A 30-gene classifier distinguishes low-risk MDS HSPCs from healthy HSPCs

Abstract

Myelodysplastic syndromes (MDS) are a group of malignant clonal disorders that are characterized by functional impairment of hematopoiesis, morphologic dysplasia, and genetic heterogeneity. While less likely to transform to acute leukemia, lower-risk MDS (LR-MDS) include patients with IPSS-M moderate low risk, low risk, and very low risk patients and have a limited median survival of 3 to 10 years. Further, there is growing interest in discovering translational targets of LR-MDS pathophysiology. Clonal populations within the hematopoietic stem and progenitor (HSPC) to myeloid differentiation spectrum are widely considered to be a major contributor to MDS pathophysiology. A granular assessment of cell-type and lineage-specific states that contribute to LR-MDS pathophysiology remains to be elucidated. Here, we leverage single-cell transcriptomics to characterize cell states across the HSPC-myeloid differentiation landscape in LR-MDS. We develop a 30-gene score to classify LR-MDS HSPCs and identify novel molecular features of LR-MDS. The genes in our score suggest dysfunction in vesicular trafficking, which we further resolve across the myeloid differentiation axis. The gene products of vesicular trafficking-related pathways may be suitable translational targets for LR-MDS.

Figure 1.. Feature selection for the classification of LR-MDS HSPCs.

(A) Integrated UMAP of LR-MDS (n = 16) and HD (n = 8) transcriptomes. (B) GSEA results with selected pathways (FDR-adjusted p-value < 0.05). (C) Schematic of score development. (D) Network plot of hub genes and co-expressed genes (edge correlation > 0.4). (E) VPS13B and ERC1 expression in single cells, comparing MDS and HD. (F) Validation of MDSPrimID classifier on bulk RNA-seq data from an independent cohort. The validation cohort included LR-MDS samples, classified as IPSS-R Low or Int-1 (n = 26), and normal samples (n = 23). (G) Differential gene expression of CD34+ cells comparing LR-MDS and HD samples from the validation cohort. Genes from MDSPrimID that were significantly upregulated or downregulated are labeled (Log 2-Fold Change > 0.5 or < −0.5, FDR-adjusted p-value < 0.05).

Figure 2.. Resolving MDSPrimID by myeloid differentiation states.

(A) Integrated UMAP colored by HSPC and myeloid metaclusters (top) and pseudotime ordering (bottom). Gray dots represent cells not assigned to HSPC or myeloid metaclusters. (B) Gene expression resolved by pseudotime of differentially expressed MDSPrim genes between MDS and HD (Log 2-Fold Change > 1 or < −1, FDR-adjusted p-value < 0.05). Hierarchical clustering reveals two MDS clusters (MDS1 and MDS2) and one HD cluster. (C,D) Gene-wise expression plots of single cells ordered by pseudotime, organized by transcriptional regulation or vesicular trafficking.