RNA-Seq Characterization of Spinal Cord Injury Transcriptome in Acute/Subacute Phases: A Resource for Understanding the Pathology at the Systems Level

Abstract

Spinal cord injury (SCI) is a devastating neurological disease without effective treatment. To generate a comprehensive view of the mechanisms involved in SCI pathology, we applied RNA-Sequencing (RNA-Seq) technology to characterize the temporal changes in global gene expression after contusive SCI in mice. We sequenced tissue samples from acute and subacute phases (2 days and 7 days after injury) and systematically characterized the transcriptomes with the goal of identifying pathways and genes critical in SCI pathology. The top enriched functional categories include “inflammation response,” “neurological disease,” “cell death and survival” and “nervous system development.” The top enriched pathways include LXR/RXR Activation and Atherosclerosis Signaling, etc. Furthermore, we developed a systems-based analysis framework in order to identify key determinants in the global gene networks of the acute and sub-acute phases. Some candidate genes that we identified have been shown to play important roles in SCI, which demonstrates the validity of our approach. There are also many genes whose functions in SCI have not been well studied and can be further investigated by future experiments. We have also incorporated pharmacogenomic information into our analyses. Among the genes identified, the ones with existing drug information can be readily tested in SCI animal models. Therefore, in this study we have described an example of how global gene profiling can be translated to identifying genes of interest for functional tests in the future and generating new hypotheses. Additionally, the RNA-Seq enables splicing isoform identification and the estimation of expression levels, thus providing useful information for increasing the specificity of drug design and reducing potential side effect. In summary, these results provide a valuable reference data resource for a better understanding of the SCI process in the acute and sub-acute phases.

Group II mGluRs suppress hyperexcitability in mouse and human nociceptors

“…Results were integratively analyzed with publicly available human fetal spinal cord from the ENCODE project [13] (Replicate 1 (male): ENCFF001RNA, ENCFF001RNB, Replicate 2 (female): ENCFF001RNC, ENCFF001RND) RNA-seq data. Publicly available RNA-seq data was obtained for mouse adult, female DRG (strain C57BL/6: GEO datasets GSM1150934, GSM1150935) [22] and adult, female spinal cord (strain C57Bl/6J: GEO datasets GSM1103369, GSM1103370) [7]. Paired-end datasets were converted to single-end datasets by merging read libraries.…”

RNA Editing—Systemic Relevance and Clue to Disease Mechanisms?

“…Regarding GluA2 under-editing, which was more pronounced in glioblastoma compared to neighboring non-tumor tissue (Hwang et al, 2016), and taking into account that brain tumor cells can release glutamate by transferrin-mediated iron accumulation (Chirasani et al, 2009), reduced RNA editing and increased calcium signaling through GluA2 may contribute to aggressiveness of tumor growth and expansion. Regarding spinal cord injury in a mouse model (Chen et al, 2013), decreased RNA editing of GluA2 in the epicenter of the injured site actually points to a disease-promoting mechanism, as cellular calcium overload should promote neurodegeneration.…”

Building an RNA Sequencing Transcriptome of the Central Nervous System

“…(B) The workflow for the analysis framework in identifying potentially important genes. Adapted from Chen and others (2013) with permission and modifications.…”