Characterizing Stroke Clots Using Single-Cell Sequencing

Background: Ischemic stroke result in significant morbidity and mortality. By examining gene expression of cells comprising stroke clots, we aim to gain valuable insights into the underlying mechanisms of this disease and identify potential biomarkers of stroke etiology. Methods: We employed single-cell RNA sequencing to analyze 10 clot samples from patients diagnosed with large vessel occlusion stroke. We aimed to identify and compare the immune cell compositions and gene expression profiles between stroke clots (atrial fibrillation vs carotid atherosclerosis). We also used MAGMA and GWAS summary statistics from the GIGASTROKE consortium to assess associations association between genetic variants and cell type-specific gene expression within the stroke subtypes. Results: Our analysis revealed distinct immune cell populations, including monocytes, macrophages, dendritic cells, neutrophils, and T-cells in both clot types. Notably, we observed significant differences in gene expression within the mononuclear phagocytic system cells between clots from atrial fibrillation and carotid atherosclerosis patients.We identified specific genes associated with atherosclerosis and stroke-related processes, such as CD74, HLA-DRB1*01, HTRA1, C1Q, CD81, and CR1 clots from carotid atherosclerosis patients. In atrial fibrillation clots, CD8 T-cells and NK-cells show upregulated expression of genes such as GZMH, GZMB, S100A4, FCGBP2, HLA-A, TIMP1, CLIC1, and IFITM2, indicating their involvement in cytotoxic activities and potential tissue damage. The MAGMA approach highlighted significant genetic associations within leukocytes, particularly in atrial fibrillation and carotid clots, underscoring the potential roles of B-cells, T-cells, and macrophages in clot pathogenesis. Conclusions: This study illuminates the immune and transcriptomic landscape within clots, offering potential biomarkers and lays the foundation for future research.