The Application of Omics Technologies to Study Axon Regeneration and CNS Repair

Traumatic brain and spinal cord injuries cause permanent disability. Although progress has been made in understanding the cellular and molecular mechanisms underlying the pathophysiological changes that affect both structure and function after injury to the brain or spinal cord, there are currently no cures for either condition. This may change with the development and application of multi-layer omics, new sophisticated bioinformatics tools, and cutting-edge imaging techniques. Already, these technical advances, when combined, are revealing an unprecedented number of novel cellular and molecular targets that could be manipulated alone or in combination to repair the injured central nervous system with precision. In this review, we highlight recent advances in applying these new technologies to the study of axon regeneration and rebuilding of injured neural circuitry. We then discuss the challenges ahead to translate results produced by these technologies into clinical application to help improve the lives of individuals who have a brain or spinal cord injury.

• Publication year

  2019

• Venue

  F1000Research

• Publication date

  2019-03-20

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.12688/f1000research.17084.1PMID 30941204PMCID 6429978
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Promoting Axon Regeneration in Adult CNS by Targeting Liver Kinase B1.

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• Multi-omics approaches to disease

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• Enhanced neuronal regeneration in the CAST/Ei mouse strain is linked to expression of differentiation markers after injury

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• Maximizing functional axon repair in the injured central nervous system: Lessons from neuronal development

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• Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity

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• Gut Microbiota: The Conductor in the Orchestra of Immune-Neuroendocrine Communication.

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