Work

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

Year: 2026

Type: article

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.

Source: Genome biology

DOI: 10.1186/s13059-026-03996-1

Authors: Anja Hess, Alexander Kovacsovics, Fabian Bachinger, Ludovic Vallier, Helene Kretzmer, Alexander Meissner