Molecular Mediators of Cell-free DNA biogenesis - PROJECT SUMMARY/ABSTRACT Liquid biopsies are currently in clinical use for many cancers. The majority of liquid biopsies are measuring and identifying naked, cell-free DNA (cfDNA) molecules in the blood that are shed from all cells into the circulation. When cancer cells shed their DNA into the bloodstream, this is known as circulating tumor DNA (ctDNA), but a major impediment to maximizing the utility of liquid biopsies is the fact that the percentage of ctDNA is relatively small in a patient’s blood, even those with metastatic disease and/or a heavy tumor burden. Improvements in technology have pushed the limits of detection such that even one ctDNA molecule in a million normal cfDNA molecules can be identified from blood. However, it is often not feasible to obtain even thousands of cfDNA molecules from a single blood draw, thus limiting the clinical sensitivity of liquid biopsies. Therefore, even though there are currently commercial tests available for testing minimal residual disease after curative intent therapies for early stage cancers, as well as tests for detecting cancer in asymptomatic persons as a primary cancer screening tool, none of these tests have a high enough negative predictive value (NPV) to safely say that a negative test truly means the individual is without cancer. The overarching goal of this research program is to increase the clinical sensitivity of ctDNA liquid biopsies, such that they could truly distinguish between patients with and without cancer. To do so, will require a better understanding of the mediators of cfDNA biogenesis. Despite years of research on cfDNA and ctDNA, there is still a paucity of knowledge regarding how cfDNA is released from cells, and factors that influence its degradation. If such knowledge were discovered, then new drugs could be developed to increase the amount of ctDNA from cancer cells thus vastly improving the sensitivity and NPV of liquid biopsies. In this proposal, these unmet needs will be addressed based upon new preliminary data via the following specific aims: Aim 1): Elucidating the role of the RNA binding protein Sam68 in mediating cfDNA release, Aim 2): Pharmacologic optimization of cfDNA release and stability for increasing ctDNA detection and Aim 3): Identifying genetic mediators of cfDNA release influenced by the local microenvironment. The completion of these aims will yield new insights and knowledge regarding how ctDNA is regulated at the cellular level, as well as how extrinsic factors including local tumor microenvironments affect ctDNA’s half-life. Moreover, these studies will leverage existing and new knowledge that will ultimately enable us to increase ctDNA levels for diagnostic purposes. By improving the sensitivity of current ctDNA tests, liquid biopsies might one day be able to determine if patients are cured of their disease. Additionally, a negative liquid biopsy screening test would also be able to determine with high confidence that an individual truly is without cancer. This would a represent major step forward in our ability to utilize ctDNA for the management of patients with cancer.
