Neuropilins (NRPs) are receptors for the major chemorepulsive axonal guidance cue semaphorins (Sema). The interaction of Sema3A/NRP1 during development leads to the collapse of growth cones. Here we show that Sema3A also induces death of cultured cortical neurons through NRP1. A specific NRP1 inhibitory peptide ameliorated Sema3A-evoked cortical axonal retraction and neuronal death. Moreover, Sema3A was also involved in cerebral ischemia-induced neuronal death. Expression levels of Sema3A and NRP1, but not NRP2, were significantly increased early during brain reperfusion following transient focal cerebral ischemia. NRP1 inhibitory peptide delivered to the ischemic brain was potently neuroprotective and prevented the loss of motor functions in mice. The integrity of the injected NRP1 inhibitory peptide into the brain remained unchanged, and the intact peptide permeated the ischemic hemisphere of the brain as determined using MALDI-MS-based imaging. Mechanistically, NRP1-mediated axonal collapse and neuronal death is through direct and selective interaction with the cytoplasmic tyrosine kinase Fer. Fer RNA interference effectively attenuated Sema3A-induced neurite retraction and neuronal death in cortical neurons. More importantly, down-regulation of Fer expression using Fer-specific RNA interference attenuated cerebral ischemia-induced brain damage. Together, these studies revealed a previously unknown function of NRP1 in signaling Sema3A-evoked neuronal death through Fer in cortical neurons.Injured central nervous system axons have a very limited capacity to regenerate due to the presence of a plethora of growth inhibitory ligands secreted from oligodendrocytes/myelin, reactive astrocytes, and fibroblasts in the damaged tissue (1-6). Neurons must integrate this multitude of inhibitory molecular cues, generated as a result of cortical damage, into a functional response. More often than not the response is one of growth cone collapse, axonal retraction, and neuronal death. Therefore, chemorepulsive factors likely contribute either directly or indirectly to neuronal death in the injured adult brain (7-10). Indeed, the expression of Sema3A, a major chemorepulsive factor, has been reported in several brain injury models, such as peripheral nerve injury, spinal cord injury, cerebral ischemia, and Alzheimer disease (1, 3, 11-16). In addition, Sema3A expression has been shown to increase vascular permeability, which may indirectly contribute to neuronal damage (17).The biological activities of Sema3A during development are complex and context-dependent. Although best known for its role as an axonal growth cone repellent, Sema3A also serves as a chemoattractant during cortical layer development by guiding the radial migration of layer II/III cortical neurons (18) and the growth of apical dendrites toward the pial surface (19). In contrast, Sema3A is also important in stereotyped pruning of long hippocampal axon branches (20), causing dorsal root ganglia axon retraction (21), and evoking apoptosis of sensory neurons (22-2...