Dissecting cell-free DNA fragmentation variation in tumors using cell line-derived xenograft mouse

TL;DR

This study explores how cell-free DNA fragmentation patterns differ in tumors using a mouse model to separate tumor DNA from non-tumor DNA.

Contribution

The study introduces a novel approach using CDX mouse models to isolate and analyze pure ctDNA fragmentation patterns.

Findings

Short cfDNA fragments are enriched in both CDX-cfDNA and ctDNA compared to normal plasma cfDNA.

CDX-cfDNA fragmentation features distinguish different tumor cell lines, while ctDNA features distinguish anatomical sites.

Both non-tumor cfDNA and ctDNA contribute to increased fragmentation variation in tumors.

Abstract

Cell-free DNA (cfDNA) is increasingly studied for its diverse applications in non-invasive detection. Non-randomly cleaved by nucleases and released into the bloodstream, cfDNA exhibits a variety of intrinsic fragmentation patterns indicative of cell status. Particularly, these fragmentation patterns have recently been demonstrated to be effective in predicting cancer and its tissue-of-origin, owing to increased variation of fragmentation features observed in tumor patients. However, there remains a lack of detailed exploration of altered cfDNA fragmentation profiles in tumors, which consist of a mixture of both non-tumor cfDNA and circulating tumor DNA (ctDNA). Hence, we leveraged the human tumor cell line-derived xenograft (CDX) mouse model, where different tumor cell lines were implanted into different anatomical sites, to isolate pure ctDNA and separately investigate the fragment properties of CDX-cfDNA and ctDNA. We found an enrichment of short cfDNA fragments in both CDX-cfDNA and ctDNA compared to normal plasma cfDNA, with more elevated short fragments in ctDNA. Moreover, the CDX-cfDNA fragmentation features distinguished between CDX models of different tumor cell lines, while the ctDNA fragmentation features conversely discriminate between CDX models of different anatomical sites. The results suggested that both non-tumor cfDNA and ctDNA contribute to the increased variation observed in tumors, and that cfDNA fragmentation may be highly variable and susceptible to regulations by both original cells and cells within the local niche.

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