Single cell RNA sequencing of aortic CX3CR1-derived monocyte/macrophage from atherosclerotic aorta during progression and regression

In atherosclerosis progression and regression, monocytes or monocyte-derived macrophages are the major immune cells in the plaque. It is important to understand the fate and characteristics of monocyte/macrophage during the plaque progression and regression. To characterize the fate of monocytes/macrophages, we performed single cell RNA sequencing of fate-mapped aortic CX3CR1-derived monocytes/macrophages from Cx3cr1CreERT2-IRES-YFP/+Rosa26floxed-tdTomato/+ mice with AAV-PCSK9 injection and fed a Western Diet. The single cell RNA-seq analyses revealed the heterogeneity of aortic macrophages and identified a stem-like cell cluster in atherosclerotic aorta. Single cell RNA sequencing of aortic sorted TdTomato+CD11b+Dump- cells (Dump- are excluding CD3+, CD19+, CD49b+, Siglec-F+, Ly6G+ cells) from atherosclerotic Cx3cr1CreERT2-IRES-YFP/+Rosa26floxed-tdTomato/+ mice (n=8, 1012 AAV-PCSK9 at 8wk old mice, then WD for 18 wks). Then 4 mice continue on WD for further 2wks as progression group, 3157 cells identified, Using Illumina HiSeq4000. The other 4 mice were switched into chow diet for further 2wks and also i.p. treated with ApoB-ASO (50 mg/kg, 2 doses/wk, 2wks) as regression group, 2198 cells identified, Using Illumina HiSeq4000.