The goal of this proposal is to develop a novel high-throughput platform for understanding gene regulatory elements in order to identify new drug targets for common diseases. The human genome encodes approximately 50,000 genes. Understanding how those genes are regulated and how this correlates to complex cell phenotypes has long been a major focus of our team. Follow-up projects to the Human Genome Project, such as the NIH-funded Encyclopedia of DNA Elements (ENCODE) and the Roadmap Epigenomics Project, have identified millions of putative regulatory elements across the human genome for many human cell types and tissues. Importantly, genome wide association (GWA) studies have strongly indicated that non- coding regulatory elements determine the gene expression patterns responsible for most complex diseases including cancer, cardiovascular disease, diabetes, and neurological disorders. However, the function of these regulatory elements and their relationships to these disease phenotype are largely unknown. Additionally, conventional screening technologies for perturbing cellular processes, such as small molecules and RNA interference, cannot directly target genomic regulatory elements. To address this critical limitation and illuminate the fundamental genomic basis of these cell phenotypes, we have recently developed epigenome- editing technologies for directly and precisely activating and repressing genomic regulatory elements in their natural chromosomal location. More recently, we have developed a novel and robust method for using these tools for high-throughput identification and quantification of gene regulatory element activity. Here, we propose to apply these methods to the discovery and validation of regulatory elements associated with cancer and cardiovascular disease as demonstration of this novel platform technology for understanding the genetic basis of complex disease. This technology will be critical to translating modern advances in genetics and genomics into new drug targets, diagnostics, and personalized medicine catered to each patient genome.
Public Health Relevance Statement: Project Narrative The purpose of this STTR Phase I application is to develop novel methods to identify and characterize gene regulatory elements and non-coding DNA mutations associated with complex disease with the goal of discovering new classes of drug targets and developing functionally informed diagnostics. The academic partner (Duke University) has accumulated years of experience with characterizing regulatory elements and DNA variants using genome and epigenome editing strategies. The small business partner (Element Genomics, Inc.) will be involved in developing novel high-throughput methods and bioinformatics pipelines to robustly characterize 1000's of regulatory elements from any region of the genome, and will show how perturbing these regulatory elements contributes to altered phenotype. We propose to develop these methods by focusing on two model genes that have been shown to be involved in human disease. The results from these Phase I studies will be used for future Phase II studies to identify novel small molecule drugs that impact the expression of those genes.
Project Terms: abstracting; Acetyltransferase; Address; base; Binding; Bioinformatics; Businesses; Cardiovascular Diseases; Cell Line; Cell physiology; cell type; Cells; Chemicals; Cholesterol; chromosomal location; Clinical Trials Design; Complex; CRISPR/Cas technology; Data; Databases; Deoxyribonuclease I; design; Development; Diabetes Mellitus; Diagnostic; Disease; disease phenotype; Disease susceptibility; DNA; DNA Sequence Alteration; DNase I hypersensitive sites sequencing; DNase-I Footprinting; Drug Design; Drug Targeting; Elements; Encyclopedia of DNA Elements; Engineering; epigenome; epigenomics; ERBB2 gene; experience; follow-up; Funding; Future; Gene Expression; Gene Expression Profile; gene function; Gene Targeting; Genes; Genetic; Genetic Determinism; Genome; genome wide association study; Genomics; Goals; Guide RNA; Heterogeneity; high throughput analysis; high throughput screening; High-Throughput Nucleotide Sequencing; Human; Human Cell Line; human disease; Human Genome; Human Genome Project; human genome sequencing; improved; Individual; Industry; innovation; interest; Libraries; Location; malignant breast neoplasm; Malignant Neoplasms; Maps; Methods; Modeling; Mutation; nervous system disorder; new technology; new therapeutic target; novel; novel therapeutics; Nucleotides; Oncogenes; Open Reading Frames; Patients; Performance; personalized medicine; Pharmaceutical Preparations; Pharmacotherapy; Phase; phase 1 study; phase 2 study; Phenotype; Preclinical Drug Evaluation; Proteins; Regulatory Element; Reporter; Reporter Genes; research study; response; RNA Interference; screening; Screening Result; Signal Pathway; Site; Small Business Technology Transfer Research; small molecule; Small RNA; Sorting - Cell Movement; Technology; Tissues; tool; trait; Transcript; transcription factor; Translating; treatment response; United States National Institutes of Health; Universities; Untranslated RNA; Validation; Variant; Variation (Genetics); Work
