Single-cell transcriptomic profile of CD45+ cells in atherosclerotic plaques of mice with myeloid-specific Lipa overexpression and on Ldlr-/- background [scRNA-seq]

Macrophages within atherosclerotic plaques display significant heterogeneity. We used single-cell RNA-sequencing (scRNA-seq) to analyze the relative abundance and transcriptomic signature of macrophage subclusters in atherosclerotic aortas of mice with myeloid-specific Lipa overexpression on the Ldlr-/- background and fed a Western diet for 16 weeks. We generated mice for Lipa overexpression (LipaTg/wt) on C57BL/6 background by inserting Lipa open reading frame (NM_001111100) into the Rosa26 locus. To achieve myeloid-specific Lipa overexpression, we bred LipaTg/Tg, Ldlr-/- mice with LysMCre+/-, Ldlr-/- mice. The LysMCre+/-, LipaTg/wt, Ldlr-/- mice (LipaTg) demonstrate myeloid-specific Lipa overexpression, where eGFP acts as a marker for cells with successful cre-loxp recombination leading to subsequent Lipa overexpression. Aortas were harvested from LipaTg mice fed a Western diet for 16 weeks and subsequently enzymatically digested into single cells. Given that LysMCre-mediated recombination is not 100% for transgenic overexpression, we leveraged this feature to sort CD45+eGFP- plaque cells (no Lipa overexpression) and CD45+eGFP+ plaque cells (with Lipa overexpression) dissociated from aortas of LipaTg mice. These sorted CD45+GFP- and CD45+GFP+ cells, pooled from five male mice, were subjected to scRNA-seq immediately.