# Non-disruptive in vitro monitoring of cellular states with cell-free DNA methylation

## TL;DR

Researchers use cell-free DNA methylation to non-invasively monitor cell states and responses in lab settings.

## Contribution

A novel non-disruptive method for tracking cellular changes using cell-free DNA methylation and sequencing.

## Key findings

- Cell-free DNA methylation signatures reflect cell type and treatment responses in vitro.
- Oxford Nanopore sequencing enables rapid assessment of CpG methylation dynamics.
- The method supports non-disruptive monitoring of bioreactor-based differentiation processes.

## Abstract

Individual CpG methylation signatures characterize each mammalian cell type, thereby offering a powerful readout for clinical and diagnostic applications. Here, we apply this principle to in vitro cellular systems, using cell-free DNA released into the culture medium to track epigenomic responses to small-molecule treatments and bioreactor-based directed differentiation. Coupled with Oxford Nanopore sequencing, our approach enables rapid assessment of global CpG methylation dynamics and enhancer states. This strategy provides a streamlined method that can be readily applied and customized for non-disruptive monitoring of various in vitro screening modalities.

The online version contains supplementary material available at 10.1186/s13059-026-03996-1.