The World Health Organization (WHO) estimated the number of spinal cord injuries to be between 250,000 and 500,000 new cases every year, with an increasing incidence over the years. In the USA alone, about 282,000 persons are living with SCI. All these cases suffer from loss of sensory and motor functions to some degree, and there is no definitive treatment until now that can restore these functions. Moreover, one-third of these patients experience insidious damage to the neural tissues and a decline in the quality of their lives due to the development of post-traumatic intraspinal cystic lesions. The strategies for restoring neurological functions are long-term solutions, retrospective, and require the synergy of different therapeutic approaches.

Along with these strategies, simple proactive strategies are required to prevent SCI complications. Molecular mechanisms involved in spinal cord development and disease seem very promising targets for both strategies, yet they are mostly unclear. Better exploitation of these molecular mechanisms can help researchers find definitive solutions for urgent and long-term problems, even without a full understanding of them. Therefore, the primary objective of this study was to prove the utility of some of the mechanisms involved in spinal cord development and disease while attempting to explain how they work, when possible. The overall hypothesis of this work is that molecular mechanisms involved in the spinal cord development and disease can be exploited for improving the outcome of SCI treatment. First, the focus was on utilizing the molecular signaling and cues retained in the subcutaneous environment throughout adulthood for priming aNSPCs encapsulated in chitosan-based hydrogel and helping nascent neurons acquire region-specific identity based on the region of implantation of the bioscaffold. To investigate this hypothesis, I implanted three bioscaffolds in the subcutaneous tissues in the back of rats in the cervical, thoracic, and lumbar region for four, six, and eight weeks. After harvesting the scaffolds, the response of aNSPCs was evaluated using IHC and RTqPCR. Evaluation of the cell response required isolating RNA from aNSPCs encapsulated in the chitosan hydrogel, which was proved to be challenging due to physicochemical interactions between chitosan and RNA. Therefore, I investigated the pH-dependent isolation of RNA from a chitosan-based hydrogel. This experiment hypothesized that pH manipulation of the homogenization solution could improve isolated RNA yield and quality. Second, a molecular mechanism implicated in the expansion of the cystic lesions after SCI was investigated. The upregulation of BGT-1 and its substrate betaine was associated with intraspinal cystic lesions. Therefore, I hypothesized that inhibition of BGT1 in spinal cord tissues could counteract cystic cavity expansion after SCI.

Along with this goal, micro-CT utility for an estimation of intraspinal cysts was investigated in comparison to conventional histology. A significant difference was found between histology and micro-CT when both were used to estimate the syrinx size. In this dissertation, I tried to demonstrate the nature of the Integrated Biosciences Ph.D. program, which cuts through across the boundaries of traditional departments and approaches a problem from different perspectives.