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bioRxiv · 10.1101/2024.04.01.587514

Somatic epimutations enable single-cell lineage tracing in native hematopoiesis across the murine and human lifespan

Scherer, M.·Singh, I.·Braun, M.·Szu-Tu, C.·Kardorff, M.·Ruehle, J.·Froemel, R.·Beneyto-Calabuig, S.·Raffel, S.·Rodriguez-Fraticelli, A.·Velten, L.
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Abstract

Current approaches to lineage tracing of stem cell clones require genetic engineering or rely on sparse somatic DNA variants, which are difficult to capture at single-cell resolution. 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 droplet-based method for transgene-free lineage tracing, and apply it to study hematopoiesis, capturing hundreds of clonal trajectories across almost 100,000 single-cells. Using ground-truth genetic barcodes, we demonstrate that EPI-clone accurately identifies clonal lineages throughout hematopoietic differentiation. Applied to unperturbed hematopoiesis, we describe an overall decline of clonal complexity during murine ageing and the expansion of rare low-output stem cell clones. In aged human donors, we identified expanded hematopoietic clones with and without genetic lesions, and various degrees of clonal complexity. Taken together, EPI-clone enables accurate and transgene-free single-cell lineage tracing at scale.

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Scherer, M., Singh, I., Braun, M., Szu-Tu, C., Kardorff, M., Ruehle, J., Froemel, R., Beneyto-Calabuig, S., Raffel, S., Rodriguez-Fraticelli, A., Velten, L.. 2024-04-01. Somatic epimutations enable single-cell lineage tracing in native hematopoiesis across the murine and human lifespan. https://doi.org/10.1101/2024.04.01.587514

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