Fig. 2: Transcriptomic and proteomic features of SF3B1^MUT bone marrow-derived basophilic (basoE) and polychromatophilic (polyE) erythroblasts.

Erythroid precursors were expanded in culture from SF3B1^MUT, SF^WT MDS and controls samples. a Schematic representation of the protocol. b Erythroid differentiation evaluated on May-Grünwald Giemsa-stained cytospins. Histograms representing the proportion of erythroid precursors in up to 7 controls, 11 SF3B1^MUT and 7 SF^WT independent samples at days (d)7-8, 9-10, 11-13 and 14-16. Results are expressed as means ± standard error of the mean. 2-way ANOVA for multiple comparisons. Controls versus SF3B1^MUT, P = 0.017; controls versus SF^WT, P = 0.012. c Variant allele frequencies of SF3B1 mutation in erythroblasts at d7, d11-13 and d14-15 of 14 independent SF3B1^MUT samples. d Volcano plot representing up- and down-regulated transcripts in SF3B1^MUT basoE and polyE compared to SF^WT ones. Two-sided Wald-test and BH-adjusted P value < 0.05. e Venn diagram representing the numbers of differentially expressed genes between SF3B1^MUT and SF^WT samples at basoE and polyE stages. f Gene Ontology (GO) enrichment analysis of up- and down-regulated genes in SF3B1^MUT versus SF^WT erythroblasts. Fisher’s exact test corrected by false discovery rate (FDR) < 0.05. Specific terms to basoE or polyE as blue or red bars, respectively, shared terms as violet bars. g Gene set Enrichment Analysis (GSEA) showing terms deregulated in SF3B1^MUT basoE. h Barplots representing numbers and types of differential splicing events in SF3B1^MUT versus SF3B1^WT basoE and polyE with ΔPSI > | 0.10| using two-sided Wald-test and BH-adjusted P value < 0.05. Bars over 0 indicate events upregulated and bars under 0 indicate events downregulated in SF^WT erythroblasts. i Venn diagram of intron retention reductions (IRR) in SF3B1^MUT basoE and polyE. j. GO terms overrepresented among genes with IRR in SF3B1^MUT basoE and polyE. Fisher’s exact-test corrected by FDR < 0.05. k Volcano plots representing differentially expressed proteins in SF3B1^MUT versus SF^WT samples at proE/basoE and polyE stages (Wald-test, BH-adjusted P value < 0.05). l Cytoscape representation of Ingenuity Pathway Analysis showing deregulated pathways in SF3B1^MUT versus SF3B1^WT samples (P values < 0.05 by Student t-test) either basoE-specific (blue dots), polyE-specific (red dots) or shared (violet dots). Scale: dot size proportional to –log10 (adjusted-P value). Source data are provided as a Source Data file.