Single-cell transcriptomic atlas reveals temporal dynamics driving chronic peripheral nerve degeneration

Peripheral nerve injury often results in irreversible functional deficits that are caused by chronic denervation. Although surgical techniques for nerve repair have advanced, a lack of understanding of the cellular dynamics in the distal nerve microenvironment has impeded the development of effective interventions. In the present study, we constructed a longitudinal single-nucleus transcriptomic atlas of distal sciatic nerve stumps from rats with complete transection injuries across five time points (0, 14, 28, 60, and 90 days postinjury). Sequencing of 63,033 nuclei revealed dynamic state transitions that spanned multiple cell types throughout nerve degeneration. At 14 days post-injury, Schwann cells proliferated and adopted a repair phenotype, whereas immune cells persisted following Wallerian degeneration alongside transient apoptosis in other stromal populations. Diverse cell types sustained robust functional activity supporting axonal regeneration until 28 days post-injury. By 60 days post-injury, persistent denervation triggered the irreversible deterioration of cellular states with minimal changes in cell numbers; this was marked by a loss of Schwann cell regenerative capacity and a pro-inflammatory shift in immune responses. By 90 days post-injury, accelerated apoptosis caused pronounced cellular loss, including a severe decline in Schwann cells. Cell–cell communication analysis identified Schwann cells as central signaling hubs that are essential for coordinating multicellular responses and regulating the microenvironment. Critically, our findings identify 28 days post-injury as a critical threshold for effective nerve regeneration. Within 28 days of injury, distal nerve segments maintain a cellular microenvironment that is capable of actively supporting regeneration; however, beyond 28 days post-injury, this supportive capacity markedly declines because of progressive chronic changes in the Schwann cell phenotype and axonal microenvironment. These results provide mechanistic insights into the pathophysiology of chronic denervation and establish a foundation for targeted interventions that are designed to extend the regenerative window and overcome barriers to nerve repair.