Fig. 2: Heterogeneous cellular states in AML and LAM.

a UMAP plot of AML cells only showing two distinct clusters (cluster 1 and cluster 2) and two transitional clusters (0 and 3). b Violin plots of highly expressed genes of each cluster. The y axis represents the normalized gene expression value. c Stemness score calculated using 50 tumor stem cell marker genes for each cluster (see method). d Inferred purine metabolism flux in SLS and IS populations relative to matched normal mesenchymal cells using pseudo-bulk RNA-seq generated from single-cell transcriptomes. Relative levels of hypoxanthine (HX) and inosine/deoxyinosine (Ino/dlno) are upregulated in SLS. e Feature plots of expression of dormancy marker genes in the tumor cell population. f Analysis of NR2F1 expression and regulon activity in AML cells. Left panel: expression of NR2F1 in cluster 1 and 2; right panel: NR2F1 regulon activity based on 41 downstream target genes. Note: only cluster 1 and cluster 2 were compared for regulon activity. Other clusters are colored in gray. g NR2F1 expression and regulon activity in LAM patient-derived TSC2-deficient cells 621-101 cells with and without estrogen treatment. Left panel: t-SNE plot of cells from estradiol treated group (red) and cells from control group (blue); middle panel: expression of NR2F1; right panel: NR2F1 regulon activity. h Expression of MDK and TAGLN in AML cell clusters. i Triple staining for MDK, TAGLN, and CTSK. Representative images of 5 samples. j Quantification of co-staining of MDK, TAGLN, and CTSK shows little co-localization of MDK and TAGLN (first bar), while both TAGLN and MDK co-localize with the tumor marker gene CTSK (second and third bars). The y axis represents area of overlap (arbitrary unit). k Re-clustering of the LAM cells from 5 LAM lungs, revealing four clusters. l Average expression of SLS (left) and IS (right) marker genes in the LAM clusters. An SLS population (cluster 2 in K), IS population (cluster 1 in K), and an intermediate state (Cluster 0 and 3 in K) were identified. m SLS population (Cluster 2) and intermediate state LAM cells (Cluster 0 and 3) show high stemness scores. n Expression and regulon analysis of NR2F1 in LAM cells. Left panel: NR2F1 expression; right panel: NR2F1 regulon activity corresponding to the degree of regulation of 23 downstream target genes. o Feature plot showing expression of MDK and VEGFD in LAM cells.