Methylation-based lineage tracing in cancer Open Access

The evolutionary history of cancers is encoded in molecular patterns that provide critical insights into the mechanisms of tumor progression. However, reconstructing cancer lineages in patient tumors remains challenging, as conventional sequencing captures only static snapshots of an ongoing evolutionary process. DNA methylation at CpG sites is a heritable epigenetic mark that accumulates stochastic errors - termed epimutations - at rates far exceeding those of somatic DNA mutations. These epimutations serve as a 'molecular clock' and can be harnessed for retrospective lineage tracing. When applied at single-cell resolution, methylation-based lineage tracing enables the reconstruction of cancer phylogenies and provides a powerful framework for studying the dynamics of treatment resistance, cell-state heritability, and metastasis directly in human tumors. In this review, we outline the strengths and challenges of single-cell DNA methylation-based lineage tracing, highlight key insights gained from its application with an emphasis on hematological cancers where relevant, and discuss its future potential in advancing our understanding of cancer evolution.