A Systems-Level Analysis of the Peripheral Nerve Intrinsic Axonal Growth Program

Abstract

SUMMARY The regenerative capacity of the injured CNS in adult mammals is severely limited, yet axons in the peripheral nervous system (PNS) regrow, albeit to a limited extent, after injury. We reasoned that coordinate regulation of gene expression in injured neurons involving multiple pathways was central to PNS regenerative capacity. To provide a framework for revealing pathways involved in PNS axon regrowth after injury, we applied a comprehensive systems biology approach, starting with gene expression profiling of dorsal root ganglia (DRGs) combined with multi-level bioinformatic analyses and experimental validation of network predictions. We used this rubric to identify a drug that accelerates DRG neurite outgrowth in vitro and optic nerve outgrowth in vivo by inducing elements of the identified network. The work provides a functional genomics foundation for understanding neural repair and proof of the power of such approaches in tackling complex problems in nervous system biology.

Intrinsic mechanisms of neuronal axon regeneration

“…Although overexpression of ATF3 can promote peripheral nerve regeneration 109 , it fails to do so in several models of CNS injury 110,111 . Conversely, JUN overexpression can promote regeneration in cultured cortical 110,112,113 and DRG neurons 114 ; however, as described above, its activation downstream of DLK also promotes cell death in RGCs 66 . Whereas neuronal JUN is clearly necessary for peripheral axon regeneration 115 , JNK-mediated phosphorylation of JUN appears to not be required for its full function in facial nerve regeneration 116 .…”

“…Bioinformatics approaches to integrate discoveries related to regenerative capacity across multiple laboratories could help to drive drug discovery, but such studies remain difficult to interpret because of the lack of cell-type-specific data. Although a recent study identified pathways and small molecules that can enhance growth of injured neurons 114 , the effects observed were small, and future multilevel bioinformatics analyses will benefit from novel neuron-specific data sets. Furthermore, how injured neurons can reprogramme themselves to regrow their axons while maintaining their competency to form synapses and how they can stop growth once regeneration is complete is still not understood.…”

“…Whereas neuronal JUN is clearly necessary for peripheral axon regeneration 115 , JNK-mediated phosphorylation of JUN appears to not be required for its full function in facial nerve regeneration 116 . Importantly, co-expression of ATF3 and JUN can cooperate to improve regeneration in DRG neurons to a greater extent than can be achieved by the expression of either transcription factor alone 114 . However, this cooperative effect does not occur in cortical neurons 110 .…”

“…Importantly, studies have also shown that each of the core transcription factors regulates the expression of the others, reinforcing cell fate 152 . Whereas one recent study identified a core network of hub transcription factors involved in peripheral regeneration 114 , their downstream targets and whether they regulate the expression of the other transcription factors in the context of regeneration are still unclear. Similarly, it is unlikely that the transcription factors that drive the pro-regenerative network are activated simultaneously.…”

An omic approach to spinal cord injury mechanisms

“…Successful axonal regeneration employs networks of interrelated genes concomitant to the activated state of the neuron, including transcription activators and functional networks related to growth-specific signaling pathways [3][4][5][6][7] . A recent study using RNA sequencing technology indicated that successfully regenerating peripheral neurons coordinately express genes within regeneration networks 8 . This coordinated regulation of molecules is considered a hallmark feature of successful regeneration.…”