Abstract
Aims: Atherosclerosis is a major global health challenge, with limited diagnostic and therapeutic options. Macrophages drive disease progression, but their tissue-specific phenotypes and functions remain poorly defined. This study aims to elucidate macrophage-driven mechanisms by characterizing their functional diversity across key metabolic and vascular tissues. Methods and results: We used single-cell RNA sequencing (scRNA-seq) and translating ribosome affinity purification sequencing (TRAP-seq) to profile macrophage-specific gene programmes in a mouse model of atherosclerosis across the aorta, adipose tissue, and liver. Our data highlight tissue-specific macrophage gene programmes and identify markers that are shared across mouse and human plaques. First, we identified soluble Trem2 as a potential circulating biomarker for differentiating between asymptomatic and symptomatic individuals. Secondly, we leveraged the pronounced expression of Folr2 and Slc7a7 to explore the potential of folate and glutamine as positron emission tomography (PET) tracers for disease burden assessment through in vivo PET imaging. Finally, we show that knockout of Slc7a7 inhibits acetylated low-density lipoprotein uptake and dampens the gene signature linked to lipid-associated macrophages. This suggests that glutamine signalling may play a critical role in foam cell formation, a key event in atherosclerosis. Conclusion: Our findings provide novel insights into macrophage-specific gene programmes during atherosclerosis progression and identify a set of promising biomarkers that can serve as a resource for future studies. These findings could significantly contribute to improving the diagnosis, monitoring, and treatment of atherosclerosis.