Improving Circulating Tumor DNA-based Liquid Biopsy Through Understanding Molecular Regulators of Cell Free DNA Release

Abstract

Liquid biopsy is a promising technique that is already impacting clinical decision making by supplementing traditional tumor biopsy as a way to derive molecular information about various cancers. However, it has potential to provide much greater impact through avenues such as early detection and minimal disease detection. Most studies attempt to elevate liquid biopsy to the levels of sensitivity and specificity required to be used for these approaches by adding additional analytes or increasing the quality of sequencing performed as part of the assay. However, few have attempted to identify and modify regulators of the cfDNA life cycle to increase the presence of ctDNA and therefore improve liquid biopsy accuracy. We sought to address this gap in knowledge by determining the most relevant mechanisms of cell-free DNA release, of which many have been proposed, including apoptosis, necrosis, and active release. In chapter II of this dissertation, I include the materials and methods used in this work. Chapters III and IV are data chapters primarily derived from work about to be published in Communications Biology. In Chapter III of this dissertation, we define a model system for the release of cell-free DNA and create and perform a novel screen for mediators of cell-free DNA release in two cell lines. In Chapter IV, we validate the hits identified in our screen using genetic and drug studies and determine that apoptotic processes are the major regulator of cell-free DNA release. Finally, in Chapter V, I discuss limitations, implications, and future directions that could be taken based on this work.