An in vitro CRISPR screen of cell-free DNA identifies apoptosis as the primary mediator of cell-free DNA release

ABTRACT

Clinical circulating cell-free DNA (cfDNA) testing is now routine, however test accuracy remains limited. By understanding the life-cycle of cfDNA, we might identify opportunities to increase test performance. Here, we profile cfDNA release across a 24-cell line panel and utilize a cell-free CRISPR screen (cfCRISPR) to identify mediators of cfDNA release. Our panel outlines two distinct groups of cell lines: one which releases cfDNA fragmented similarly to clinical samples and purported as characteristic of apoptosis, and another which releases larger fragments associated with vesicular or necrotic DNA. Our cfCRISPR screens reveal that genes mediating cfDNA release are primarily involved with apoptosis, but also identify other subsets of genes such as RNA binding proteins as potential regulators of cfDNA release. We observe that both groups of cells lines identified primarily produce cfDNA through apoptosis. These results establish the utility of cfCRISPR, genetically validate apoptosis as a major mediator of DNA release in vitro, and implicate ways to improve cfDNA assays.

Optimisation of a novel glass-alginate hydrogel for the treatment of intracranial aneurysms

The current gold standard for aneurysm treatment is endovascular coiling. However, recurrence is observed in over 20% of cases. A novel hydrogel has been developed to treat aneurysms. This hydrogel is composed of a polymeric alginate, a novel ion releasing glass and glucono-delta-lactone. This is an internally setting alginate hydrogel, wherein the setting rate can be controlled by both the glass and the alginate chemistry. The aim of this work is to examine the effect of each component of the hydrogel and optimise the composition of the hydrogel, specifically the alginate molecular weight, M/G ratio and concentration. The effects of gamma sterilisation will also be examined. The results show that alginate concentration, chemical composition and molecular weight affect the compressive strength, working time, hardening time and deliverability of the hydrogel. Gamma irradiation of the alginate reduces the molecular weight, which has a negative effect on the usability of this hydrogel.