Integrative single-cell and spatial transcriptome analysis reveals the functions of TREM2high macrophages and infarct border dynamics post-myocardial infarction

This study employs an integrative approach combining single-cell RNA Sequencing (scRNA-seq), spatial transcriptomics (ST), and bulk RNA Sequencing to investigate the complex cellular and molecular dynamics following myocardial infarction (MI). Quality control, batch correction, dimensionality reduction, clustering, and annotation were performed on scRNA and ST data. The Milo tool was used to analyze differential cell abundance. Developmental trajectory inference was conducted using the Monocle2 algorithm, and cell-cell communication was explored using CellPhoneDB and NicheNet. SCENIC analysis identified active transcription factors (TFs) in macrophage subtypes. Additionally, deconvolution was used to assess the spatial distribution of cell types. The functional roles of different myocardial regions were explored through cell communication patterns. Mouse MI and ischemia-reperfusion (I/R) models were established by ligating the left anterior descending (LAD) coronary artery. Molecular changes were analyzed using RT-qPCR, Western blot, immunohistochemistry and immunofluorescence. In vitro, AC16 cardiomyocytes (CMs) and THP-1-derived M2 macrophages were subjected to oxygen-glucose deprivation/reoxygenation (OGD/R) and co-culture experiments to study TREM2-mediated effects. Cell viability and Apoptosis were assessed using CCK-8 and flow cytometry, respectively. The study identified dynamic changes in the proportions of immune cell types at different time points post-MI. ST revealed distinct immune cell infiltration patterns in the infarct, border, and remote zones, with macrophages progressively infiltrating the infarct region over time. Functional enrichment analysis highlighted key pathways involved in inflammation, cell proliferation, and extracellular matrix remodeling across different cardiac regions. The study also identified Trem2^high macrophages as key players in tissue repair. SCENIC analysis uncovered TFs regulating macrophage subtypes, emphasizing their roles in immune regulation and tissue reconstruction. Finally, cell-cell communication analysis revealed complex signaling networks influencing immune responses and tissue repair. Our results demonstrated that the expressions of Trem2 were significantly increased in the IZ groups in the MI and I/R model, and co-culture with TREM2-overexpressing M2 macrophages significantly enhanced the proliferative capacity and reduced Apoptosis in AC16 CMs under OGD/R conditions, indicating a critical role of Trem2 in the I/R response and CMs survival. This comprehensive analysis provides a detailed map of the cellular and molecular landscape post-MI, highlighting the temporal and spatial dynamics of immune cells and their regulatory networks.

Cardiac repair; Immune cells; Myocardial infarction; Single-cell RNA sequencing; Spatial transcriptomics.