Fig. 6: MSC treatment causes major transcriptional changes in AMs to dampen lung inflammation and asthma.
From: Mesenchymal stromal cell apoptosis is required for their therapeutic function
a Unsensitised or OVA-sensitised mice received MSCs on day (D) 5, 6 and 7. AMs from BALF were FACS purified for RNA-sequencing either prior to (D8) or following (D12) OVA challenge. PCA analysis of genes from D8 and D12 treatment groups. Plots were generated using the top 100 variable genes within samples. Each dot represents data from 5 pooled samples. b Venn diagram showing number of overlapping DEGs among different treatment groups in D12, obtained by setting a filter of 1 CPM (counts per millions) and FDR of 0.05. c Classification of DEGs (obtained from b) by KEGG pathway enrichment. d Heatmap showing genes with an FDR of 0.05 that are broadly associated with M1/M2 macrophage polarisation. e Volcano plot comparing DEGs from D12 SEN versus D12 SEN + MSC groups. Gene expression changes with a fold-change greater or less than 1.5 were shown as red dots. Selected genes highlighted in green represent genes that were upregulated in UNS versus SEN and downregulated in SEN + MSC, whereas those in orange represent genes that were downregulated in UNS versus SEN and upregulated in SEN + MSC. Selected genes in black indicate interferon regulated genes identified via Interferome. f GSEA plots showing enrichment of genes from the Interferon-Alpha Response (ES: 0.66824204, NES: 2.684128, FDR q value: 0.0, nominal p value: 0.0), Interferon-Gamma Response (ES: 0.59893006, NES: 2.6195564, FDR q value: 0.0, nominal p value: 0.0), Oxidative Phosphorylation (ES: −0.74083024, NES: −3.1281621, FDR q value: 0.0, nominal p value: 0.0), Fatty Acid Metabolism (ES: −0.48348597, NES: −1.9388303, FDR q value: 1.6666666E-4, nominal p value: 0.0), and Glycolysis (ES: −0.4049271, NES: −1.6384116, FDR q value: 0.013858369, nominal p value: 0.0016447369) hallmark gene sets in D12 SEN + MSC compared to D12 SEN. Unbiased GSEA was performed using software from the Broad Institute75 against hallmark gene sets (n = 50) and C2 curated gene sets (n = 4063) from the Molecular Signatures Database (MSigDB). Significant enrichment was defined as a p ≤ 0.05 and FDR < 0.25. Interferon regulated genes were identified using the Interferome v2.01 database76. Source data are provided as a Source Data file.
