Fig. 2: Expression of IL-1 pathway genes are upregulated in MPN.

a Expression of IL-1R pathway gene signatures is tested for enrichment by Gene Set Enrichment Analysis (GSEA) in peripheral blood CD34⁺ HSPCs from PMF patients (n = 23) and bone marrow CD34⁺ HSPCs from normal controls (n = 15). Comparisons with p-value <0.05 and FDR q-value <0.05 were considered significant. Analysis of publicly available dataset¹⁹. Affymetrix data were dowloaded as normalized expression levels from Gene Expression Omnibus database (GSE53482)¹⁹ using the GEOquery package (R, Vienna, Austria. https://www.R-project.org/). The normalization of the expression data was checked by boxplot representation. Gene Set Enrichment Analysis (GSEA) was performed with the GSEAv4.1.0 software (Broad Institute). All gene sets were obtained from GSEA website (https://www.gsea-msigdb.org). Enrichment map was used for visualization of the GSEA results. Normalized Enrichment score (NES) and False discovery rate (FDR) p-values were applied after a 10,000 gene set permutations. b Heatmap representation of expression levels of IL-1R pathway genes in CD34⁺ HSPCs from PMF patients (n = 23) and normal controls (n = 15). Analysis of publicly available dataset¹⁹. c Heatmap representation of the differential expression of IL-1 signaling pathway genes in hematopoietic stem cells (HSC; Lin⁻Sca1⁺cKit⁺CD48⁻CD150⁺), megakaryocyte-erythroid precursors (MEP or pre-MegE; Lin⁻Sca1⁻cKit⁺CD41⁻CD16⁻105⁻CD150⁺) and megakaryocyte progenitors (MkP; Lin⁻Sca1⁻cKit⁺CD41⁺CD150⁺) between VF (n = 3) and WT (n = 3) mice is shown (left). Barcode plots showing custom Gene Set Enrichment Analysis (GSEA) of the Biocarta IL-1R pathway in HSC, pre-MegE (or MEP) and MkP from VF vs WT (right). Source data are provided as a Source Data file.