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<p>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.</p>

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年2月17日

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

摘要

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.