Abstract Background Acute pulmonary embolism (APE) is a life-threatening clinical condition characterized by thrombus formation within the pulmonary arteries, with high morbidity and mortality rates. Recent studies have indicated that immune cells play crucial roles in thrombus formation and pathological progression. However, the cellular composition and immunological features within APE thrombi remain poorly understood. This study aimed to characterize the cellular composition and immune cell features of thrombi from patients with APE using single-cell RNA sequencing (scRNA-seq) and to explore the potential roles of distinct immune cell subpopulations in the pathogenesis of APE. Methods Thrombus samples were collected from five patients diagnosed with APE and subjected to single-cell RNA sequencing. Cell types and subpopulations were identified and annotated to delineate the cellular composition of APE thrombi. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to evaluate the functional characteristics of different cell subsets. In addition, Monocle3 and CellChat were employed to investigate cellular differentiation trajectories and intercellular communication networks. Results The analysis identified multiple cell types within APE thrombi, including monocyte, macrophages, neutrophils, T cells, NK cells, and mast cells, with a markedly increased proportion of monocyte and macrophages. Functional characterization revealed significant heterogeneity among macrophages, which could be categorized into four major subtypes: inflammatory, lipid metabolism-related, proliferative, and complement-activated macrophages. Among them, the lipid metabolism-related macrophages exhibited enhanced lipid metabolic activity and reduced secretion of inflammatory factors, suggesting a transitional state from inflammatory macrophages toward complement-associated macrophages.Meanwhile, neutrophils also demonstrated a high degree of transcriptional diversity, encompassing resting, activated, cytotoxic, and antigen-presenting neutrophil subsets, each corresponding to different stages of the inflammatory response. Conclusion APE thrombi exhibit a complex immune cell composition and remarkable functional heterogeneity. Both macrophages and neutrophils play vital roles during the initiation, progression, and resolution of inflammation, and their diverse functional states may jointly contribute to thrombus formation and disease development. This abstract is funded by: National Key Research and Development projects of China (2023YFC2509500) and the Program of National Natural Science Foundation of China (82570413), the Noncommunicable Chronic Diseases-National Science and Technology Major Project (2024ZD0526700, 2024ZD0528600), the the Pujiang Talent Program (22OHD064), and the Program of Shanghai Pulmonary Hospital (2025-0554-YB-15, LYRC202415).
Sun et al. (Fri,) studied this question.