Fig. 1: Biomarker and transcriptome profiling of primary AML and MDS patient samples. | Nature Communications

Fig. 1: Biomarker and transcriptome profiling of primary AML and MDS patient samples.

From: Allogeneic CD33-directed CAR-NKT cells for the treatment of bone marrow-resident myeloid malignancies

Fig. 1

a Experiment design to profile primary AML and MDS patient bone marrow (BM) samples using flow cytometry and single cell RNA sequencing (scRNA-seq). 8 AML and MDS primary samples were included for flow cytometry analyses. Data from Gene Expression Omnibus database (GSE235923)49 and NCBI Sequence Read Archive (PRJNA720840)50 were included for scRNA-seq analyses. Created in BioRender. LI, Y. (2025) https://BioRender.com/o37h997. b Diagram showing the progression from leukemia stem cells (LSCs) to myeloblast cells (MBCs) in myeloid malignancies, along with associated biomarkers. Created in BioRender. FANG, Y. (2025) https://BioRender.com/f57l159c–e Profiling AML and MDS blast cells using flow cytometry. c FACS detection of the subpopulations of AML blast cells, and their expression of CAR target (CD33), NKT TCR target (CD1d), and NKR ligands (i.e., CD112, MICA/B, and ULBP-1). Two representative data sets from AML samples #1 and #2 are presented. d Quantification of the proportions of the three subpopulations of AML and MDS blast cells. The combined percentage of these subpopulations totals 100%. e Quantification of the expression of CAR target, NKT TCR target, and NKR ligands on the three subpopulations of AML and MDS blast cells (n = 7 for LSPC, and n = 8 for CMP and MBC; n represents different patient samples). f–k Profiling AML blast cells using scRNA-seq. Data from Gene Expression Omnibus database (GSE235923) were analyzed. f Combined UMAP plot showing the formation of four major cell clusters. 19 primary AML blast samples were analyzed. g UMAP plots showing the expression distribution of the CD34, CD38, and stem genes SOX4 and CD99. h Bar graphs showing the cell cluster proportions of the 19 primary AML blast samples. Expression of cancer stem cell (CSC) gene signature (i) and NKR ligand gene signature (j) in the indicated cell clusters. UMAP plots showing the gene expression distributions and violin plots showing the gene expression levels are presented. Data from the 19 primary AML blast samples are shown. k Violin plots showing the expression distribution of NKR ligand gene signature in the 19 primary AML blast samples. Representative of 1 (d–k) and 8 (c) experiments. In the violin plots (i, j), box and whisker plots exhibit the minimum, lower quartile, median, upper quartile and maximum expression levels of each type of cell. Source data and exact p values are provided as a Source Data file.

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