Exploration of plaque rupture-associated pathways in acute myocardial infarction based on in silico perturbation of NK-cell transcription factor activity

Background Natural killer (NK) cells may be involved in the immune and inflammatory responses underlying plaque rupture (PR) and non-plaque rupture (NPR) in acute myocardial infarction (AMI); however, their transcriptional differences remain incompletely characterized. Objectives This study aimed to characterize NK-cell transcriptional features associated with PR and to explore differences in inferred pathway and transcription factor (TF) activity between PR and NPR. Methods The publicly available single-cell RNA-sequencing (scRNA-seq) dataset GSE269269, including five PR and five NPR samples, was analyzed using the Seurat package. Intercellular communication patterns were inferred by CellChat. NK-cell expression counts were aggregated at the sample level to generate pseudobulk expression profiles for differential expression analysis and PR score calculation. Hallmark gene set enrichment analysis (GSEA) and PROGENy were employed to evaluate pathway-associated transcriptional activities, whereas DoRothEA and VIPER were used to infer TF activities. Exploratory in silico perturbation analysis was performed to evaluate the potential effects of selected TF perturbations. Results A total of 76,050 cells were classified into 10 major cell types, with NK cells representing the largest proportion in most samples. Sample-level NK-cell analyses revealed group-associated differences in transcriptional programs, inferred pathway activities, and TF activities. PR samples showed relatively higher inferred TGF-β, EGFR, and JAK-STAT pathway activities and lower hypoxia-related activity. IRF4 and PPARG activities were higher in PR, whereas CREB1, HIF1A, E2F1, ARID3A, and HOXB13 activities were lower. In silico perturbation analysis revealed TF-specific changes in PR score, identifying several potential TF candidates for further validation. Conclusions This exploratory analysis identified PR-associated differences in NK-cell transcriptional programs, pathway activities, and TF activities. These computational findings are hypothesis-generating and require further validation in independent cohorts and experimental models.