Fig. 3: Single cell landscape of CD34+ differentiation in Bthal.

Analysis of 10x Genomics scRNA-seq from CD34⁺ HSPCs and phenotypic HSC/MPP isolated from BM of Bthal patients or HD. A UMAP for 36,878 single cells from 6 Bthal patients and 6 HDs. Indicated lineage groups were derived from the conflation of clusters with similar cell identities annotated based on label transfer from Zeng et al. ⁴³ (HSC, MPP, MEP, Meg precursors, MEP, Erythroid, EoBasoMast precursor, Cycling prog, GMP, Mono, MDP, MLP, CLP, B cell precursor). Original cluster annotation is shown in Fig. S7A. B Bar graph of the relative composition of HSPC groups shown in A in Bthal and HD. P values by two-tailed unpaired t-test; mean ± SEM is shown. C Top panels: UMAPs colored by the expression of a dormant HSC signature (left) and CDK6 gene expression (right). Bottom panels: Gaussian kernel density estimates plotted in the UMAP for HD (left) and Bthal (right) CD34+ cells on UMAP. D Ridge plot of pseudotime values assigned to phenotypic HSC/MPPs of Bthal and HD. P-value by two-side Welsh t-test. Selected pathways E MSigDB hallmark, F published genesets related to stemness and lineage commitment) significantly enriched (padj<0.05) by GSEA in the populations indicated on the y axis. Red: enriched in Bthal; Blue: enriched. A list of all enriched pathways is provided in Supplementary Data 6, 7. Terms with adjusted p.value (Benjamini-Hochber correction) less than 0.05 were considered significantly enriched. Representative examples of genes differentially expressed along the Ery (G) or monocytic (H) differentiation trajectory as identified by tradeSeq. Purple lines: Bthal; yellow lines: HD. Source data are provided as Source Data file.