Integrative single cell RNA and spatial profiling identify mechanisms of neonatal brain hemorrhage pathophysiology and repair.

Precise control of cell-cell communication networks within brain neurovascular units (NVUs) promotes normal tissue physiology. Dysregulation of these networks can lead to pathologies including uncontrolled angiogenesis, endothelial barrier disruption, and intracerebral hemorrhage (ICH). The cellular and molecular mechanisms underlying ICH pathogenesis and subsequent tissue repair processes remain poorly understood. Here we employed fixed single cell RNA profiling coupled with spatial in situ gene expression profiling to characterize NVU signaling pathways associated with ICH in Itgb8/β8 integrin mutant mice. In this model, early neonatal stages of ICH were characterized by downregulation of extracellular matrix (ECM)-associated signaling factors (Adamtsl2, Htra3, and Lama4) linked to canonical TGFβ activation and signaling in endothelial cells. Conversely, the progressive resolution of ICH involved upregulation of neuroinflammatory signaling networks (Gas6 and Axl) alongside activation of iron metabolism pathway components (Hmox1, Cp, and Slc40a1) in microglia/macrophages. Integrated computational modeling identifies additional ligand-receptor signaling networks between perivascular glial cells and angiogenic endothelial cells. Collectively, these findings illuminate the molecular signaling networks that promote NVU maturation and provide novel mechanistic insights into the pathways controlling ICH pathogenesis and repair in Itgb8 mutant mice.