Transcriptome analyses reveal molecular mechanisms underlying functional recovery after spinal cord injury

Abstract

Spinal cord injury (SCI) is considered incurable because axonal regeneration in the central nervous system (CNS) is extremely challenging, due to harsh CNS injury environment and weak intrinsic regeneration capability of CNS neurons. We discovered that neurotrophin-3 (NT3)-loaded chitosan provided an excellent microenvironment to facilitate nerve growth, new neurogenesis, and functional recovery of completely transected spinal cord in rats. To acquire mechanistic insight, we conducted a series of comprehensive transcriptome analyses of spinal cord segments at the lesion site, as well as regions immediately rostral and caudal to the lesion, over a period of 90 days after SCI. Using weighted gene coexpression network analysis (WGCNA), we established gene modules/ programs corresponding to various pathological events at different times after SCI. These objective measures of gene module expression also revealed that enhanced new neurogenesis and angiogenesis, and reduced inflammatory responses were keys to conferring the effect of NT3-chitosan on regeneration.S pinal cord injury (SCI) is a debilitating medical condition that often leads to permanent impairment of sensory and motor functions. SCI is considered almost incurable because axons in the central nervous system (CNS), unlike those in the peripheral nervous system (PNS), are believed not to regenerate. The innate ability of mature CNS neurons to regenerate is much weaker than that of PNS neurons (1). In addition, myelin debris in the injured CNS is more inhibitory toward axonal growth compared to that in the PNS (2). Moreover, the mode of immune cell infiltration and microglia activation are different in CNS versus PNS, resulting in a different cellular microenvironment, which crucially influences the outcome, i.e., PNS axons regenerate, while CNS axons do not (3).Over the years, SCI research has focused on ways to promote the long-distance growth of CNS motor axons, mainly by neutralizing inhibitory myelin components and/or changing the neuronal intrinsic program to enable better regeneration (4). Unfortunately, however, although numerous studies have been carried out following this line of strategy, no major breakthroughs translatable to therapy have been achieved. In recent years, efforts toward promoting long distance axonal growth have been complemented with alternative approaches aimed at using exogenous stem cells to generate local new neurons that form nascent relay neural networks to pass ascending and descending neurotransmission signals with or without long-distance axonal growth (5-7).SCI is a complex medical condition. The primary lesion includes the physical traumatic wounding of both white and gray matter, breakdown of the vasculature system, and acute immune reactions, which is followed by secondary lesions, such as demyelination, additional immune cell infiltration, inflammation, glial scar formation, impaired neurotransmission, and neuronal apoptosis (8). Secondary lesions are intermingled with intrinsic repair processes, including remyelina...

NT3-chitosan elicits robust endogenous neurogenesis to enable functional recovery after spinal cord injury

“…Through inhibition of new endogenous neurogenesis, behavioral recovery was partially impaired, as were MEP and SEP amplitudes, demonstrating the contribution of nascent relay neuronal networks created via activation of endogenous NSCs and subsequent neurogenesis. Moreover, we also found that the NT3-chitosan tube not only acted on neural cells, but also elicited inhibition of the inflammatory immune process (22), both of which could contribute to better nerve regeneration and adult neurogenesis.…”

“…S6E). Since these BrdU cells in the LC group were not labeled with Nestin or Tuj1, they were most likely infiltrating inflammatory immune cells (22). Moreover, the fact that those cells did not infiltrate into the middle part of the chitosan tubes at such early time points in the ET and NT3 groups suggests that the chitosan tubes with or without NT3 likely created an anti-inflammatory environment early after injury and, when coupled with NT3, supported new neurogenesis and axonal regeneration (22).…”

In vitro response of macrophages to ceramic scaffolds used for bone regeneration

“…Another major limitation is that we evaluated only a small subset of the thousands of genes involved in bone regeneration. Moreover, although gene expression has been shown to be an excellent indicator of cell identity and physiological state [55], especially for discerning macrophage activation [56][57][58], additional work is needed to confirm phenotypic changes in macrophages on a functional level. Finally, we investigated only the effects of these scaffolds on macrophages, but other immune cells, including dendritic cells and resident tissue macrophages, as well as cells specific to bone repair, would be expected to interact with macrophages and have major effects on bone regeneration.…”

Harness the power of endogenous neural stem cells by biomaterials to treat spinal cord injury

“…In an accompanying paper by Duan et al [3] from the same group, the authors used genomic analysis to probe the mechanism underlying the activation of endogenous NSCs, and to search for possible prohibitive factors that could hamper regeneration of neurons after SCI. Using an ingenuous analytical method called the Weighted Gene Coexpression Analysis (WGCNA), the authors found a gene expression pattern which suggested that the NT-3 chitosan bio-tube may dampen inflammatory immune processes [3], enhance formation of blood vessels, and promote de novo neurogenesis.…”

“…Using an ingenuous analytical method called the Weighted Gene Coexpression Analysis (WGCNA), the authors found a gene expression pattern which suggested that the NT-3 chitosan bio-tube may dampen inflammatory immune processes [3], enhance formation of blood vessels, and promote de novo neurogenesis. WGCNA analysis involves identification of gene modules that are representative of pathological events, and potentially allows definition of diagnostic hallmarks and targets for future therapeutic interventions.…”