Cross-Cohort Optimal Transport Maps Macrophage Plasticity and Competing Routes to Inflammation and Fibrosis in Human Atherosclerotic Plaques (opens in new tab)

Single-cell transcriptomics has revealed extensive macrophage heterogeneity in atherosclerotic plaques, but how macrophages move between states, and whether transition mechanisms depend on cellular origin, remain unclear. Here we develop a computational framework that reconstructs directed cell-state transition networks from cross-sectional single-cell RNA-sequencing data by combining optimal transport with RNA velocity and systematic cross-cohort validation. Applying this approach to seven h...