Retrospective cell lineage reconstruction in humans by using short tandem repeats

Cell Reports: Methods

Ehud Shapiro¹  Guy Rom²  Liming Tao²  Shiran Amir²  Asaf Ben Arie²  Ofir Raz²  Zipora Marx²  Noa Chapal-Ilani²  Tamir Biezuner²  Lilach Milo²  Ron Levy²  Barak Oron²  Rivka Adar²  Amos Onn²  Veronika Berman²  Ruth Halaban³  Sandra Huber⁴  Zbigniew T. Czyz⁴  Melanie Werner-Klein⁴  Julia Greindl-Junghans⁴  Christoph A. Klein⁴  Manjusha S. Ghosh⁴ 

[1] Division of Personalized Tumor Therapy, Fraunhofer Institute for Experimental Medicine and Toxicology Regensburg, Am Biopark 9, 93053 Regensburg, Germany;Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel;Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520-8059, USA;Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany;

关键词: single-cell genomics;    cell lineage reconstruction;    molecular inversion probes;    short tandem repeats;   

DOI  :  

来源: DOAJ

【 摘 要 】

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. 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.

【 授权许可】

Unknown