Fig. 2: Identifying CAR T cell targets on JMML LSCs by scRNAseq and mass spectrometry.

A Top: UMAP depicting assigned clusters. Bottom: the average expression of HSC markers in different assigned clusters. Y-axis shows genes while circle size and colors represent percent of cells expressing the gene or expression level, respectively. B UMAP with cell type identification overlay. C Volcano plot intersecting mass spectrometry of JMML (n = 9) vs. healthy control (n = 3) CD34+ cells with upregulated surface proteins highlighted (positive log2FC, FDR < 0.05; Wilcoxon signed-rank test with Benjamini–Hochberg correction). “MS + RNA” denotes significant proteins and genes upregulated by both mass spectrometry and scRNAseq, respectively. “+GTEx” denotes genes/proteins with median TPM < 20 in the GTEx database (except hematopoietic tissues). D Heatmap of differentially upregulated genes in JMML vs. normal control of the HSC cells using the FindMarkers function with the Wilcoxon rank sum test. Only cell surface and upregulated genes (FDR < 0.05) are shown. Genes associated with cell surface markers are labeled to the right. Hierarchical clustering of all HSC cells and their respective group assignment are labeled on top. Genes with TPM < 5 on at least 75% of all normal GTEx samples are further annotated to the right. Average Exp average expression, C_Monocytes classical monocytes, mDCs myeloid dendritic cells, N_Monocytes non-classical monocytes, ISG+ ISG expressing immune cells, MS/Mass Spec mass spectrometry, RNA scRNAseq.