Barath, Abhijeet

Abstract Understanding the function of non-coding genomic sequence variants represents a challenge for biomedicine. Many diseases are products of gene-by-environment interactions with complex mechanisms. This study addresses these themes by mechanistic characterization of non-coding variants that influence gene expression only after drug or hormone exposure. Using glucocorticoid signaling as a model system, we integrated genomic, transcriptomic, and epigenomic approaches to unravel mechanisms by which variant function could be revealed by hormones or drugs. Specifically, we identified cis-regulatory elements and 3D interactions underlying ligand-dependent associations between variants and gene expression. One-quarter of the glucocorticoid-modulated variants that we identified had already been associated with clinical phenotypes. However, their affected genes were ‘unmasked’ only after glucocorticoid exposure and often with function relevant to the disease phenotypes. These diseases involved glucocorticoids as risk factors or therapeutic agents and included autoimmunity, metabolic and mood disorders, osteoporosis and cancer. For example, we identified a novel breast cancer risk gene, MAST4, with expression that was repressed by glucocorticoids in cells carrying the risk genotype, repression that correlated with MAST4 expression in breast cancer and treatment outcomes. These observations provide a mechanistic framework for understanding non-coding genetic variant-chemical environment interactions and their role in disease risk and drug response.

The comprehensive microscopic, spectroscopic, and in vitro voltammetric analysis presented in this work, which builds on the well-studied properties of carbon-based materials, facilitates potential ways for improvement of carbon fiber microelectrodes (CFMs) for neuroscience applications. Investigations by both, scanning electron microscopy (SEM) and confocal Raman spectroscopy, confirm a higher degree of structural ordering for the fibers exposed to carbonization temperatures. An evident correlation is also identified between the extent of structural defects observed from SEM and Raman results with the CFM electrochemical performance for dopamine detection. To improve CFM physico-chemical surface stability and increase its mechanical resistance to the induced compressive stress during anticipated in vivo tissue penetration, successful coating of the carbon fiber with boron-doped diamond (BDD) is also performed and microspectroscopically analyzed here. The absence of spectral shifts of the diamond Raman vibrational signature verifies that the growth of an unstrained BDD thin film was achieved. Although more work needs to be done to identify optimal parameter values for improved BDD deposition, this study serves as a demonstration of foundational technology for the development of more sensitive electrochemical sensors, that may have been impractical previously for clinical applications, due to limitations in either safety or performance.