Pilot projects 2004
Project 1: Identification of polymorphisms in smoking induced genes
PI: Charles M. Perou, Ph.D., Assistant Professor of Genetics and of Pathology & Laboratory Medicine
Project 2: Development of an infectivity assay for noroviruses using tissue engineering
Project 3: Pilot feasibility study of farm endotoxin, asthma, and gene-environment interaction
Project 4: Environmental determinants of physical activity and obesity
Project 5: Oxidative stress in the obese/diabetic heart
Project 6: Melanoma expression signatures and heterogeneity
Project 7: Genetic and early life origins of obesity, metabolic and cancer-related risk factors among Filipinos
Project: Identification of polymorphisms in smoking induced genes
The diversity of clinical behaviors of squamous cell carcinoma of the head and neck (SCCHN; cancer of the oral cavity, pharynx, and larynx) poses a challenge to the prevention and treatment of this disease. Our laboratory has used genome-wide expression profiles to classify SCCHN into four distinct and reproducible subtypes. These subtypes showed statistically significant differences in recurrence-free survival. One subtype showed high expression of antioxidant enzymes that are involved in xenobiotic metabolism including Glutathione S-Transferase M3, Thioredoxin Reductase 1, Glutathione Peroxidase 2, Aldo-Keto Reductase 1, and two genes involved in the pentose phosphate cycle (Transaldolase 1 and Phosphogluconate Dehydrogenase). We propose a unique translational study to: 1) “resequence” these four of these genes from 80 SCHHN tumors to identify Single Nucleotide Polymorphisms (SNP) and determine haplotype structure and 2) to evaluate the population allele frequencies for these SNP using samples from an ongoing UNC SCCHN case-control study. The proposed “resequencing” project will not only provide clues to the importance of genetic variation in these smoking-related genes but will also provide polymorphic markers for evaluation in many other population studies.
Project: Development of an infectivity assay for noroviruses using tissue engineering
Noroviruses (NoVs) are the leading causes of acute gastroenteritis in humans. The inability to replicate NoVs in cell culture has been a serious barrier to understanding their basic virology. Recently, it has been shown that humans possessing certain ABH histo-blood group antigens are susceptible to norovirus infection and that humans lacking these antigens cannot be infected. In addition to the need for the presence of an appropriate ABH histo-blood group antigen on cells two additional restrictions could be: 1) the need to use authentic gastrointestinal cells and culture conditions as hosts, since NoVs are observed in vivo in gastrointestinal tissue (small intestine), and 2) a possible need for the viruses to replicate in a stem/progenitor cell compartment and then be able to mature along with the host cells to an appropriate adult cell stages to yield the mature virus. We propose to test the relevance of ABH histo-blood group antigen, the use of gastrointestinal-derived cell types, and/or a lineage-stage culture model system to see if any (or all) of the variables are critical to enable NoVs to replicate ex vivo.
If our approach is successful, this research will become a cornerstone for NoV research. A culture system for human NoV would represent a major advance for the field, and therefore should lead to competitive applications and funding opportunities.
Project: Pilot feasibility study of farm endotoxin, asthma, and gene-environment interaction
Asthma is the most common chronic childhood disease. What causes asthma is still not clearly understood. The current paradigm is the “hygiene hypothesis,” which postulates that high exposure to microbial products found on farms, such as endotoxin, stimulates the young immune system to develop Th1 response pathways instead of Th2 pathways and thereby protects against the development of asthma. Recent discoveries indicate the protective mechanisms involve a gene-environment interaction between farm endotoxin exposure and toll receptors (microbial pattern recognition receptors). The RO1 has the goals to 1) evaluate the role of gene-environment interaction in the development of asthma, 2) examine cytokine response profiles (representing either a TH1 or TH2 polarization) associated with high levels of exposure to farm endotoxin. The purpose of the proposed pilot study is to demonstrate our ability to collect and analyze 1) buccal cells for haplotype analyses of toll 2 receptors, 2) nasal lavage samples for Th1 and TH2-like cytokine profiles, and 3) and home endotoxin samples. Understanding the protective immune response mechanisms in asthma is critical to the development of preventative strategies for childhood asthma.
Project: Environmental determinants of physical activity and obesity
Background. With minimal research, particularly longitudinal analysis, there is an increasing call for population-wide environmental/policy interventions to increase physical activity.
Specific Aims. We will link contemporaneous geographic locations of respondents with physical environment variables and data from the Coronary Artery Risk Development in Young Adults Study [CARDIA], a longitudinal study of 5,115 black and white young adults aged 18-30 years at baseline. The specific aim of the pilot is to develop and validate new physical environment measures from existing databases linked to respondents= geographic locations. Future aims include estimating the dynamic effects of patterns and changes in environment variables on activity.
Methods. We will geocode street addresses for respondents from the CARDIA dataset and build an extensive GIS database of activity-related environmental factors (e.g., park and recreation facilities, transport options, accessibility variables, crime, climate, and community design) using a range of federal, commercial, and public databases. We will develop complex longitudinal and spatial analytical models to explore relationships between environmental factors and activity, adjusting for self-selectivity of residential location choice. This will be the first longitudinal study of its kind.
Project: Oxidative stress in the obese/diabetic heart
An obesogenic environment exists in the US in which obesity and diabetes flourish. Obesity and subsequent diabetes leads to a concomitant increase in heart disease. Hearts from obese and diabetic rodents exhibit deranged fatty acid (FA) metabolism, with increased rates of mitochondrial and peroxisomal FA oxidation and accumulation of triacylglycerol (TAG). The presence of hydrogen peroxide, elevated catalase, and a diminished ratio of reduced gluatathione (GSH) to oxidized glutathione (GSSG) indicate the presence of oxidative stress. Hyperlipidemia is associated with increased tissue concentrations of lipid peroxides (TBARS); therefore, excess myocardial TAG may contribute to elevated levels of TBARS in the obese/diabetic heart. We hypothesize that altered FA metabolism in the obese/diabetic heart induces oxidative damage which results in the observed heart disease. Mice will be fed either a high fat, high sucrose diet to induce obesity/diabetes or a control diet. We will evaluate the following: a) extent of myocardial TAG accumulation, b) up-regulation of peroxisomal oxidation, c) oxidative state of the heart (GSH/GSSG ratio), d) extent of lipid peroxidation (TBARS/MDA; Nutrient Assessment Facility Core), e) extent of DNA damage (8-OH-dG and M1G; Biomarkers Facility Core), and f) up-regulation of base excision repair (BER) genes. Results from these studies will provide preliminary data for an RO1 proposal investigating obesity/diabetes-induced heart disease.
Project: Melanoma expression signatures and heterogeneity
Melanoma is an environmentally-induced cancer which has increased in incidence at an alarming rate during the past few decades. A primary cause of melanoma is DNA damage due to ultraviolet radiation (UV) from sunlight. However, the wavelength, intensity, and pattern of UV exposure on the human body that lead to malignant melanoma have not been sufficiently characterized; and, based upon tumor site, histology, and different genetic alterations that occur, it is likely that melanoma is a heterogeneous disease with differing etiologies related to different exposures. Further studies of etiology would be greatly facilitated by a better understanding of melanoma heterogeneity, and we hypothesize that some of this heterogeneity can be elucidated through gene expression profiling. We propose to do gene expression profiling in the context of known mutations in melanoma. This pilot project would begin that process by identifying gene expression patterns associated with BRAF mutation in frozen and formalin-fixed paraffin-embedded melanoma tissues. This pilot study will provide the foundation for future studies of melanomagenesis in the context of environmental exposures.
Project: Genetic and early life origins of obesity, metabolic and cancer-related risk factors among Filipinos
The proposed research focuses on the identification of early life exposures, genetic main effects, and gene-environment interactions contributing to the development of obesity and other components of the metabolic syndrome among Filipino young adults. We use detailed, prospectively collected data from The Cebu Longitudinal Health and Nutrition Survey, an ongoing sociodemographic study to which we will add blood collection for analysis of DNA and plasma biomarkers of CVD risk. The sample includes about 2000 individuals born in 1983-84, and their mothers. This rich data set allows us to examine interactions of prenatal and early life nutritional exposures, selected genotypes, and diet and physical activity as determinants of outcomes. We also include genetic and phenotypic data on the mothers of young adults. Our ultimate research goal is to model a wide range of obesity-related phenotypes reflected in weight gain trajectories from the prenatal period to adulthood, subcutaneous fat patterning, other markers of central obesity, and a suite of biomarkers of CVD risk (insulin resistance using HOMA, fasting glucose and insulin, leptin, C-reactive protein and other markers of inflammation, and serum lipids).
Funded by NIEHS Grant # P30 ES010126