Simulating cell-free chromatin using preclinical cancer models for liquid biopsy applications

Area of Science:

• Epigenetics
• Molecular Biology
• Cancer Research

Background:

• Cell-free DNA (cfDNA) circulates in blood as cell-free chromatin (cfChromatin), retaining epigenetic information like nucleosome positioning.
• cfChromatin holds potential as a cancer biomarker source for liquid biopsies.
• Challenges in liquid biopsy research include low tumor-derived cfChromatin abundance and limited clinical samples.

Purpose of the Study:

• To develop a framework for simulating cfChromatin nucleosomal distributions.
• To validate simulated cfChromatin as a preclinical tool for liquid biopsy research.
• To improve cell-free chromatin immunoprecipitation and sequencing (cfChIP-seq) methods.

Main Methods:

• Conditioned media from nuclease-treated tissue cultures were used to simulate cfChromatin.
• Whole-genome sequencing (WGS) was employed to analyze nucleosome positioning.
• Simulated cfChromatin profiles were compared with plasma cfChromatin from mouse xenografts and human patients.

Main Results:

• Inferred nucleosome positioning in simulated cfChromatin reflected cell-type-specific gene expression and chromatin accessibility.
• Nucleosome profiles from simulated cfChromatin were concordant with plasma cfChromatin in xenografted mice.
• Simulated cfChromatin exhibited stronger tumor-specific signals compared to patient plasma, which is diluted by hematopoietic cfChromatin.
• Simulated cfChromatin facilitated the identification of repressive and bivalent chromatin domains predictive of transcriptional activity using cfChIP-seq.

Conclusions:

• Simulated cfChromatin is a valuable and scalable preclinical tool for advancing liquid biopsy research.
• The developed framework effectively models cfChromatin nucleosomal distributions and epigenetic features.
• This approach overcomes limitations associated with low tumor cfChromatin abundance and sample scarcity in clinical settings.