Fig. 7: Distinct MDS transcriptome signature and changes in cellular composition during disease progression measured by single-cell transcriptome analysis.

A Analysis of scRNA-Seq data. Uniform Manifold Approximation and Projection for Dimensional Reduction (UMAP) map for individual samples. Each dot in the map represents a cell and is coloured according to cluster assignment. B Histogram showing the proportion of cells in each cell cycle phase within each cluster as identified by the expression of cell cycle-regulated genes. C 13 clusters based on the expression of specific genes. Cluster annotation was based on manual curation of marker genes. Each dot in the map represents a cell and is coloured according to cluster assignment. L = Low risk, H = high risk. D Table representing the number of cells in each cluster. Blue squares, clusters reduced during disease progression; red squares, clusters increased during disease progression; green squares, no change during disease progression. E Normalized enrichment scores (NES) calculated using gene set enrichment analysis (GSEA) with gene sets related to HSC and LSC signatures in single-cell RNA-Seq clusters 6 and 7, showing significant association with HSC and LSC signatures in these clusters (as indicated by a positive NES and Adjusted p-value < 0.1). NES and p-values were calculated using a permutation-based test (one-sided) using the GSEA software¹⁰⁹. F Expression of indicated genes projected on the UMAP map. Colour intensity represents expression data log2 normalized unique molecular identifier (UMI) counts. G Dot plots showing the scaled expression level of the indicted transcription factors in low-risk and high-risk MDS samples. Colours represent the scaled expression and size encodes the proportion of gene-expressing cells. H Dot plots showing the scaled expression level of the indicted myeloid genes in control and low-risk samples. Colours represent the scaled expression and size encodes the proportion of gene-expressing cells. I Monocle pseudo-time trajectory for MDS specific, myeloid, and erythroid cells projected on the UMAP map of scRNA clusters. Cells are coloured according to their pseudo-time value.