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. 2023 Feb;33(2):218–231. doi: 10.1101/gr.277015.122

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© 2023 Mishra et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 5. — Using scEpiSearch for 2D embedding to track the dedifferentiated state of leukemia cells from blood-cancer patients. (A) scEpiSearch-based 2D embedding of single-cell open chromatin profiles of three types of cells: blood cells collected from patients with mixed MPAL, PBMC, from healthy (normal) individuals, and progenitors of blood cells (derived from bone marrow). The scATAC-seq profiles of MPAL and PBMCs were published by Granja et al. (2019), and progenitor cell epigenome profiles are from a different study. In the embedding plot by scEpiSearch, most of the PBMCs are far from progenitor cells and closer to B cells. MPAL cells are closer to progenitor cells. Some MPAL cells overlap with blood cell progenitors, highlighting their highly undifferentiated state. The same 2D embedding plot from scEpiSearch is shown with a different color for cells according to the source of data and patient. (B) scEpiSearch based 2D embedding of single-cell open chromatin profile of MPAL cells with HSC from fetal and young mice. (C) Results from other tools for the 2D embedding of the single-cell open-chromatin profile of three types of cells: blood cells collected from patients with MPAL, PBMCs from healthy individuals, and progenitors of blood cells. Other methods either mixed up the locations of different types of hematopoietic progenitor cells or could not colocalize B and T cells with PBMCs.