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. 2024 Jan 2;15:32. doi: 10.1038/s41467-023-44137-7

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 7 — a Percentage of cells with detected somatic nuclear mutations across 22 hematopoietic cell types in 9 AML cases for a total of 17,911 cells. Arrow indicates NK cells. MK - megakaryopoiesis, Ery erythropoiesis, T/NK T and NK cells. b Percentage of cells with detected somatic nuclear mutations across hematopoietic cell compartments in AML1002. TP53^R179H and TP53^P278S are enriched in NK cells (purple). c Longitudinal clinical amplicon sequencing of bulk bone marrow-derived DNA demonstrates separation of NK-associated mutations (TP53^R179H and TP53^P278S) from AML-associated mutations in AML1002 (IDH2^R140Q, TET2^I1873T, U2AF1^S34Y, and JAK2^V617F). d PCR scheme demonstrating the amplification strategy of CAR transcripts with a CD28-specific primer. The coverage plot demonstrates the amplification of wildtype CD28 (blue) and fusion transcripts spanning into the CAR domain (red). e Read distribution with nanoranger on the Oxford Nanopore platform (ONT) compared to short-read sequencing (Illumina) as number of reads per cell barcode (left). The bar plot (right) shows the number of cells in which a CAR transcript was detected with both technologies (+/+), only with Illumina (-/+) or only with ONT (+/-). ND not detected. f Quantification of cells that only have wildtype CD28 transcripts (blue, CD28 only) versus cells with at least one CAR transcript (red, CAR, and CD28) in one CAR T cell infusion product. g, h Identification of CAR T cells with high expression of CAR transcripts by comparison with wildtype CD28 expression levels (g). Projection of CAR T cell detection on UMAP annotated by predicted cell types based on the PBMC reference dataset provided by Seurat (h). Data shown for four infusion products and four PBMC samples at day 7 after CAR T cell infusion. Red arrows indicate cells with high CAR expression. i Expression levels of CAR transcripts across ten predicted cell types in a total of 6504 cells. Expression levels of CAR transcripts compared to exhaustion score (calculated from expression of PDCD1, CTLA4, TIGIT, HAVCR2, TOX, LAG3, and ENTPD1) (j) and percentage clonal expansion of the native T cell receptor (TCR) relative to all detected TCRs within the library (k).