Scientists at the Van Andel Institute have created a new, transformative technique, scDEEP-mC. This new creative approach allows for high-resolution, multiplexed analysis of single cell epigenetics. An example of the detail this novel approach provides is previously unachievable in high-throughput analysis of genome-wide allele-resolved methylation. It has been invaluable for gaining insight into the ways in which epigenetics drives cancer and other diseases. Those unexpected results were recently released in the journal Nature Communications on July 15, 2025.
The scDEEP-mC technique further improves upon existing methods. It allows scientists to study hemi-methylation, producing extremely granular maps of DNA methylation in single cells. This advancement brings the most effective single-cell DNA methylation method ever created. This dramatically increases researchers’ ability to profile DNA methylation in a comprehensive manner.
Details of the Study
Nathan Spix, Ph.D., who co-authored the study that describes scDEEP-mC. He is currently a postdoctoral fellow of the Laird Lab at the Van Andel Institute. In doing so, the research team wanted to build off previous methodologies. Specifically, they aimed to increase the resolution and coverage of DNA methylation profiling at a single-cell resolution.
ScDEEP-mC leverages advanced technologies to achieve high-resolution mapping of DNA methylation, which is crucial for understanding how epigenetic modifications influence gene expression and cellular behavior. By offering a more nuanced view of methylation patterns, the technique opens new avenues for exploring how these factors contribute to various diseases, including cancer.
The study has been assigned DOI: 10.1038/s41467-025-61589-1 and can be accessed online. Researchers and practitioners who want to dig more deeply should take a look at the entire paper published in Nature Communications.
Implications for Research
The implications of scDEEP-mC are huge, especially as epigenetics research continues exploring how epigenetic patterns shape health and disease. This powerful technique enables the rigorous probing of DNA methylation with a level of precision never before attainable. Armed with these tools, scientists are finally able to discover poorly understood correlations between tissue methylation patterns and cancer progression.
In addition, the emerging ability to discern hemi-methylation further compounds this aspect of the research. Knowing if and how methylation occurs to both alleles of a gene can offer invaluable information on regulation and expression. As such, scDEEP-mC is positioned to be an important pilot for subsequent larger studies. This will assist researchers in decoding the notoriously complex mechanisms of genetic and epigenetic interactions.
Researchers at the National Cancer Institute are pioneering methods to use epigenetics in the fight against cancer and other diseases. In this pursuit, scDEEP-mC is an empowering resource that could lead to fundamental discoveries and help improve precision therapeutic strategies.
Future Directions
The Van Andel Institute’s research team is eager to turn their eyes toward the future. They aim to continue validating and refining scDEEP-mC through continued studies. They would like to expand the technique’s use to other biological systems, such as developmental biology and regenerative medicine.
The researchers hope to leverage scDEEP-mC to advance our understanding of fundamental biological processes. They intend for it to fuel the creation of epigenetics-based targeted therapies for diseases driven by epigenetic changes. Equal parts exciting and confusing, epigenetics is quickly making its way toward becoming an essential area of research. Methods such as scDEEP-mC will be integral in determining the future of biomedical research.