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. 2021 Mar 30;35(5):1365–1379. doi: 10.1038/s41375-021-01231-3

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 7 — A Two-dimensional UMAP projection of the transcriptomes of CD45+ lymphocyte cells pooled from three time points from bone marrow. A total of 22,407 cells are annotated in 21 distinct clusters, 7 of which that can be annotated as CD8+ T cells but only 2 as CD4+ T cells. B Dot plot showing the canonical markers used to annotate the clusters. C Focused two-dimensional UMAP projection of re-embedded CD8+ lymphocyte cells. The encircled dots are the TCRBV04-03 clone colored by different time points, where turquoise is the diagnostic (sample 1), yellow is follow-up (sample 2), and red is from relapse (sample 3). Most of the TCRBV04-03 clonotype cells can be classified as 1 CD8+ T_EMRA. D The proportion of TCRBV04-03 clonotype cells from the total CD8+ repertoire from the single-cell TCRab data. E The relative abundances of TCRBV04-03 clone’s phenotype during treatment. F Volcano plot showing differentially expressed genes between clonotype of interest (to the right, significant shown in red) and cells from other clonotypes from the 1 CD8+ T_EMRA cluster (to the left, significant shown in blue). G Gene set enrichment analysis (GSEA) results from the differential expression analysis. Shown here are GO categories enriched (FDR qval < 0.05) to the TCRBV04-03 clone.