Retrospective cell lineage reconstruction in humans by using short tandem repeats

Summary Cell lineage analysis aims to uncover the developmental history of an organism back to its cell of origin. Recently, novel in vivo methods utilizing genome editing enabled important insights into the cell lineages of animals. In contrast, human cell lineage remains restricted to retrospective approaches, which still lack resolution and cost-efficient solutions. Here, we demonstrate a scalable platform based on short tandem repeats targeted by duplex molecular inversion probes. With this human cell lineage tracing method, we accurately reproduced a known lineage of DU145 cells and reconstructed lineages of healthy and metastatic single cells from a melanoma patient who matched the anatomical reference while adding further refinements. This platform allowed us to faithfully recapitulate lineages of developmental tissue formation in healthy cells. In summary, our lineage discovery platform can profile informative somatic mutations efficiently and provides solid lineage reconstructions even in challenging low-mutation-rate healthy single cells.
Graphical abstract
Highlights • A human cell lineage discovery platform based on somatic STR mutations • The platform has been validated with a high resolution of ex vivo cell lineage tree • A melanoma lineage tree inferred from STR agrees with sampling location • Lineage trees of healthy cells support separation of embryonic germ layers
Motivation Human cell lineage trees can provide answers to the most profound open questions in human biology and medicine. Obtaining this knowledge is a long journey worth taking. We pioneered the concept, the mathematical foundations, and the implementation of the human cell lineage discovery method utilizing naturally acquired microsatellite mutations by individual cells, to reconstruct trees among human cells. We kept improving its power. From 128 microsatellites per cell to 2,000, we have now reached a panel of over 50,000 loci, barcoded and sequenced cost effectively. Retrieving this unprecedented amount of microsatellite data would enable precise cell lineage tree reconstruction.
Tao et al. present a biological-computational cell lineage discovery platform that enables efficient acquisition of tens of thousands of short tandem repeat targets in human single cells and tailored cell lineage reconstruction with its integrated bioinformatic pipeline and database management system.