Fig. 3: Identification of a distinct inflammatory MSC population in BM of CHIP and MDS.

A Spider plot showing stromal cell types in Control (green), CHIP (purple), and MDS (orange). Proportions are probit-transformed; black outlines indicate significant differences compared to Control. Statistical test: Fisher’s exact test. B Giemsa-stained BM sections from Control, CHIP, and MDS patients. Scale bars: 100 µm. C Scatter plot quantifying BM cellularity (cell/adipocyte ratio) across conditions (Control n = 30, CHIP n = 9, MDS n = 16 patients) (see Supplementary Fig. 5A–C). Medians with 95% confidence intervals are shown. Statistical test: one-way ANOVA, Tukey’s test. D Dot plot of extracellular matrix (ECM)-related and inflammatory gene markers (from⁷⁴) across stromal cell populations. Circle size represents percentage of cells expressing the gene, while color intensity represents scaled expression. E Violin plots of stromal genes upregulated in MDS and detected in the NanoString data. F Immunofluorescence of BM sections showing IL-1R1 (red) and CD271 (yellow) co-staining in Control, CHIP, and MDS. Insets highlight areas containing inflammatory IL-1R1⁺CD271⁺ stromal cells. DAPI (blue) stains nuclei. Scale bars: 25 µm. G Bar graph quantifying IL-1R1⁺ MSCs across Control (n = 2), CHIP (n = 3), and MDS (n = 3) samples. Medians with 95% confidence intervals are shown. Statistical test: one-way ANOVA, Tukey’s test. H, I Flow cytometry of CD44 expression on Lin^–CD271⁺CD73⁺ MSCs from Control (n = 5), CHIP (n = 5), and MDS (n = 13) samples. MDS samples are divided into splice (n = 9, SF3B1, SRSF2) and non-spliceosome (n = 4) mutated. Histogram (H) and percentage of CD44⁺ MSCs (I). Means with SD are shown. Statistical test: one-way ANOVA, Dunnett test. J, K Violin plots of inflammatory signature scores in stromal cells, stratified by condition (J) and cell subtypes (K). The signature score represents the cumulative expression of inflammation-related genes. Statistical test: two-sided Wilcoxon rank-sum test. L UMAP integration of our scRNA-seq dataset with three published human BM datasets (healthy, AML, and MM^47,74,83) using Harmony¹⁷⁷. The stromal cells are colored by inflammatory signature scores. Arrowhead marks iMSCs. M UMAP of stromal cell populations in Control, CHIP, and MDS from BM aspirates (left), healthy digested hip bones (middle)⁴⁷, and AML⁸³ and MM BM aspirates (right)⁷⁴. Cluster labels follow original published annotations, inflammation-associated clusters are labeled iMSC. A, J, K P values were adjusted using Benjamini–Hochberg procedure. Source data are provided in the Source Data file and Supplementary Data 7.