Fig. 1: Global proteomics analysis highlights key changes of proteins steering MK maturation.
From: Critical shifts in lipid metabolism promote megakaryocyte differentiation and proplatelet formation
a, Multiomics workflow for the quantitative assessment of the lipidome and proteome of maturating MKs. b, Representative immunofluorescence staining of GPIb (platelet glycoprotein Ib β-chain, green) expressed in the late stage of MK maturation and platelets (n = 6). Nuclei were stained with DRAQ5 dye (blue). Scale bar, 10 µm (upper panel) or 100 µm (lower panels). c, Fuzzy c-means clustering of regulated proteins from day 0 to day 7. Number of proteins and their median are denoted in individual plots, and only a selection of clusters is shown. Note that over 2,229 proteins are not regulated and therefore not considered. The assignment of proteins to clusters can be found in the Source data. Threshold, 85. d, Diagram showing nonregulated (light gray) and significantly regulated proteins comparing day 7 versus day 0, with the latter being divided into three sections: upregulated (red) or downregulated (blue) proteins with a log2(fold change) of ≥2 or ≤−2, respectively, and other regulated proteins (dark gray) with log2(fold change) between −2 and +2. e, Pathway enrichment analysis of significantly regulated proteins with log2(fold change) of ≥2 or ≤−2 showing the top 15 enriched pathways of only upregulated (red) or downregulated (blue) proteins. Pathways were sorted by their fold enrichment independent of the number of proteins involved. Pathway enrichment analysis was performed using the open-source DAVID bioinformatics tool. f,g, Bar graphs of various MK differentiation markers (f) and lipid-related enzymes (g) displayed with their associated lipid category. Proteomics data were combined from three independent experiments with four pooled mice per biological replicate. Means are displayed with the standard deviations represented as error bars. A two-sided t-test was used for statistical analysis. Benjamini–Hochberg correction was applied to P values using an FDR cutoff of <0.05 (*P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001). Oxi, oxylipin.
