Figure 1.

Mechanistic and functional characteristics of common gene expression between VSMC and MΦ, DC in response to IFNα + LPS and IFNγ + LPS. (A) Venn diagrams based on RNA-seq results showing intersection between lists of up-regulated (FC > 2) genes in VSMC, MΦ, and DC after combined stimulation with IFNα (8 h) + LPS (4 h) and IFNγ (8 h) + LPS (4 h). The gene lists for these Venn diagrams are shown in Table S1. Common 579 IFNα + LPS and 536 IFNγ + LPS-induced genes between three cell types were highlighted by violet frames. (B) Heatmap plots depicting expression pattern of commonly up-regulated, 579 IFNα (8 h) +LPS (4 h)- and 536 IFNγ (8 h) + LPS (4 h)-induced genes in VSMC, resulting from RNA-seq. Three main columns on each heatmap represent one particular treatment condition [IFNα (8 h), IFNγ (8h), LPS (4 h), IFNα (8 h) + LPS (4 h), or IFNγ (8 h) + LPS (4 h)]. Increasing brightness of red color indicates a higher gene expression level (gene expression is presented as log2 FC in comparison to control). (C) Box-plot representation of gene expression distribution for commonly up-regulated genes by IFNα (8 h) + LPS (4 h) and IFNγ (8 h) + LPS (4 h) resulting from RNA-seq (gene expression is presented as log2 FC in comparison to control) in VSMC. The line within each box represents the median and the lower and upper boundaries of each box indicate first and third quartiles, respectively. (D) Comparison of commonly up-regulated genes by IFNα (8h) + LPS (4 h) and IFNγ (8 h) + LPS (4 h) from RNA-seq, showing 64.21% overlap between the gene lists. (E) GO analysis of commonly up-regulated genes by IFNα (8 h) + LPS (4 h) and IFNγ (8 h) + LPS (4 h) (RNA-seq) revealed a strong enrichment for terms reflecting pro-inflammatory and pro-atherogenic biological functions. P-value < 0.05. (F) Venn diagram distribution of promoter located (−950/+50 bp) GAS, ISRE, and NFκB binding sites among commonly up-regulated genes by IFNα (8 h) + LPS (4 h) and IFNγ (8 h) + LPS(4 h) from RNA-seq experiment.