Integrated scRNA-seq analysis identifies conserved transcriptomic features of mononuclear phagocytes in mouse and human atherosclerosis

Abstract

RationaleAccumulation of mononuclear phagocytes (monocytes, macrophages and dendritic cells) in the vessel wall is a hallmark of atherosclerosis. Although single-cell RNA-sequencing (scRNA-seq) has shed new light on immune cell transcriptional diversity in atherosclerosis, it is still unknown whether the transcriptional states of mononuclear phagocytes are conserved between mouse and human atherosclerosis.ObjectiveTo integrate and compare macrophage and dendritic cell transcriptomes in mouse and human atherosclerosis.Methods and resultsWe integrated 12 scRNA-seq datasets of immune cells isolated from healthy or atherosclerotic mouse aortas, and scRNA-seq data from 11 patients (n=4 coronary vessels, n=7 carotid endarterectomy specimens) from two independent studies. Integration of mouse data recovered previously described macrophage populations and identified novel subpopulations with discrete transcriptomic signatures within populations of aortic resident (Lyve1), inflammatory (Il1b), as well as foamy (Trem2hi) macrophages. We identified unique transcriptomic features distinguishing aortic intimal resident macrophages from atherosclerosis-associated Trem2hi macrophages. Also, populations of Xcr1+ type 1 classical dendritic cells (cDC1), Cd209a+ cDC2 and mature DCs (Ccr7, Fscn1) were detected. In humans, we uncovered macrophage and dendritic cell populations with gene expression patterns similar to those observed in mice in both vascular beds. In particular, core transcripts of the foamy/Trem2hi signature (TREM2, SPP1, GPNMB, CD9) mapped to a specific population of macrophages in human lesions. Cross-species data integration demonstrated transcriptionally proximal macrophage and dendritic cell populations in mice and humans.ConclusionsWe demonstrate conserved transcriptomics features of macrophages and dendritic cells in atherosclerosis in mice and humans, emphasizing the relevance of mouse models to study mononuclear phagocytes in atherosclerosis.

Trafficking of Mononuclear Phagocytes in Healthy Arteries and Atherosclerosis

“…This might be owed to a more important role of local macrophage proliferation than monocyte recruitment in advanced atherosclerosis, similar to what has been observed in mice. In line with this, advanced atherosclerotic plaques contain a significant fraction of proliferating macrophages (71,(215)(216)(217)(218)(219). Another striking similarity between the human and mouse plaque macrophages relates to their phenotype.…”

“…Novel multiparametric analysis methods have established the high plasticity and different nuances in the macrophage functional outfit (67)(68)(69), also in the aortic wall. Recent integrated analyses of scRNA-seq datasets from healthy and atherosclerotic mouse aortas revealed the presence of 5 major macrophage subsets (70,71). As described in more detail below, these subsets are (I) inflammatory, (II) triggering receptor expressed on myeloid cells 2 (TREM2) + , (III) interferon inducible, (IV) resident-like and (V) cavity macrophages.…”

“…As described in more detail below, these subsets are (I) inflammatory, (II) triggering receptor expressed on myeloid cells 2 (TREM2) + , (III) interferon inducible, (IV) resident-like and (V) cavity macrophages. These five subsets can be found both in the atherosclerotic and healthy aorta, although the complexity of macrophage phenotypes increases in atherosclerotic aortas ( 70 , 71 ). Strikingly, by employing scRNA-seq in Rank Cre Rosa26 eYFP mice we were able to map the transcriptional heterogeneity in adventitial macrophages to their origin.…”

“…Phenotype and functions of macrophages are governed by transcriptional regulation. It has been suggested that the transcriptional programs of intima-resident macrophages and recruited monocyte-derived macrophages converge on a similar foamy macrophage profile early in hypercholesterolemia ( 16 , 71 ). But developing atherosclerotic plaques harbour many heterogenous subsets of macrophages.…”

“…But developing atherosclerotic plaques harbour many heterogenous subsets of macrophages. As described above, efforts to integrate the various scRNA-seq studies of the murine atherosclerotic plaque have defined 5 distinct macrophage subsets: (I) inflammatory, (II) TREM2 + , (III) interferon inducible, (IV) resident-like and (V) cavity macrophages ( 70 , 71 ). Inflammatory macrophages show elevated expression levels of pro-inflammatory cytokines like interleukin 1β and tumor necrosis factor.…”