Somatic epimutations enable native single-cell clonal tracking on hematopoietic cell state landscapes across the murine and human lifespan
Current approaches to track stem cell clones through differentiation require genetic engineering or rely on sparse somatic DNA variants. Here, we show that targeted single-cell measurements of DNA methylation at single-CpG resolution deliver joint information about cellular differentiation state and clonal identities. We develop EPI-clone, a method for transgene-free lineage tracing based on microfluidic, targeted single-cell DNA methylation analysis. Applied to mouse and human hematopoiesis, we captured hundreds of clonal differentiation trajectories across tens of individuals and almost 400,000 single-cells. Using ground-truth genetic barcodes, we demonstrate that EPI-clone accurately identifies clonal lineages throughout hematopoietic differentiation while at the same time providing cell state resolution similar to transcriptomic data. Applied to unperturbed hematopoiesis in murine ageing, we demonstrate that myeloid bias and low output of old HSCs are restricted to a small number of expanded developmental clones, while many functionally young-like clones persist in old age. In human ageing, we demonstrate that clones carrying CHIP mutations are part of a spectrum of age-related expansions of low-output clones. EPI-clone is compatible with the multiplexed readout of surface protein, somatic variants and RNA from the same single cell. Taken together, EPI-clone enables accurate and transgene-free single-cell lineage tracing on hematopoietic cell state landscapes at scale. Overall design: Single-cell DNA methylation data was generated using scTAM-seq providing single-CpG, single-cell resolution. Data is provided as a count matrix showing the number of sequencing read per amplicon (CpG) in each of the single cells.