A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages

Atherosclerosis is a systemic and chronic inflammatory disease propagated by monocytes and macrophages. Yet, our knowledge on how transcriptional profiles of these cells evolve in time and space is limited. We aimed at characterizing gene expression changes in site-specific macrophages, i.e. atherosclerotic aorta versus remote peritoneal cavity, and in circulating monocytes during the course of atherosclerosis initiation and progression in Apoe deficient mice. Constructing a comparative directory of cell type- and disease stage-specific whole transcriptome information, we identified a distinctive gene regulation profile of aortic macrophages. Overall 1149 differentially expressed genes (DEG) were involved in the biological modulation of aortic macrophages, and they were further categorized into regulated early, late, and transitorily throughout the disease course. The commonality of gene regulation was surprisingly low among the three investigated cell types. Through complementary interrogation of murine and human single cell RNA sequencing datasets, we showcased the practicality of our directory, using the selected gene, Glycoprotein Nmb (Gpnmb), whose expression in aortic macrophages, and a subset of foamy macrophages in particular, strongly correlated with disease advancement during atherosclerosis initiation and progression. Our study provides a unique toolset to explore gene regulation of macrophage-related biological processes in and outside the atheromatous plaque at early and advanced disease stages for pathomechanistic insight and therapeutic target screening. Overall design: We acquired three cell types (circulating monocytes, peritoneal macrophages, aortic macrophages) from atherosclerotic mice with different disease severity (baseline, early atheroma, advanced atheroma). Atheroma formation was controled by feeding Apoe-deficient mice high cholesterol diet for different durations (chow diet, 1 month feeding, 6 month feeding). The study aimed to investigate gene regulation changes of systemic and lesional monocytes/macrophages during atheroma initiation and progression. There were four replicates for each cell type and each disease stage.