Spinal cord injury (SCI) is a devastating disease without effective treatment. The chronic SCI remains the most difficult to treat. The pathologic hallmarks in chronic SCI include increased astrogliosis and inhibitory molecules that hinder axonal regeneration. However, the understanding of the detailed molecular pathways is still very limited. For example, how inhibitory molecules are regulated and maintained in the chronic phase remains unclear. Current therapeutics for gliosis is not ideal, and new molecular targets are urgently needed. Previous studies have usually focused on a small number of genes and pathways at a time, and thus did not provide a comprehensive view of the complex mechanisms underlying SCI pathophysiology. Although, during the last decade, microarray studies have provided valuable insights into SCI, microarray suffers from limitations in resolution, dynamic range and accuracy. Recent advances in RNA-Sequencing technology make it possible to globally map transcribed regions and quantitatively analyze expression at an unprecedented level of sensitivity and specificity. Based on our preliminary studies of differential expression using RNA-Seq during acute and subacute SCI phases in mouse contusive injury models, we propose to investigate the intricate relationship of genes and pathways in the spinal cord tissue and the predominant component of the glial scar (purified astrocytes) in chronic SCI by using integrated RNA-Seq and network analyses. We hypothesize that novel genes and pathways that regulate or maintain inhibitory molecules in reactive astrocytes (chondroitin sulphate proteoglycans, tenascins, ephrin-B2 and Slit proteins etc.) are critical for the chronic SCI inhibitory environment associated with glial scar. Specifically, we propose to derive a better understanding of the progression of SCI pathophysiology by characterizing gene and splicing isoform changes in SCI subchronic/chronic phases at both temporal and spatial levels. Additionally, we will use an innovative strategy of integrated network analysis to identify novel genes of interest (GOIs) and pathways involved in gliosis as new molecular targets. We will also incorporate pharmacogenomic information into our analyses that will serve as a powerful tool for translation. Finally, we will test GOIs potentially involved in neuron inhibition of reactive astrocytes by loss- and gain-of-function assays in a glia scar model for their functional effects. Our study is the first to propose that the mechanisms of chronic SCI and gliosis be investigated at the systems level using RNA-Seq, and key genes be identified via innovative pathway and network analyses and be tested by functional assays. The advantage of the genome-wide analysis is that, as a de novo discovery approach, it can identify critical missing links in the disease processes that were not previously appreciated. Importantly, we will generate a comprehensive data resource of SCI gene expression which will be extremely valuable for the research community (jiaqianwulab.org/SCI browser/data). The successful completion of this project will lead to the discovery of novel molecular targets and shift the research and clinical paradigms.

Public Health Relevance

Spinal cord injury (SCI) is one of the most debilitating diseases without effective treatment, and the majority of SCI patients are in the chronic phase. Using innovative interdisciplinary approaches, our goal is to investigate astrocytes' contribution to the injury environment by studying the intricate relationship of genes and pathways that regulate or maintain the inhibitory molecules associated with glial scar, as well as to identify important functional molecular targets to decrease neuron inhibition and promote axonal regeneration. The novel concepts and approaches that we develop will move the SCI field forward and have immediate and substantial impact on developing effective therapies.

Agency
National Institute of Health (NIH)
Institute
National Institute of Neurological Disorders and Stroke (NINDS)
Type
Research Project (R01)
Project #
1R01NS088353-01A1
Application #
8886116
Study Section
Clinical Neuroplasticity and Neurotransmitters Study Section (CNNT)
Program Officer
Jakeman, Lyn B
Project Start
2015-03-15
Project End
2020-02-29
Budget Start
2015-03-15
Budget End
2016-02-29
Support Year
1
Fiscal Year
2015
Total Cost
$328,559
Indirect Cost
$109,809
Name
University of Texas Health Science Center Houston
Department
Neurosurgery
Type
Schools of Medicine
DUNS #
800771594
City
Houston
State
TX
Country
United States
Zip Code
77030
You, Yanan; Cuevas-Diaz Duran, Raquel; Jiang, Lihua et al. (2018) An integrated global regulatory network of hematopoietic precursor cell self-renewal and differentiation. Integr Biol (Camb) 10:390-405
Dong, Xiaomin; Cuevas-Diaz Duran, Raquel; You, Yanan et al. (2018) Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFR?+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis. J Vis Exp :
Liu, Ying; Zheng, Yiyan; Li, Shenglan et al. (2017) Human neural progenitors derived from integration-free iPSCs for SCI therapy. Stem Cell Res 19:55-64
Duran, Raquel Cuevas-Diaz; Yan, Han; Zheng, Yiyan et al. (2017) The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury. Sci Rep 7:41008
Jiang, Nan; Xiang, Lusai; He, Ling et al. (2017) Exosomes Mediate Epithelium-Mesenchyme Crosstalk in Organ Development. ACS Nano 11:7736-7746
Cuevas-Diaz Duran, Raquel; Wei, Haichao; Wu, Jia Qian (2017) Single-cell RNA-sequencing of the brain. Clin Transl Med 6:20
Dong, Xiaomin; You, Yanan; Wu, Jia Qian (2016) Building an RNA Sequencing Transcriptome of the Central Nervous System. Neuroscientist 22:579-592
Dong, Xiaomin; Chen, Kenian; Cuevas-Diaz Duran, Raquel et al. (2015) Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination. PLoS Genet 11:e1005669
Yan, Qinghong; Weyn-Vanhentenryck, Sebastien M; Wu, Jie et al. (2015) Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. Proc Natl Acad Sci U S A 112:3445-50