A research team from Van Andel Institute has published an innovative breakthrough in Nature Communications, developing a high-resolution single-cell DNA methylation analysis technology called scDEEP-mC. This groundbreaking method provides a powerful new tool for studying the epigenetic mechanisms of diseases such as cancer.

DNA methylation, a key epigenetic modification, regulates gene expression without altering the DNA sequence and is closely linked to cell differentiation, development, and disease onset. Traditional methylation detection methods are limited by technical resolution and can only provide average data from cell populations. In contrast, scDEEP-mC is the first to achieve high-precision methylation profiling at the single-cell level.

"This technology allows us to observe dynamic methylation changes in individual cells across different stages of DNA replication—something that was previously impossible," said co-first author Dr. Nathan Spix. scDEEP-mC can not only identify rare cell subpopulations but also be applied to epigenetic clock analysis, hemi-methylation studies, and whole-chromosome X-inactivation mapping.

The technology holds significant promise for early cancer diagnosis. By detecting abnormal methylation in pre-cancerous cells, it may enable the development of more accurate early screening methods. Furthermore, the cell-to-cell epigenetic heterogeneity revealed by scDEEP-mC offers new insights into the evolution of the tumor microenvironment.

The research team plans to apply this technology to additional disease models to explore the precise roles of methylation modifications in disease initiation and progression. This innovation will also advance personalized medicine, providing support for precision therapies based on epigenetic signatures.