We propose to establish the feasibility of a potentially transformative approach, applicable to a wide variety of human diseases, which we refer to as Enhancer Therapy. This approach is based on the discovery of the functional importance of eRNAS; non-coding RNAs that are transcribed from tissue and disease-specific enhancers. Remarkably, we find that knockdown of these eRNAs using derivatized anti-sense oligonucleotides (ASOs) reduces expression of nearby target genes in macrophages and breast cancer cells. These findings, in concert with the clinical development of ASO technology by Isis Pharmaceuticals, open a pathway for the development of ASOs that result in tissue specific inhibition of pathogenic gene expression in humans. We therefore propose to investigate the feasibility of 'Enhancer Therapy' using inflammation and breast cancers as initial models, with the following approach: (i) We will use established and novel genome-wide methods to generate atlases of enhancers and enhancer RNAs in mouse and human tissues and cell types that are relevant to both pathological conditions and normal tissue homeostasis; (ii) Using these atlases, we apply GRO-seq and our recently developed 3D-DSL methodology to generate high-resolution maps of the interconnections of specific enhancers of interest with their target genes; (iii) We will next select cell-specific enhancers that express eRNAs and interact with disease-relevant genes to use as models for eRNA targeting. In collaboration with ISIS Pharmaceuticals, we will develop corresponding ASOs that specifically reduce expression of target eRNAs in primary mouse macrophages and human breast cancers suitable for use in vivo. The functional consequences of eRNA knockdown will be ascertained by appropriate secondary assays, e.g., suppression of inflammatory gene expression in macrophages and proliferation/metastasis of breast cancer cells. (iv) Using the results of these in vitro studies, we will proceed to test ASOs for their ability to reduce expression of selected target genes in cells and in vivo in a cell/tisse specific manner and explore appropriate disease models. Our goal is to directly test the novel idea that inhibition of eRNA expression can result in a therapeutic outcome, thereby establishing a transformative approach to treatment of human disease.
We will focus on macrophages and breast cancer cells as the primary target cells for studies of feasibility of Enhancer Therapy. These two cell types provide models that are relevant to a broad range of inflammatory diseases, such as atherosclerosis and type 2 diabetes, and cancer, which collectively account for a substantial fraction of overall morbidity and mortality in industrialized societies.
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