Cross-Cohort Optimal Transport Maps Macrophage Plasticity and Competing Routes to Inflammation and Fibrosis in Human Atherosclerotic Plaques
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 human atherosclerotic plaque cohorts, we generate an integrated atlas of 81,633 monocytes and macrophages and identify 15 statistically significant pairwise transitions, of which 11 directed transitions organize into three biological axes: monocyte fate diversification, inflammatory reactivation, and fibrotic remodeling. The strongest transition links scavenging macrophages to inflammatory macrophages, suggesting that plaque inflammation is driven predominantly by reactivation of tissue-adapted macrophages rather than by direct differentiation of newly recruited monocytes. By tracking gene expression changes along the OT target-association gradient, we find that macrophage plasticity follows an origin-dependent spectrum. Tissue-resident macrophages, in particular scavenging macrophages, acquire inflammatory programs while preserving and reinforcing their resident scavenging identity, a mechanism we term transcriptional layering, whereas monocyte-derived transitions proceed through selective loss of source-identity modules. Despite these distinct routes, transitions converging on the same fate activate shared destination-specific regulatory circuits, with inflammatory and fibrotic programs governed by mutually antagonistic transcription factor networks. These findings identify inflammatory reactivation of scavenging macrophages as a dominant transition axis in human atherosclerosis and suggest that macrophage origin constrains how disease-associated programs are acquired. More broadly, this framework provides a general strategy for quantifying cell-state transitions and dissecting plasticity mechanisms in chronic inflammatory disease.