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Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression
Jian-Da Lin, Hitoo Nishi, Jordan Poles, Xiang Niu, Caroline Mccauley, Karishma Rahman, Emily J. Brown, Stephen T. Yeung, Nikollaq Vozhilla, Ada Weinstock, Stephen A. Ramsey, Edward A. Fisher, P’ng Loke
Jian-Da Lin, Hitoo Nishi, Jordan Poles, Xiang Niu, Caroline Mccauley, Karishma Rahman, Emily J. Brown, Stephen T. Yeung, Nikollaq Vozhilla, Ada Weinstock, Stephen A. Ramsey, Edward A. Fisher, P’ng Loke
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Research Article Cardiology Immunology

Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression

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Abstract

Atherosclerosis is a leading cause of death worldwide in industrialized countries. Disease progression and regression are associated with different activation states of macrophages derived from inflammatory monocytes entering the plaques. The features of monocyte-to-macrophage transition and the full spectrum of macrophage activation states during either plaque progression or regression, however, are incompletely established. Here, we use a combination of single-cell RNA sequencing and genetic fate mapping to profile, for the first time to our knowledge, plaque cells derived from CX3CR1+ precursors in mice during both progression and regression of atherosclerosis. The analyses revealed a spectrum of macrophage activation states with greater complexity than the traditional M1 and M2 polarization states, with progression associated with differentiation of CXC3R1+ monocytes into more distinct states than during regression. We also identified an unexpected cluster of proliferating monocytes with a stem cell–like signature, suggesting that monocytes may persist in a proliferating self-renewal state in inflamed tissue, rather than differentiating immediately into macrophages after entering the tissue.

Authors

Jian-Da Lin, Hitoo Nishi, Jordan Poles, Xiang Niu, Caroline Mccauley, Karishma Rahman, Emily J. Brown, Stephen T. Yeung, Nikollaq Vozhilla, Ada Weinstock, Stephen A. Ramsey, Edward A. Fisher, P’ng Loke

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Figure 7

Validation of the presence of a “stem-like” cell cluster from an independent study of atherosclerotic mice.

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Validation of the presence of a “stem-like” cell cluster from an indepen...
A recently published single-cell data set from Kim et al. (ref. 40; “Kim”) from sorted CD45+ cells isolated from whole aortas of Ldlr–/– mice fed WD for 12 weeks was combined with our progression and regression data sets (Lin Progression, Lin Regression) with Seurat merging and aligned with canonical correlation analysis (CCA). (A) t-SNE visualization of the 8906 single cells from both data sets after Louvain clustering and colored by sub-cluster.(B) SingleR method was used for unbiased cell classifications of each sub-cluster against the ImmGen database and colored and labeled accordingly on the t-SNE plot. (C) t-SNE plot colored based on experimental group and data sets, showing that cluster 6 includes cells from all 3 experiments. (D) Cluster composition by cell numbers of experimental groups and data sets (red, Kim Ldlr–/–; green, Lin Progression; blue, Lin Regression) in total single cells. (E) Violin plot and heatmap showing the highest expression of cell cycle (“Stemness”) genes in cluster 6. (F) Violin plot and heatmap showing the expression of CX3CR1 in cluster 6.

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