Single-cell multimodal profiling of monocytes reveals diverse phenotypes and alterations linked to cardiovascular disease risks

Monocytes are a critical innate immune system cell type that serves homeostatic and immunoregulatory functions. They have been identified historically by the cell surface expression of CD14 and CD16. However, recent single-cell studies have revealed that they are much more heterogeneous than previously realized. We utilized cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and single-cell RNA sequencing (scRNA-seq) to describe the comprehensive transcriptional and phenotypic landscape of 437,126 monocytes. This high-dimensional multimodal approach identified vast phenotypic diversity and functionally distinct subsets, including IFN-responsive, MHCIIhi, monocyte-platelet aggregates, as well as non-classical, sand several subpopulations of classical monocytes. Using flow cytometry, we validated the existence of MHCII+CD275+ MHCIIhi, CD42b+ monocyte-platelet aggregates, CD16+CD99- non-classical monocytes, and CD99+ classical monocytes. Each subpopulation exhibited unique characteristics, developmental trajectories, transcriptional regulation, and tissue distribution. In addition, alterations associated with cardiovascular disease (CVD) risk factors, including race, smoking, and hyperlipidemia were identified. Moreover, the effect of hyperlipidemia was recapitulated in mouse models of elevated cholesterol. This integrative and cross-species comparative analysis provides a new perspective on comparison of alterations in monocytes in pathological conditions and offers insights into monocyte-driven mechanisms in CVD and the potential for monocyte subpopulation targeted therapies. Single-cell RNA sequencing (scRNA-seq) was performed on blood monocytes from 118 subjects that were generally healthy.

单核细胞是先天免疫系统的关键细胞类群，兼具稳态维持与免疫调控功能。既往人们通过CD14与CD16的细胞表面表达特征对其进行鉴定。然而，近期的单细胞研究表明，单核细胞的异质性远高于此前认知。我们采用转录组与表位测序细胞索引技术（cellular indexing of transcriptomes and epitopes by sequencing，CITE-seq）与单细胞RNA测序（single-cell RNA sequencing，scRNA-seq），对437126个单核细胞的完整转录组与表型图谱进行了系统性描述。该高维多模态分析策略揭示了单核细胞广泛的表型多样性与功能迥异的亚群，包括干扰素应答型、MHCII高表达型、单核细胞-血小板聚集体，以及非经典单核细胞与数类经典单核细胞亚群。我们通过流式细胞术验证了MHCII+CD275+ MHCII高表达亚群、CD42b+单核细胞-血小板聚集体、CD16+CD99-非经典单核细胞以及CD99+经典单核细胞的存在。各亚群均具备独特的生物学特征、发育轨迹、转录调控模式与组织分布特征。此外，我们还鉴定出与心血管疾病（cardiovascular disease，CVD）危险因素（包括种族、吸烟与高脂血症）相关的单核细胞表型改变。不仅如此，高脂血症的相关效应在高胆固醇血症小鼠模型中得到了重现。这项整合性跨物种比较分析，为病理状态下单核细胞的表型改变研究提供了全新视角，同时揭示了单核细胞介导的心血管疾病发病机制，并为针对单核细胞亚群的靶向治疗策略提供了理论依据。本研究对118名健康志愿者的外周血单核细胞开展了单细胞RNA测序（scRNA-seq）。