24 25 45 KEYWORDS 46 Atherosclerotic plaque, T cells, macrophages, cerebrovascular events, Stroke, CyTOF, 47 scRNA-seq, CITE-seq, cell-cell interactions, IL-1β, PD-1, T cell exhaustion. 48 49 alterations of individual immune cells that contribute to human disease and its CV 89 complications. 90 91 RESULTS 92 Single-Cell Immunophenotyping of Human Atherosclerosis: Study Design 93 To map the immune microenvironment of atherosclerotic lesions, identify mirroring 94 immune changes in blood and pinpoint cell-specific alterations associated with clinical CV 95 events (i.e. stoke and TIA), we performed a large-scale CyTOF mass-cytometry 96 analysis 41 combined with Cellular Indexing of Transcriptomes and Epitopes by 97 Sequencing (CITE-seq) 42 and single-cell scRNA-seq analysis of plaques from a total of 98 46 prospectively enrolled patients undergoing carotid endarterectomy (Fig.