first year, trainee support will shift to their graduate program, mentor, or other funding; however, trainees will continue participation in program-related functions thus maintaining a strong bond to a community of scholars of underrepresented backgrounds in addition to their home programs. Trainees affiliated with this program will be highly successful in academia, industry, government and other professional settings in health-related disciplines.

PROJECT SUMMARY Texas A&M University has a long history of training in the genetic sciences, with the first graduate degree having been awarded in 1919. The first Interdisciplinary Program (IDP) in Genetics was the first IDP established at Texas A&M in 1983, and has been at the forefront of diversifying not only the trainee pool that will contribute to a diversified workforce, but is also leading in the preparedness of students for diverse career paths. The Genetics IDP preceptors have world-renowned research programs providing unique opportunities for trainees to perform dissertation research in laboratories using cutting-edge technologies that are addressing important and impactful questions in modern genetics that impact human health and well-being, while also having extensive mentoring and career development opportunities. This innovative training program aims to be a model for ?preparing diverse scientists for a diverse workforce?. The Genetics IDP has developed several initiatives and partnerships that have resulted in a dramatic increase in diversity of applicants and matriculates to the program. Similar to the need for a diverse genetics workforce, efforts are needed to diversify preparedness for future workforce needs and career opportunities. Modern training in genetics and the sub-discipline of genomics not only requires mastering classical Mendelian and quantitative genetics, but expertise in big data, interpersonal interactions that is essential for convergence research, and project management that can be applied to diverse career opportunities. The training program is designed to train the next generation of scholar in modern genetics by providing contemporary skills and exposure to the increasingly broad range of career opportunities that these scholars will pursue in order to have a profound impact on the future of genetic sciences. The goals of the training program are to: 1) Provide doctoral students with balanced research and training opportunities that span the continuum from basic science to applied applications and the scientific knowledge needed to excel in modern genetic sciences irrespective of career path; 2) Offer a rigorous didactic training that provides the fundamentals in Mendelian and quantitative genetics, statistics and experimental design, rigor and reproducibility, biostatistics, big data computation skills, and a core set of competencies in communication, interpersonal interactions, and leadership and team science that will be required for successful careers in academia, industry and government; and 3) Ensure that trainees develop appreciation for, familiarity with, and exposure to various career opportunities for well-trained geneticists through mentorship and introduction to experts in various fields.

PROJECT SUMMARY The incidence of cardiometabolic disease has soared during last half-century despite national efforts to improve health through universal dietary recommendations. A critical limitation of this approach is the lack of consideration given to dietary response differences based on an individual?s genetics, which is essential for the nascent field of precision nutrition. The long-term goal of this proposal is to develop the foundation and an experimental platform to support in-depth biological analyses of precision nutrition interventions. The objective of this proposal is to develop an experimental genetic reference platform that models human genetic diversity into a model for precision nutrition. Although largely relying on a discovery-driven approach, the central hypothesis is that a major failing of public health efforts has been generalization of dietary recommendations and that through matching dietary recommendations to an individual?s metabolic needs, cardiovascular health will be greatly improved at the individual and population level. This hypothesis is based on published and unpublished work. The rationale is that completion of these studies will identify genetic and metabolic factors and high-level mechanisms by which diet influences differential cardiometabolic health that can be used to develop new paradigms for precision nutrition. The proposed work will also provide a repository of data and samples from the Collaborative Cross, a publicly available mouse genetic reference population. The central hypothesis will be tested by pursuing three aims: 1) Identify cardiometabolic health traits that are influenced by gene-by-diet (GxD) interactions; 2) Determine the genetic architecture regulating diet-dependent effects on cardiometabolic health; and 3) Validate a precision nutrition paradigm to predict effects of diet on cardiometabolic disease. These aims will be pursued using an innovative combination of a novel, publicly available mouse genetic reference population and human relevant diets for which substantial epidemiological data exists on their cardiometabolic effects. The proposed research is significant because it will determine the health impact that individual genetic variation has on response to common diets and identify those characteristics that are influenced by GxD interactions. It is also significant because it will provide a public database of physiological responses and a sample repository of tissues for future molecular analyses, providing a critical foundation for the nascent field of precision nutrition. The expected outcome of this project is a comprehensive understanding of how diet influences cardiometabolic health in an experimental genetic reference population, an essential first step to support future projects in precision nutrition. The resulting data will have an important positive impact because it will provide a paradigm shift toward precision nutrition by: a) identifying cardiometabolic phenotypes influenced by GxD responses; b) elucidating the genetic architecture and high-level mechanisms of unique responses to diet; c) validating putative diet responses through confirmatory studies; and d) generating a rich database of GxD responses and a sample repository for use by the research community.